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 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(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(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(job_mapper, iso_job_tbl, iso_job_member_tbl,
worklist_series_iso_request_tbl):
"Mapper factory."
m = mapper(IsoJob, iso_job_tbl,
inherits=job_mapper,
polymorphic_identity=JOB_TYPES.ISO,
properties=dict(
iso_job_stock_racks=relationship(IsoJobStockRack,
back_populates='iso_job',
cascade='all, delete-orphan'),
iso_job_preparation_plates=relationship(
IsoJobPreparationPlate,
back_populates='iso_job',
cascade='all, delete-orphan'),
isos=relationship(Iso, secondary=iso_job_member_tbl,
back_populates='iso_job',
cascade='all, delete-orphan',
single_parent=True),
worklist_series=relationship(WorklistSeries,
cascade='all, delete-orphan',
uselist=False, single_parent=True,
secondary=worklist_series_iso_request_tbl)
)
)
return m
def create_mapper(job_mapper, iso_job_tbl, iso_job_member_tbl,
worklist_series_iso_request_tbl):
"Mapper factory."
m = mapper(IsoJob,
iso_job_tbl,
inherits=job_mapper,
polymorphic_identity=JOB_TYPES.ISO,
properties=dict(iso_job_stock_racks=relationship(
IsoJobStockRack,
back_populates='iso_job',
cascade='all, delete-orphan'),
iso_job_preparation_plates=relationship(
IsoJobPreparationPlate,
back_populates='iso_job',
cascade='all, delete-orphan'),
isos=relationship(Iso,
secondary=iso_job_member_tbl,
back_populates='iso_job',
cascade='all, delete-orphan',
single_parent=True),
worklist_series=relationship(
WorklistSeries,
cascade='all, delete-orphan',
uselist=False,
single_parent=True,
secondary=worklist_series_iso_request_tbl)))
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(supplier_molecule_design_tbl,
single_supplier_molecule_design_tbl,
pooled_supplier_molecule_design_tbl):
"Mapper factory."
ssmd = single_supplier_molecule_design_tbl
psmd = pooled_supplier_molecule_design_tbl
m = mapper(SupplierMoleculeDesign, supplier_molecule_design_tbl,
id_attribute='supplier_molecule_design_id',
properties=dict(
supplier=
relationship(Organization,
uselist=False),
supplier_structure_annotations=
relationship(SupplierStructureAnnotation,
back_populates=
'supplier_molecule_design'),
molecule_design=\
relationship(MoleculeDesign,
uselist=False,
secondary=ssmd,
back_populates='supplier_molecule_designs'),
molecule_design_pool=\
relationship(MoleculeDesignPool,
uselist=False,
secondary=psmd,
back_populates='supplier_molecule_designs')
),
)
return m
def create_mapper(molecule_design_tbl, molecule_design_structure_tbl,
single_supplier_molecule_design_tbl,
molecule_design_gene_tbl, refseq_gene_tbl):
"Mapper factory."
md = molecule_design_tbl
ssmd = single_supplier_molecule_design_tbl
mdg = molecule_design_gene_tbl
rsg = refseq_gene_tbl
m = mapper(MoleculeDesign, molecule_design_tbl,
id_attribute='molecule_design_id',
properties=dict(
molecule_type=relationship(MoleculeType), #, lazy='joined'),
chemical_structures=relationship(
ChemicalStructure,
secondary=molecule_design_structure_tbl,
back_populates='molecule_designs'),
supplier_molecule_designs=
relationship(SupplierMoleculeDesign,
secondary=ssmd,
back_populates='molecule_design'),
genes=relationship(Gene, viewonly=True, secondary=mdg,
primaryjoin=(mdg.c.molecule_design_id ==
md.c.molecule_design_id),
secondaryjoin=(mdg.c.gene_id == rsg.c.gene_id),
foreign_keys=(mdg.c.molecule_design_id, mdg.c.gene_id),
back_populates='molecule_designs',
),
),
polymorphic_on=molecule_design_tbl.c.molecule_type_id,
polymorphic_identity=MOLECULE_TYPE,
)
return m
def create_mapper(experiment_metadata_type_tbl):
"Mapper factory."
m = mapper(ExperimentMetadataType,
experiment_metadata_type_tbl,
id_attribute='experiment_metadata_type_id',
slug_expression=lambda cls: func.lower(cls.id))
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(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(experiment_design_tbl,
worklist_series_experiment_design_tbl):
"Mapper factory."
m = mapper(
ExperimentDesign,
experiment_design_tbl,
id_attribute='experiment_design_id',
properties=dict(rack_shape=relationship(RackShape, uselist=False),
experiment_design_racks=relationship(
ExperimentDesignRack,
back_populates='experiment_design',
cascade="all, delete, delete-orphan"),
experiments=relationship(
Experiment,
back_populates='experiment_design',
cascade_backrefs=False),
experiment_metadata=relationship(
ExperimentMetadata,
back_populates='experiment_design',
uselist=False),
worklist_series=relationship(
WorklistSeries,
uselist=False,
cascade='all, delete, delete-orphan',
secondary=worklist_series_experiment_design_tbl,
single_parent=True)),
)
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(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(molecule_design_set_mapper, molecule_design_pool_tbl,
pooled_supplier_molecule_design_tbl,
supplier_molecule_design_tbl, molecule_design_set_gene_tbl):
"Mapper factory."
mdp = molecule_design_pool_tbl
psmd = pooled_supplier_molecule_design_tbl
smd = supplier_molecule_design_tbl
mdsg = molecule_design_set_gene_tbl
m = mapper(MoleculeDesignPool,
molecule_design_pool_tbl,
inherits=molecule_design_set_mapper,
properties=dict(
molecule_type=relationship(MoleculeType,
# lazy='joined'
),
supplier_molecule_designs=
relationship(
SupplierMoleculeDesign,
secondary=psmd,
primaryjoin=psmd.c.molecule_design_set_id ==
mdp.c.molecule_design_set_id,
secondaryjoin=smd.c.supplier_molecule_design_id ==
psmd.c.supplier_molecule_design_id,
foreign_keys=[psmd.c.molecule_design_set_id,
psmd.c.supplier_molecule_design_id],
back_populates='molecule_design_pool'),
genes=relationship(Gene,
viewonly=True,
secondary=mdsg),
),
polymorphic_identity=MOLECULE_DESIGN_SET_TYPES.POOL)
event.listen(MoleculeDesignPool, 'init', check_init)
return m
def create_mapper(iso_request_mapper, lab_iso_request_tbl,
experiment_metadata_iso_request_tbl, reservoir_specs_tbl,
molecule_design_library_lab_iso_request_tbl):
"Mapper factory."
lir = lab_iso_request_tbl
emir = experiment_metadata_iso_request_tbl
rs = reservoir_specs_tbl
m = mapper(LabIsoRequest, lab_iso_request_tbl,
inherits=iso_request_mapper,
properties=dict(
requester=relationship(User, uselist=False),
rack_layout=relationship(RackLayout, uselist=False,
cascade='all,delete,delete-orphan',
single_parent=True),
experiment_metadata=relationship(ExperimentMetadata,
secondary=emir, uselist=False,
back_populates='lab_iso_request'),
molecule_design_library=relationship(
MoleculeDesignLibrary, uselist=False,
secondary=molecule_design_library_lab_iso_request_tbl),
iso_plate_reservoir_specs=relationship(ReservoirSpecs,
uselist=False,
primaryjoin=lir.c.iso_plate_reservoir_specs_id == \
rs.c.reservoir_specs_id)
),
polymorphic_identity=ISO_TYPES.LAB,
)
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(iso_request_mapper, lab_iso_request_tbl,
experiment_metadata_iso_request_tbl, reservoir_specs_tbl,
molecule_design_library_lab_iso_request_tbl):
"Mapper factory."
lir = lab_iso_request_tbl
emir = experiment_metadata_iso_request_tbl
rs = reservoir_specs_tbl
m = mapper(LabIsoRequest, lab_iso_request_tbl,
inherits=iso_request_mapper,
properties=dict(
requester=relationship(User, uselist=False),
rack_layout=relationship(RackLayout, uselist=False,
cascade='all,delete,delete-orphan',
single_parent=True),
experiment_metadata=relationship(ExperimentMetadata,
secondary=emir, uselist=False,
back_populates='lab_iso_request'),
molecule_design_library=relationship(
MoleculeDesignLibrary, uselist=False,
secondary=molecule_design_library_lab_iso_request_tbl),
iso_plate_reservoir_specs=relationship(ReservoirSpecs,
uselist=False,
primaryjoin=lir.c.iso_plate_reservoir_specs_id == \
rs.c.reservoir_specs_id)
),
polymorphic_identity=ISO_TYPES.LAB,
)
return m
def create_mapper(iso_request_tbl, worklist_series_iso_request_tbl,
iso_request_pool_set_tbl):
"Mapper factory."
wsir = worklist_series_iso_request_tbl
m = mapper(IsoRequest, iso_request_tbl,
id_attribute='iso_request_id',
properties=
dict(owner=column_property(iso_request_tbl.c.owner,
comparator_factory=CaseInsensitiveComparator
),
isos=relationship(Iso, back_populates='iso_request'),
worklist_series=relationship(WorklistSeries,
uselist=False, secondary=wsir,
cascade='all,delete,delete-orphan',
single_parent=True),
molecule_design_pool_set=relationship(
MoleculeDesignPoolSet,
secondary=iso_request_pool_set_tbl,
uselist=False, single_parent=True,
cascade='all,delete,delete-orphan')
),
polymorphic_on=iso_request_tbl.c.iso_type,
polymorphic_identity=ISO_TYPES.BASE,
)
return m
def create_mapper(molecule_design_set_mapper, molecule_design_pool_tbl,
pooled_supplier_molecule_design_tbl,
supplier_molecule_design_tbl, molecule_design_set_gene_tbl):
"Mapper factory."
mdp = molecule_design_pool_tbl
psmd = pooled_supplier_molecule_design_tbl
smd = supplier_molecule_design_tbl
mdsg = molecule_design_set_gene_tbl
m = mapper(
MoleculeDesignPool,
molecule_design_pool_tbl,
inherits=molecule_design_set_mapper,
properties=dict(
molecule_type=relationship(
MoleculeType,
# lazy='joined'
),
supplier_molecule_designs=relationship(
SupplierMoleculeDesign,
secondary=psmd,
primaryjoin=psmd.c.molecule_design_set_id ==
mdp.c.molecule_design_set_id,
secondaryjoin=smd.c.supplier_molecule_design_id ==
psmd.c.supplier_molecule_design_id,
foreign_keys=[
psmd.c.molecule_design_set_id,
psmd.c.supplier_molecule_design_id
],
back_populates='molecule_design_pool'),
genes=relationship(Gene, viewonly=True, secondary=mdsg),
),
polymorphic_identity=MOLECULE_DESIGN_SET_TYPES.POOL)
event.listen(MoleculeDesignPool, 'init', check_init)
return m
def create_mapper(iso_plate_tbl):
"Mapper factory."
m = mapper(IsoPlate,
iso_plate_tbl,
id_attribute='iso_plate_id',
polymorphic_on=iso_plate_tbl.c.iso_plate_type,
polymorphic_identity=ISO_PLATE_TYPES.ISO_PLATE,
properties=dict(rack=relationship(Rack, 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(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(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 create_mapper(molecule_tbl, molecule_supplier_molecule_design_tbl):
"Mapper factory."
# ssmd = single_supplier_molecule_design_tbl
# smd = supplier_molecule_design_tbl
# mcl = molecule_tbl.alias()
# prd_sel = \
# select([distinct(smd.c.product_id)],
# and_(mcl.c.molecule_design_id ==
# molecule_tbl.c.molecule_design_id,
# smd.c.supplier_id == molecule_tbl.c.supplier_id,
# smd.c.is_current
# ),
# from_obj=[mcl.join(ssmd,
# ssmd.c.molecule_design_id ==
# mcl.c.molecule_design_id)
# .join(smd,
# smd.c.supplier_molecule_design_id ==
# ssmd.c.supplier_molecule_design_id)]
# )
# msmd = molecule_supplier_molecule_design_vw
msmd = molecule_supplier_molecule_design_tbl
m = mapper(
Molecule,
molecule_tbl,
id_attribute='molecule_id',
properties=dict(
supplier=relationship(Organization),
molecule_design=relationship(
MoleculeDesign,
uselist=False,
# lazy='joined'
),
# Loading the product ID like this is faster than loading it
# through the supplier molecule design.
# product_id=column_property(prd_sel.as_scalar(), deferred=True),
supplier_molecule_design=relationship(
SupplierMoleculeDesign,
uselist=False,
secondary=msmd,
# primaryjoin=ssmd.c.molecule_design_id ==
# molecule_tbl.c.molecule_design_id,
# secondaryjoin=and_(smd.c.supplier_molecule_design_id ==
# ssmd.c.supplier_molecule_design_id,
# smd.c.is_current,
# smd.c.supplier_id == molecule_tbl.c.supplier_id),
# foreign_keys=(ssmd.c.molecule_design_id,
# ssmd.c.supplier_molecule_design_id),
## remote_side=msmd.c.molecule_id,
viewonly=True),
sample_molecules=relationship(SampleMolecule,
back_populates='molecule'),
),
)
return m
def create_mapper(stock_rack_mapper, iso_job_stock_rack_tbl):
"Mapper factory."
m = mapper(
IsoJobStockRack,
iso_job_stock_rack_tbl,
inherits=stock_rack_mapper,
properties=dict(iso_job=relationship(
IsoJob, uselist=False, back_populates='iso_job_stock_racks'), ),
polymorphic_identity=STOCK_RACK_TYPES.ISO_JOB,
)
return m
def create_mapper(user_preferences_tbl):
"Mapper factory."
m = mapper(UserPreferences,
user_preferences_tbl,
id_attribute='user_preferences_id',
properties=dict(user=relationship(
User,
uselist=False,
back_populates='user_preferenceses',
cascade='save-update'), ))
return m
def create_mapper(iso_plate_mapper, iso_aliquot_plate_tbl):
"Mapper factory."
m = mapper(IsoAliquotPlate, iso_aliquot_plate_tbl,
inherits=iso_plate_mapper,
properties=dict(
iso=relationship(Iso, uselist=False,
back_populates='iso_aliquot_plates'),
),
polymorphic_identity=ISO_PLATE_TYPES.ALIQUOT,
)
return m
def create_mapper(iso_plate_mapper, iso_aliquot_plate_tbl):
"Mapper factory."
m = mapper(
IsoAliquotPlate,
iso_aliquot_plate_tbl,
inherits=iso_plate_mapper,
properties=dict(iso=relationship(
Iso, uselist=False, back_populates='iso_aliquot_plates'), ),
polymorphic_identity=ISO_PLATE_TYPES.ALIQUOT,
)
return m
def create_mapper(stock_rack_mapper, iso_sector_stock_rack_tbl):
"Mapper factory."
m = mapper(
IsoSectorStockRack,
iso_sector_stock_rack_tbl,
inherits=stock_rack_mapper,
properties=dict(iso=relationship(
Iso, uselist=False, back_populates='iso_sector_stock_racks'), ),
polymorphic_identity=STOCK_RACK_TYPES.SECTOR,
)
return m
def create_mapper(iso_plate_tbl):
"Mapper factory."
m = mapper(IsoPlate, iso_plate_tbl,
id_attribute='iso_plate_id',
polymorphic_on=iso_plate_tbl.c.iso_plate_type,
polymorphic_identity=ISO_PLATE_TYPES.ISO_PLATE,
properties=dict(
rack=relationship(Rack, uselist=False),
)
)
return m
def create_mapper(iso_mapper, stock_sample_creation_iso_tbl):
"Mapper factory."
m = mapper(StockSampleCreationIso, stock_sample_creation_iso_tbl,
inherits=iso_mapper,
properties=dict(
iso_sector_preparation_plates=relationship(
IsoSectorPreparationPlate,
back_populates='iso',
cascade='all,delete,delete-orphan')),
polymorphic_identity=ISO_TYPES.STOCK_SAMPLE_GENERATION)
return m
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(iso_mapper, stock_sample_creation_iso_tbl):
"Mapper factory."
m = mapper(StockSampleCreationIso,
stock_sample_creation_iso_tbl,
inherits=iso_mapper,
properties=dict(iso_sector_preparation_plates=relationship(
IsoSectorPreparationPlate,
back_populates='iso',
cascade='all,delete,delete-orphan')),
polymorphic_identity=ISO_TYPES.STOCK_SAMPLE_GENERATION)
return m
def create_mapper(user_preferences_tbl):
"Mapper factory."
m = mapper(UserPreferences, user_preferences_tbl,
id_attribute='user_preferences_id',
properties=dict(
user=relationship(User, uselist=False,
back_populates='user_preferenceses',
cascade='save-update'),
)
)
return m
def create_mapper(stock_rack_mapper, iso_stock_rack_tbl):
"Mapper factory."
m = mapper(IsoStockRack, iso_stock_rack_tbl,
inherits=stock_rack_mapper,
properties=dict(
iso=relationship(Iso, uselist=False,
back_populates='iso_stock_racks'),
),
polymorphic_identity=STOCK_RACK_TYPES.ISO,
)
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(worklist_series_tbl):
"Mapper factory."
m = mapper(WorklistSeries,
worklist_series_tbl,
id_attribute='worklist_series_id',
properties=dict(worklist_series_members=relationship(
WorklistSeriesMember,
uselist=True,
collection_class=list,
back_populates='worklist_series',
cascade='all,delete,delete-orphan')))
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(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(worklist_series_tbl):
"Mapper factory."
m = mapper(WorklistSeries, worklist_series_tbl,
id_attribute='worklist_series_id',
properties=dict(
worklist_series_members=relationship(WorklistSeriesMember,
uselist=True, collection_class=list,
back_populates='worklist_series',
cascade='all,delete,delete-orphan')
)
)
return m
def create_mapper(iso_job_preparation_plate_tbl):
"Mapper factory."
m = mapper(IsoJobPreparationPlate, iso_job_preparation_plate_tbl,
id_attribute='iso_job_preparation_plate_id',
properties=dict(
rack=relationship(Rack, uselist=False),
rack_layout=relationship(RackLayout, uselist=False),
iso_job=relationship(IsoJob, uselist=False,
back_populates='iso_job_preparation_plates'),
),
)
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(job_tbl):
"Mapper factory."
m = mapper(Job, job_tbl,
id_attribute='job_id',
properties=dict(
user=relationship(User, uselist=False),
),
polymorphic_on=job_tbl.c.job_type,
polymorphic_identity=JOB_TYPES.BASE,
)
return m
def create_mapper(rack_position_tbl):
"Mapper factory."
m = mapper(RackPosition, rack_position_tbl,
id_attribute='rack_position_id',
slug_expression=lambda cls: func.lower(cls._label), # pylint: disable=W0212
properties=
dict(_label=rack_position_tbl.c.label,
_row_index=rack_position_tbl.c.row_index,
_column_index=rack_position_tbl.c.column_index
),
)
return m
def create_mapper(job_tbl):
"Mapper factory."
m = mapper(
Job,
job_tbl,
id_attribute='job_id',
properties=dict(user=relationship(User, uselist=False), ),
polymorphic_on=job_tbl.c.job_type,
polymorphic_identity=JOB_TYPES.BASE,
)
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(iso_mapper, iso_tbl, iso_library_plate_tbl):
"Mapper factory."
m = mapper(LabIso,
iso_tbl,
inherits=iso_mapper,
polymorphic_identity=ISO_TYPES.LAB,
properties=dict(
library_plates=relationship(LibraryPlate,
secondary=iso_library_plate_tbl,
back_populates='lab_iso',
cascade='all')))
return m
def create_mapper(iso_mapper, iso_tbl, iso_library_plate_tbl):
"Mapper factory."
m = mapper(LabIso, iso_tbl,
inherits=iso_mapper,
polymorphic_identity=ISO_TYPES.LAB,
properties=dict(
library_plates=relationship(LibraryPlate,
secondary=iso_library_plate_tbl,
back_populates='lab_iso',
cascade='all')
)
)
return m
def create_mapper(rack_position_set_tbl, rack_position_set_member_tbl):
"Mapper factory."
m = mapper(
RackPositionSet,
rack_position_set_tbl,
id_attribute="rack_position_set_id",
slug_expression=lambda cls: cls._hash_value, # pylint: disable=W0212
properties=dict(
_positions=relationship(RackPosition, collection_class=set, secondary=rack_position_set_member_tbl),
_hash_value=rack_position_set_tbl.c.hash_value,
),
)
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(job_mapper, job_tbl, experiment_tbl):
"Mapper factory."
m = mapper(
ExperimentJob,
job_tbl,
inherits=job_mapper,
properties=dict(
experiments=relationship(Experiment,
order_by=experiment_tbl.c.experiment_id,
back_populates='job',
cascade='save-update, merge, delete')),
polymorphic_identity=JOB_TYPES.EXPERIMENT)
return m
def create_mapper(executed_liquid_transfer_tbl):
"Mapper factory."
m = mapper(ExecutedLiquidTransfer, executed_liquid_transfer_tbl,
id_attribute='executed_liquid_transfer_id',
properties=dict(
user=relationship(User, uselist=False),
planned_liquid_transfer=relationship(PlannedLiquidTransfer,
uselist=False),
),
polymorphic_on=executed_liquid_transfer_tbl.c.transfer_type,
polymorphic_identity=TRANSFER_TYPES.LIQUID_TRANSFER
)
return m
