def create_view(metadata, molecule_design_pool_tbl,
stock_sample_tbl, sample_tbl, container_tbl):
"""
stock_info_view factory.
"""
mdp = molecule_design_pool_tbl
ss = stock_sample_tbl
c = container_tbl
s = sample_tbl
stock = select([
(literal('mdp')
+ cast(mdp.c.molecule_design_set_id, String)
+ literal('c')
+ cast(coalesce(ss.c.concentration * 1e6, 0),
String)).label('stock_info_id'),
mdp.c.molecule_design_set_id,
# We need to set the label explicitly here because
# mdp.c.molecule_type_id is really mdp.c.molecule_type.
mdp.c.molecule_type_id.label('molecule_type_id'),
# pylint: disable=E1101
coalesce(ss.c.concentration, 0).label('concentration'),
coalesce(func.count(c.c.container_id), 0).label('total_tubes'),
coalesce(func.sum(s.c.volume), 0).label('total_volume'),
coalesce(func.min(s.c.volume), 0).label('minimum_volume'),
coalesce(func.max(s.c.volume), 0).label('maximum_volume')
# pylint: enable=E1101
],
from_obj=
mdp.outerjoin(ss, ss.c.molecule_design_set_id ==
mdp.c.molecule_design_set_id) \
.outerjoin(s, s.c.sample_id == ss.c.sample_id) \
.outerjoin(c,
and_(c.c.container_id == s.c.container_id,
c.c.item_status ==
_STOCK_CONTAINER_ITEM_STATUS))
).group_by(mdp.c.molecule_design_set_id,
ss.c.concentration).alias('ssi')
fkey_mds = ForeignKey(mdp.c.molecule_design_set_id)
fkey_mds.parent = stock.c.molecule_design_set_id
stock.c.molecule_design_set_id.foreign_keys.add(fkey_mds)
fkey_mt = ForeignKey(mdp.c.molecule_type_id)
fkey_mt.parent = stock.c.molecule_type_id
stock.c.molecule_type_id.foreign_keys.add(fkey_mt)
return view_factory(VIEW_NAME, metadata, stock)
def create_view(metadata, molecule_design_pool_tbl, stock_sample_tbl, sample_tbl, container_tbl):
"""
stock_info_view factory.
"""
mdp = molecule_design_pool_tbl
ss = stock_sample_tbl
c = container_tbl
s = sample_tbl
stock = (
select(
[
(
literal("mdp")
+ cast(mdp.c.molecule_design_set_id, String)
+ literal("c")
+ cast(coalesce(ss.c.concentration * 1e6, 0), String)
).label("stock_info_id"),
mdp.c.molecule_design_set_id,
# We need to set the label explicitly here because
# mdp.c.molecule_type_id is really mdp.c.molecule_type.
mdp.c.molecule_type_id.label("molecule_type_id"),
# pylint: disable=E1101
coalesce(ss.c.concentration, 0).label("concentration"),
coalesce(func.count(c.c.container_id), 0).label("total_tubes"),
coalesce(func.sum(s.c.volume), 0).label("total_volume"),
coalesce(func.min(s.c.volume), 0).label("minimum_volume"),
coalesce(func.max(s.c.volume), 0).label("maximum_volume")
# pylint: enable=E1101
],
from_obj=mdp.outerjoin(ss, ss.c.molecule_design_set_id == mdp.c.molecule_design_set_id)
.outerjoin(s, s.c.sample_id == ss.c.sample_id)
.outerjoin(c, and_(c.c.container_id == s.c.container_id, c.c.item_status == _STOCK_CONTAINER_ITEM_STATUS)),
)
.group_by(mdp.c.molecule_design_set_id, ss.c.concentration)
.alias("ssi")
)
fkey_mds = ForeignKey(mdp.c.molecule_design_set_id)
fkey_mds.parent = stock.c.molecule_design_set_id
stock.c.molecule_design_set_id.foreign_keys.add(fkey_mds)
fkey_mt = ForeignKey(mdp.c.molecule_type_id)
fkey_mt.parent = stock.c.molecule_type_id
stock.c.molecule_type_id.foreign_keys.add(fkey_mt)
return view_factory(VIEW_NAME, metadata, stock)
def create_view(metadata, molecule_design_tbl, molecule_design_structure_tbl,
chemical_structure_tbl):
"""
molecule_type_modification_view factory.
"""
md = molecule_design_tbl
mds = molecule_design_structure_tbl
chs = chemical_structure_tbl
modification = \
select([md.c.molecule_type_id.label('molecule_type_id'),
chs.c.representation.label('name'),
chs.c.chemical_structure_id],
from_obj=md \
.join(mds,
mds.c.molecule_design_id == md.c.molecule_design_id) \
.join(chs,
and_(chs.c.chemical_structure_id ==
mds.c.chemical_structure_id,
chs.c.structure_type_id ==
CHEMICAL_STRUCTURE_TYPE_IDS.MODIFICATION))
)
return view_factory(VIEW_NAME, metadata, modification)
def create_view(metadata, molecule_design_tbl, molecule_design_structure_tbl,
chemical_structure_tbl):
"""
molecule_type_modification_view factory.
"""
md = molecule_design_tbl
mds = molecule_design_structure_tbl
chs = chemical_structure_tbl
modification = \
select([md.c.molecule_type_id.label('molecule_type_id'),
chs.c.representation.label('name'),
chs.c.chemical_structure_id],
from_obj=md \
.join(mds,
mds.c.molecule_design_id == md.c.molecule_design_id) \
.join(chs,
and_(chs.c.chemical_structure_id ==
mds.c.chemical_structure_id,
chs.c.structure_type_id ==
CHEMICAL_STRUCTURE_TYPE_IDS.MODIFICATION))
)
return view_factory(VIEW_NAME, metadata, modification)
def create_view(metadata, molecule_tbl, single_supplier_molecule_design_tbl,
supplier_molecule_design_tbl):
"""
molecule_type_modification_view factory.
"""
m = molecule_tbl
ssmd = single_supplier_molecule_design_tbl
smd = supplier_molecule_design_tbl
msmd = \
select([m.c.molecule_id,
smd.c.supplier_molecule_design_id],
from_obj=m \
.join(ssmd,
ssmd.c.molecule_design_id == m.c.molecule_design_id) \
.join(smd,
and_(smd.c.supplier_molecule_design_id ==
ssmd.c.supplier_molecule_design_id,
smd.c.supplier_id == m.c.supplier_id,
smd.c.is_current))
)
fkey_m = ForeignKey(m.c.molecule_id)
fkey_m.parent = msmd.c.molecule_id
msmd.c.molecule_id.foreign_keys.add(fkey_m)
return view_factory(VIEW_NAME, metadata, msmd)
def create_view(metadata, molecule_tbl, single_supplier_molecule_design_tbl,
supplier_molecule_design_tbl):
"""
molecule_type_modification_view factory.
"""
m = molecule_tbl
ssmd = single_supplier_molecule_design_tbl
smd = supplier_molecule_design_tbl
msmd = \
select([m.c.molecule_id,
smd.c.supplier_molecule_design_id],
from_obj=m \
.join(ssmd,
ssmd.c.molecule_design_id == m.c.molecule_design_id) \
.join(smd,
and_(smd.c.supplier_molecule_design_id ==
ssmd.c.supplier_molecule_design_id,
smd.c.supplier_id == m.c.supplier_id,
smd.c.is_current))
)
fkey_m = ForeignKey(m.c.molecule_id)
fkey_m.parent = msmd.c.molecule_id
msmd.c.molecule_id.foreign_keys.add(fkey_m)
return view_factory(VIEW_NAME, metadata, msmd)