def test_reagent_get_maker_attr_3(mock_plugins):
db = Database()
db['x1'] = x1 = MockReagent(
synthesis=Fields(['m'], {'conc': '1 nM'}),
cleanups=[
Fields(['m'], {}),
Fields(['m'], {}),
],
)
assert x1.get_maker_attr('product_conc') == Quantity(1, 'nM')
assert x1.get_maker_attr('product_conc', None) == Quantity(1, 'nM')
def test_intermediate(mock_plugins):
db = Database()
db['x1'] = x1 = MockMolecule(
synthesis=Fields('m', {'conc': '1 nM'}),
cleanups=[
Fields('m', {'conc': '2 nM'}),
Fields('m', {'conc': '3 nM'}),
],
)
# Access the concentration before creating the intermediates so that a
# concentration value is cached. The intermediates will need to forget
# this value:
assert x1.conc == Quantity(3, 'nM')
i1 = x1.make_intermediate(0)
i2 = x1.make_intermediate(1)
i3 = x1.make_intermediate(2)
with pytest.raises(QueryError) as err:
x1.make_intermediate(3)
assert err.match("x1: intermediate 3 doesn't exist")
assert err.match("intermediates:")
assert err.match("0: m conc='1 nM'")
assert err.match("1: m conc='2 nM'")
assert err.match("2: m conc='3 nM'")
# Access the concentration again after creating the intermediates, to make
# sure that doing so does not somehow re-establish the cache:
assert x1.conc == Quantity(3, 'nM')
# Test that precursors are correct:
assert i2.precursor is i1
assert i3.precursor is i2
# Test that fields are correct:
assert i1.maker_args[0] == 'm'
assert i1.maker_args['conc'] == '1 nM'
assert i2.maker_args[0] == 'm'
assert i2.maker_args['conc'] == '2 nM'
assert i3.maker_args[0] == 'm'
assert i3.maker_args['conc'] == '3 nM'
# Test that makers are correct:
assert i1.maker.product_conc == Quantity(1, 'nM')
assert i2.maker.product_conc == Quantity(2, 'nM')
assert i3.maker.product_conc == Quantity(3, 'nM')
# Test that properties depending on fields are re-evaluated correctly.
assert i1.conc == Quantity(1, 'nM')
assert i2.conc == Quantity(2, 'nM')
assert i3.conc == Quantity(3, 'nM')
def test_reagent_get_maker_attr_4(mock_plugins):
db = Database()
db['x1'] = x1 = MockReagent(
synthesis=Fields(['m'], {}),
cleanups=[
Fields(['m'], {}),
Fields(['m'], {}),
],
)
with pytest.raises(QueryError, match='product_conc'):
x1.get_maker_attr('product_conc')
assert x1.get_maker_attr('product_conc', None) == None
def test_reagent_maker_err_2(mock_plugins):
db = Database()
db['x1'] = x1 = MockReagent(
# no synthesis
cleanups=[
Fields(['m'], {'conc': '2 nM'}),
Fields(['m'], {'conc': '3 nM'}),
], )
with pytest.raises(QueryError, match="no synthesis specified"):
x1.cleanup_args
with pytest.raises(QueryError, match="no synthesis specified"):
x1.cleanup_makers
def test_reagent_intermediate_repr():
x1 = MockReagent(synthesis=Fields(['m'], {}), )
i1 = x1.make_intermediate(0)
assert repr(x1) == "MockReagent(synthesis=Fields(['m'], {}))"
assert repr(
i1) == "MockReagentIntermediate(step=0, synthesis=Fields(['m'], {}))"
def test_reagent_maker_args_2():
db = Database()
db['x1'] = x1 = MockReagent(
synthesis=lambda: Fields(['m'], {'conc': '1 nM'}),
cleanups=lambda: [
Fields(['m'], {'conc': '2 nM'}),
Fields(['m'], {'conc': '3 nM'}),
],
)
assert x1.synthesis_args[0] == 'm'
assert x1.synthesis_args['conc'] == '1 nM'
assert x1.cleanup_args[0][0] == 'm'
assert x1.cleanup_args[0]['conc'] == '2 nM'
assert x1.cleanup_args[1][0] == 'm'
assert x1.cleanup_args[1]['conc'] == '3 nM'
def test_reagent_makers(mock_plugins):
db = Database()
db['x1'] = x1 = MockReagent(
synthesis=Fields(['m'], {'conc': '1 nM'}),
cleanups=[
Fields(['m'], {'conc': '2 nM'}),
Fields(['m'], {'conc': '3 nM'}),
],
)
m1 = x1.synthesis_maker
m2 = x1.cleanup_makers[0]
m3 = x1.cleanup_makers[1]
assert isinstance(m1, MockMaker)
assert m1.product_conc == Quantity(1, 'nM')
assert isinstance(m2, MockMaker)
assert m2.product_conc == Quantity(2, 'nM')
assert isinstance(m3, MockMaker)
assert m3.product_conc == Quantity(3, 'nM')
def test_f9(db, tag='f9'):
assert isinstance(db[tag], NucleicAcid)
assert db[tag].desc == "conc from cleanup"
assert db[tag].synthesis_args == Fields(['mock'], {})
assert db[tag].cleanup_args == [Fields(['mock'], {'conc': '50nM'})]
assert db[tag].conc_nM == 50
def test_f5(db, tag='f5'):
assert isinstance(db[tag], NucleicAcid)
assert db[tag].desc == "sequence from synthesis"
assert db[tag].synthesis_args == Fields(['mock'], {'seq': 'GGTCTC'})
assert db[tag].seq == 'GGTCTC'
def test_f15(db, tag='f15'):
assert isinstance(db[tag], NucleicAcid)
assert db[tag].desc == "circular from synthesis"
assert db[tag].synthesis_args == Fields(['mock'], {'circular': 'y'})
assert db[tag].is_circular == True
def test_f11(db, tag='f11'):
assert isinstance(db[tag], NucleicAcid)
assert db[tag].desc == "molecule from synthesis"
assert db[tag].synthesis_args == Fields(['mock'], {'molecule': 'ssRNA'})
assert db[tag].molecule == 'RNA'
assert db[tag].is_single_stranded == True