class TestAssertionIrreversible:
@pytest.fixture(autouse=True)
def setup_items(self):
self.reaction = Reaction("r1")
self.evidence = Evidence(entity=self.reaction,
assertion="Irreversible")
def test_not_valid_if_reaction_reversible(self):
self.reaction.lower_bound = -1000.
self.reaction.upper_bound = 1000.
assert self.evidence.is_valid() is False
def test_valid_if_irreversible(self):
self.reaction.lower_bound = 0.
self.reaction.upper_bound = 1000.
assert self.evidence.is_valid() is True
self.reaction.lower_bound = -1000.
self.reaction.upper_bound = 0.
assert self.evidence.is_valid() is True
def test_reaction_needed(self):
evidence = Evidence(assertion="Irreversible")
assert evidence.is_valid() is None
def test_fix_reaction(self):
self.reaction.lower_bound = -1000.
self.reaction.upper_bound = 1000.
status = self.evidence.fix()
assert status is True
assert self.reaction.lower_bound == 0.
assert self.reaction.upper_bound == 1000.
def test_fix_nonstandard_boundary_kept(self):
self.reaction.lower_bound = -1000.
self.reaction.upper_bound = 500.
status = self.evidence.fix()
assert status is True
assert self.reaction.lower_bound == 0.
assert self.reaction.upper_bound == 500.
class TestAssertionCatalyzingReaction:
@pytest.fixture(autouse=True)
def setup_items(self):
self.reaction = Reaction("r1")
self.gene = Gene("g1")
self.evidence = Evidence(entity=self.gene,
target=self.reaction,
assertion="Catalyzing reaction")
def test_valid_if_gene_in_reaction(self):
self.reaction.add_child(self.gene)
assert self.evidence.is_valid() is True
def test_invalid_if_gene_not_in_reaction(self):
assert self.evidence.is_valid() is False
def test_gene_needed(self):
evidence = Evidence(entity=self.gene, assertion="Catalyzing reaction")
assert evidence.is_valid() is None
def test_reaction_needed(self):
evidence = Evidence(target=self.reaction,
assertion="Catalyzing reaction")
assert evidence.is_valid() is None
def test_fix_gene_added(self):
assert self.gene not in self.reaction.genes
status = self.evidence.fix()
assert status is True
assert self.gene in self.reaction.genes
class TestAssertionPresent:
@pytest.fixture(autouse=True)
def setup_items(self):
self.reaction = Reaction("r1")
self.evidence = Evidence(entity=self.reaction, assertion="Present")
def test_valid_if_reaction_is_active(self):
self.reaction.lower_bound = -1000.
self.reaction.upper_bound = 0.
assert self.evidence.is_valid() is True
self.reaction.upper_bound = 1000.
assert self.evidence.is_valid() is True
self.reaction.lower_bound = 0.
assert self.evidence.is_valid() is True
def test_invalid_if_reaction_not_active(self):
self.reaction.lower_bound = 0.
self.reaction.upper_bound = 0.
assert self.evidence.is_valid() is False
def test_valid_if_metabolite_entity(self):
self.evidence.set_entity(Metabolite("m1"))
assert self.evidence.is_valid() is True
def test_entity_needed(self):
evidence = Evidence()
assert evidence.is_valid() is None
def test_fixing_not_implemented(self):
self.reaction.lower_bound = 0
self.reaction.upper_bound = 0
self.evidence.fix()
assert self.reaction.lower_bound == 0.
assert self.reaction.upper_bound == 0.