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
def test_entity_needed(self):
evidence = Evidence(assertion="Localization")
assert evidence.is_valid() is None
evidence.set_entity(self.gene)
assert evidence.is_valid() is None
evidence.set_target(self.compartment)
assert evidence.is_valid() is not None
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.
def test_sorting_erroneous(self):
evidence = Evidence()
assert evidence.is_valid() is None
conflicts, failing, errors = sort_evidences([evidence])
assert not conflicts
assert not failing
assert evidence in errors
def test_sorting_conflicting(self):
reaction = Reaction()
gene = Gene()
reaction.add_child(gene)
evidence1 = Evidence(entity=gene,
target=reaction,
assertion="Catalyzing reaction")
evidence2 = Evidence(entity=gene,
target=reaction,
assertion="Not catalyzing reaction")
assert evidence1.is_valid() is True
assert evidence2.is_valid() is False
conflicts, failing, errors = sort_evidences([evidence1, evidence2])
assert len(conflicts) == 1
assert set(conflicts[0]) == set([evidence1, evidence2])
assert not failing
assert not errors
class TestAssertionAbsent:
@pytest.fixture(autouse=True)
def setup_items(self):
self.reaction = Reaction("r1")
self.evidence = Evidence(entity=self.reaction, assertion="Absent")
def test_invalid_if_reaction_is_active(self):
self.reaction.lower_bound = -1000.
self.reaction.upper_bound = 0.
assert self.evidence.is_valid() is False
self.reaction.upper_bound = 1000.
assert self.evidence.is_valid() is False
self.reaction.lower_bound = 0.
assert self.evidence.is_valid() is False
def test_valid_if_reaction_not_active(self):
self.reaction.lower_bound = 0.
self.reaction.upper_bound = 0.
assert self.evidence.is_valid() is True
def test_invalid_if_metabolite_entity(self):
self.evidence.set_entity(Metabolite("m1"))
assert self.evidence.is_valid() is False
def test_entity_needed(self):
evidence = Evidence()
assert evidence.is_valid() is None
def test_fixing_not_implemented(self):
self.reaction.lower_bound = -1000
self.reaction.upper_bound = 1000
result = self.evidence.fix()
assert result is False
assert self.reaction.lower_bound == -1000.
assert self.reaction.upper_bound == 1000.
def test_sorting_failing(self):
reaction = Reaction()
gene = Gene()
evidence = Evidence(entity=gene,
target=reaction,
assertion="Catalyzing reaction")
assert evidence.is_valid() is False
conflicts, failing, errors = sort_evidences([evidence])
assert not conflicts
assert [evidence] in failing
assert not errors
def test_sorting_valid(self):
reaction = Reaction()
gene = Gene()
evidence = Evidence(entity=gene,
target=reaction,
assertion="Catalyzing reaction")
reaction.add_child(gene)
assert evidence.is_valid() is True
conflicts, failing, errors = sort_evidences([evidence])
assert not conflicts
assert not failing
assert not errors
def test_reaction_needed(self):
evidence = Evidence(assertion="Reversible")
assert evidence.is_valid() is None
def test_reaction_needed(self):
evidence = Evidence(target=self.reaction,
assertion="Not catalyzing reaction")
assert evidence.is_valid() is None
def test_gene_needed(self):
evidence = Evidence(entity=self.gene,
assertion="Not catalyzing reaction")
assert evidence.is_valid() is None
def test_error_if_gene_not_added_to_reaction(self):
gene = Gene("g1")
evidence = Evidence(entity=gene, assertion="Localization")
assert evidence.is_valid() is None
class TestAssertionLocalization:
@pytest.fixture(autouse=True)
def setup_items(self):
self.gene = Gene("g1")
self.compartment = Compartment("c")
self.metabolite1 = Metabolite("m1")
self.metabolite2 = Metabolite("m2")
self.reaction = Reaction("r1")
self.reaction.add_metabolites({
self.metabolite1: -1,
self.metabolite2: 1
})
self.reaction.add_child(self.gene)
self.evidence = Evidence(entity=self.gene,
assertion="Localization",
target=self.compartment)
def test_valid_if_metabolites_in_same_compartment_as_gene(self):
self.metabolite1.compartment = "c"
self.metabolite2.compartment = "c"
self.compartment.id = "c"
assert self.evidence.is_valid() is True
def test_invalid_if_metabolites_not_in_same_compartment(self):
self.metabolite1.compartment = "e"
self.metabolite2.compartment = "e"
self.compartment.id = "c"
assert self.evidence.is_valid() is False
def test_invalid_if_any_reaction_not_in_same_compartment(self):
self.metabolite1.compartment = "c"
self.metabolite2.compartment = "c"
self.compartment.id = "c"
assert self.evidence.is_valid() is True
met1 = Metabolite("m1")
met2 = Metabolite("m2")
react2 = Reaction("r2")
react2.add_metabolites({met1: -1, met2: 1})
react2.add_child(self.gene)
assert self.evidence.is_valid() is False
def test_error_if_gene_not_added_to_reaction(self):
gene = Gene("g1")
evidence = Evidence(entity=gene, assertion="Localization")
assert evidence.is_valid() is None
def test_entity_needed(self):
evidence = Evidence(assertion="Localization")
assert evidence.is_valid() is None
evidence.set_entity(self.gene)
assert evidence.is_valid() is None
evidence.set_target(self.compartment)
assert evidence.is_valid() is not None
def test_entity_needed(self):
evidence = Evidence()
assert evidence.is_valid() is None