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 parse_evidences_from_xml(model_node, model, progress=None):
list_of_evidences_node = model_node.find(ge_listOfEvidences)
if list_of_evidences_node is None:
return
elif progress is None:
pass
elif not progress.wasCanceled():
progress.setLabelText("Reading evidences...")
progress.setRange(0, len(list_of_evidences_node))
else:
return
for i, evidence_node in enumerate(
list_of_evidences_node.iterfind(ge_evidence)):
if progress is None:
pass
elif not progress.wasCanceled():
progress.setValue(i)
QApplication.processEvents()
else:
return
new_evidence = Evidence(internal_id=evidence_node.get("id"),
assertion=evidence_node.get("assertion"),
comment=evidence_node.get("comment"),
eco=evidence_node.get("eco"))
entity_id = evidence_node.get("entity_id")
entity_type = evidence_node.get("entity_type")
entity = get_item_from_model(entity_type, entity_id, model)
new_evidence.set_entity(entity)
# Add target item if present
target_id = evidence_node.get("target_id")
target_type = evidence_node.get("target_type")
if target_id and target_type:
target = get_item_from_model(target_type, target_id, model)
new_evidence.set_target(target)
# Add all references if present
reference_list_node = evidence_node.find(ge_listOfReferenceLinks)
if reference_list_node is not None:
for refLink_node in reference_list_node.iterfind(ge_referenceLink):
new_evidence.add_reference(
model.references[refLink_node.get("id")])
model.all_evidences[new_evidence.internal_id] = new_evidence
def test_override_target(self):
entity = Reaction()
target = Gene()
eco = "ECO:000000"
assertion = "Presence"
comment = "test comment"
reference = Reference()
evidence = Evidence(entity=entity,
eco=eco,
assertion=assertion,
comment=comment,
target=target)
evidence.add_reference(reference)
new_gene = Gene()
evidence.set_target(new_gene)
# Check disconnection of old reaction
assert evidence.target is new_gene
assert evidence not in target.evidences
class TestModelDeleteItems:
@pytest.fixture(autouse=True)
def setup_complete_model(self):
self.model = Model("model")
# Setup reaction1
self.metabolite = Metabolite("m1")
self.reaction = Reaction("r1")
self.gene = Gene("g1")
self.reaction.add_child(self.gene)
self.model.add_genes((self.gene,))
self.reaction.add_metabolites({self.metabolite: -1})
self.model.add_reactions((self.reaction,))
# Setup reaction2
self.metabolite2 = Metabolite("m2")
self.reaction2 = Reaction("r2")
self.gene2 = Gene("g2")
self.genegroup = GeneGroup()
self.genegroup.add_child(self.gene2)
self.reaction2.add_child(self.genegroup)
self.model.add_genes((self.gene2,))
self.reaction2.add_metabolites({self.metabolite2: 1})
self.model.add_reactions((self.reaction2,))
# Setup evidences
self.evidence = Evidence(assertion="Catalyzes")
self.evidence.set_entity(self.gene)
self.evidence.set_target(self.reaction)
self.reference = Reference()
self.model.add_reference(self.reference)
self.evidence.add_reference(self.reference)
self.model.add_evidence(self.evidence)
# Setup test case
self.testcase = ModelTest()
reaction_setting = ReactionSetting(self.reaction, 1000., -1000., 0.)
gene_setting = GeneSetting(gene=self.gene2, activity=False)
outcome = Outcome(self.reaction2, 0., "greater")
self.testcase.add_outcome(outcome)
self.testcase.add_setting(gene_setting)
self.testcase.add_setting(reaction_setting)
self.model.add_test(self.testcase)
self.reference2 = Reference()
self.model.add_reference(self.reference2)
self.testcase.add_reference(self.reference2)
self.model.setup_tables()
def test_setup(self):
# Test genes
gene_in_model(self.gene, self.model)
gene_in_model(self.gene2, self.model)
# Test reactions
reaction_in_model(self.reaction, self.model)
reaction_in_model(self.reaction2, self.model)
# Test metabolites
metabolite_in_model(self.metabolite, self.model)
metabolite_in_model(self.metabolite2, self.model)
# Test evidences
evidence_in_model(self.evidence, self.model)
# Test model test
case_in_model(self.testcase, self.model)
# Test references
reference_in_model(self.reference, self.model)
reference_in_model(self.reference2, self.model)
# Test connections
# Reference <-> Evidence
reference_in_item(self.reference, self.evidence)
# Reference2 <-> Testcase
reference_in_item(self.reference2, self.testcase)
# Gene1 <-> Reaction1
gene_in_reaction(self.gene, self.reaction)
gene_in_reaction(self.gene2, self.reaction2)
# Metabolite1 <-> Reaction1
metabolite_in_reaction(self.metabolite, self.reaction)
metabolite_in_reaction(self.metabolite2, self.reaction2)
# Evidence <-> Gene1/Reaction
item_in_evidence(self.gene, self.evidence)
item_in_evidence(self.reaction, self.evidence)
def test_deletion_metabolite(self):
# Action
self.model.gem_remove_metabolites((self.metabolite,))
# Test gene
gene_in_model(self.gene, self.model)
gene_in_model(self.gene2, self.model)
# Test reactions
reaction_in_model(self.reaction, self.model)
reaction_in_model(self.reaction2, self.model)
# Test metabolites
metabolite_in_model(self.metabolite, self.model, valid=False)
metabolite_in_model(self.metabolite2, self.model)
# Test evidences
evidence_in_model(self.evidence, self.model)
# Test model test
case_in_model(self.testcase, self.model)
# Test references
reference_in_model(self.reference, self.model)
reference_in_model(self.reference2, self.model)
# Test connections
# Reference <-> Evidence
reference_in_item(self.reference, self.evidence)
# Reference2 <-> Testcase
reference_in_item(self.reference2, self.testcase)
# Gene1 <-> Reaction1
gene_in_reaction(self.gene, self.reaction)
gene_in_reaction(self.gene2, self.reaction2)
# Metabolite1 <-> Reaction1
metabolite_in_reaction(self.metabolite, self.reaction, valid=False)
metabolite_in_reaction(self.metabolite2, self.reaction2)
# Evidence <-> Gene1/Reaction
item_in_evidence(self.gene, self.evidence)
item_in_evidence(self.reaction, self.evidence)
def test_deletion_metabolite2(self):
# Action
self.model.gem_remove_metabolites((self.metabolite2,))
# Test genes
gene_in_model(self.gene, self.model)
gene_in_model(self.gene2, self.model)
# Test reactions
reaction_in_model(self.reaction, self.model)
reaction_in_model(self.reaction2, self.model)
# Test metabolites
metabolite_in_model(self.metabolite, self.model)
metabolite_in_model(self.metabolite2, self.model, valid=False)
# Test evidences
evidence_in_model(self.evidence, self.model)
# Test model test
case_in_model(self.testcase, self.model)
# Test references
reference_in_model(self.reference, self.model)
reference_in_model(self.reference2, self.model)
# Test connections
# Reference <-> Evidence
reference_in_item(self.reference, self.evidence)
# Reference2 <-> Testcase
reference_in_item(self.reference2, self.testcase)
# Gene1 <-> Reaction1
gene_in_reaction(self.gene, self.reaction)
gene_in_reaction(self.gene2, self.reaction2)
# Metabolite1 <-> Reaction1
metabolite_in_reaction(self.metabolite, self.reaction)
metabolite_in_reaction(self.metabolite2, self.reaction2, valid=False)
# Evidence <-> Gene1/Reaction
item_in_evidence(self.gene, self.evidence)
item_in_evidence(self.reaction, self.evidence)
def test_delete_reaction1(self):
####
# Delete reaction
# Check:
# - gene present but removed from reaction1
# - metabolite present but removed from reaction1
# - reaction deleted
# - evidence deleted
# - testcase deleted
# - reference present but removed from evidence
# - reference2 present but removed from testcase
####
# Action
self.model.gem_remove_reactions((self.reaction,))
# Test genes
gene_in_model(self.gene, self.model)
gene_in_model(self.gene2, self.model)
# Test reactions
reaction_in_model(self.reaction, self.model, valid=False)
reaction_in_model(self.reaction2, self.model)
# Test metabolites
metabolite_in_model(self.metabolite, self.model)
metabolite_in_model(self.metabolite2, self.model)
# Test model test
case_in_model(self.testcase, self.model, valid=False)
# Test references
reference_in_model(self.reference, self.model)
reference_in_model(self.reference2, self.model)
# Test connections
# Reference <-> Evidence
reference_in_item(self.reference, self.evidence, valid=False)
reference_in_item(self.reference2, self.testcase, valid=False)
# Gene1 <-> Reaction1
gene_in_reaction(self.gene, self.reaction, valid=False)
gene_in_reaction(self.gene2, self.reaction2)
# Metabolite1 <-> Reaction1
# Check metabolite is still in reaction, but reaction not in metabolite
assert self.metabolite in self.reaction.metabolites
assert self.reaction not in self.metabolite.reactions
metabolite_in_reaction(self.metabolite2, self.reaction2)
# Evidence <-> Gene1/Reaction
item_in_evidence(self.gene, self.evidence, valid=False)
item_in_evidence(self.reaction, self.evidence, valid=False)
# Check evidence is removed when reference deleted
del self.evidence
gc.collect()
assert len(self.model.all_evidences) == 0
def test_deletion_reaction2(self):
# Check:
# - reaction2 removed
# - test case removed
# - reference removed from testcase
# - gene2 removed from reaction
# Action
self.model.gem_remove_reactions((self.reaction2,))
# Test genes
gene_in_model(self.gene, self.model)
gene_in_model(self.gene2, self.model)
# Test reactions
reaction_in_model(self.reaction, self.model)
reaction_in_model(self.reaction2, self.model, valid=False)
# Test metabolites
metabolite_in_model(self.metabolite, self.model)
metabolite_in_model(self.metabolite2, self.model)
# Test evidences
evidence_in_model(self.evidence, self.model)
# Test model test
case_in_model(self.testcase, self.model, valid=False)
# Test references
reference_in_model(self.reference, self.model)
reference_in_model(self.reference2, self.model)
# Test connections
# Reference <-> Evidence
reference_in_item(self.reference, self.evidence)
# Reference2 <-> Testcase
reference_in_item(self.reference2, self.testcase, valid=False)
# Gene1 <-> Reaction1
gene_in_reaction(self.gene, self.reaction)
gene_in_reaction(self.gene2, self.reaction2, valid=False)
# Metabolite1 <-> Reaction1
metabolite_in_reaction(self.metabolite, self.reaction)
# Check metabolite still in reaction, but reaction not in metabolite
assert self.metabolite2 in self.reaction2.metabolites
assert self.reaction2 not in self.metabolite2.reactions
# Evidence <-> Gene1/Reaction
item_in_evidence(self.gene, self.evidence)
item_in_evidence(self.reaction, self.evidence)
def test_delete_gene1(self):
# Test gene deletion
# Check:
# - Gene removed from model
# - Evidence removed from model
# Action
self.model.gem_remove_genes((self.gene,))
# Test genes
gene_in_model(self.gene, self.model, valid=False)
gene_in_model(self.gene2, self.model)
# Test reactions
reaction_in_model(self.reaction, self.model)
reaction_in_model(self.reaction2, self.model)
# Test metabolites
metabolite_in_model(self.metabolite, self.model)
metabolite_in_model(self.metabolite2, self.model)
# Test model test
case_in_model(self.testcase, self.model)
# Test references
reference_in_model(self.reference, self.model)
reference_in_model(self.reference2, self.model)
# Test connections
# Reference <-> Evidence
reference_in_item(self.reference, self.evidence, valid=False)
# Reference2 <-> Testcase
reference_in_item(self.reference2, self.testcase)
# Gene1 <-> Reaction1
gene_in_reaction(self.gene, self.reaction, valid=False)
gene_in_reaction(self.gene2, self.reaction2)
# Metabolite1 <-> Reaction1
metabolite_in_reaction(self.metabolite, self.reaction)
metabolite_in_reaction(self.metabolite2, self.reaction2)
# Evidence <-> Gene1/Reaction
item_in_evidence(self.gene, self.evidence, valid=False)
item_in_evidence(self.reaction, self.evidence, valid=False)
# Check evidence is removed when reference deleted
del self.evidence
gc.collect()
assert len(self.model.all_evidences) == 0
def test_delete_gene2(self):
# Test removal of gene2
# Check:
# - Gene2 removed from model
# - Gene2 removed from reaction2
# - Testcase deleted from model
# - Reference2 removed from testcase
# Action
self.model.gem_remove_genes((self.gene2,))
# Test genes
gene_in_model(self.gene, self.model)
gene_in_model(self.gene2, self.model, valid=False)
# Test reactions
reaction_in_model(self.reaction, self.model)
reaction_in_model(self.reaction2, self.model)
# Test metabolites
metabolite_in_model(self.metabolite, self.model)
metabolite_in_model(self.metabolite2, self.model)
# Test evidences
evidence_in_model(self.evidence, self.model)
# Test model test
case_in_model(self.testcase, self.model, valid=False)
# Test references
reference_in_model(self.reference, self.model)
reference_in_model(self.reference2, self.model)
# Test connections
# Reference <-> Evidence
reference_in_item(self.reference, self.evidence)
# Reference2 <-> Testcase
reference_in_item(self.reference2, self.testcase, valid=False)
# Gene1 <-> Reaction1
gene_in_reaction(self.gene, self.reaction)
gene_in_reaction(self.gene2, self.reaction2, valid=False)
# Metabolite1 <-> Reaction1
metabolite_in_reaction(self.metabolite, self.reaction)
metabolite_in_reaction(self.metabolite2, self.reaction2)
# Evidence <-> Gene1/Reaction
item_in_evidence(self.gene, self.evidence)
item_in_evidence(self.reaction, self.evidence)
def test_delete_testcase(self):
# Action
self.model.gem_remove_tests((self.testcase,))
# Test genes
gene_in_model(self.gene, self.model)
gene_in_model(self.gene2, self.model)
# Test reactions
reaction_in_model(self.reaction, self.model)
reaction_in_model(self.reaction2, self.model)
# Test metabolites
metabolite_in_model(self.metabolite, self.model)
metabolite_in_model(self.metabolite2, self.model)
# Test evidences
evidence_in_model(self.evidence, self.model)
# Test model test
case_in_model(self.testcase, self.model, valid=False)
# Test references
reference_in_model(self.reference, self.model)
reference_in_model(self.reference2, self.model)
# Test connections
# Reference <-> Evidence
reference_in_item(self.reference, self.evidence)
# Reference2 <-> Testcase
reference_in_item(self.reference2, self.testcase, valid=False)
# Gene1 <-> Reaction1
gene_in_reaction(self.gene, self.reaction)
gene_in_reaction(self.gene2, self.reaction2)
# Metabolite1 <-> Reaction1
metabolite_in_reaction(self.metabolite, self.reaction)
metabolite_in_reaction(self.metabolite2, self.reaction2)
# Evidence <-> Gene1/Reaction
item_in_evidence(self.gene, self.evidence)
item_in_evidence(self.reaction, self.evidence)
def test_delete_referenec(self):
# Action
self.model.gem_remove_references((self.reference,))
# Test genes
gene_in_model(self.gene, self.model)
gene_in_model(self.gene2, self.model)
# Test reactions
reaction_in_model(self.reaction, self.model)
reaction_in_model(self.reaction2, self.model)
# Test metabolites
metabolite_in_model(self.metabolite, self.model)
metabolite_in_model(self.metabolite2, self.model)
# Test evidences
evidence_in_model(self.evidence, self.model)
# Test model test
case_in_model(self.testcase, self.model)
# Test references
reference_in_model(self.reference, self.model, valid=False)
reference_in_model(self.reference2, self.model)
# Test connections
# Reference <-> Evidence
reference_in_item(self.reference, self.evidence, valid=False)
# Reference2 <-> Testcase
reference_in_item(self.reference2, self.testcase)
# Gene1 <-> Reaction1
gene_in_reaction(self.gene, self.reaction)
gene_in_reaction(self.gene2, self.reaction2)
# Metabolite1 <-> Reaction1
metabolite_in_reaction(self.metabolite, self.reaction)
metabolite_in_reaction(self.metabolite2, self.reaction2)
# Evidence <-> Gene1/Reaction
item_in_evidence(self.gene, self.evidence)
item_in_evidence(self.reaction, self.evidence)
def test_delete_reference2(self):
# Action
self.model.gem_remove_references((self.reference2,))
# Test genes
gene_in_model(self.gene, self.model)
gene_in_model(self.gene2, self.model)
# Test reactions
reaction_in_model(self.reaction, self.model)
reaction_in_model(self.reaction2, self.model)
# Test metabolites
metabolite_in_model(self.metabolite, self.model)
metabolite_in_model(self.metabolite2, self.model)
# Test evidences
evidence_in_model(self.evidence, self.model)
# Test model test
case_in_model(self.testcase, self.model)
# Test references
reference_in_model(self.reference, self.model)
reference_in_model(self.reference2, self.model, valid=False)
# Test connections
# Reference <-> Evidence
reference_in_item(self.reference, self.evidence)
# Reference2 <-> Testcase
reference_in_item(self.reference2, self.testcase, valid=False)
# Gene1 <-> Reaction1
gene_in_reaction(self.gene, self.reaction)
gene_in_reaction(self.gene2, self.reaction2)
# Metabolite1 <-> Reaction1
metabolite_in_reaction(self.metabolite, self.reaction)
metabolite_in_reaction(self.metabolite2, self.reaction2)
# Evidence <-> Gene1/Reaction
item_in_evidence(self.gene, self.evidence)
item_in_evidence(self.reaction, self.evidence)