def test_consistency_write_read():
model1 = Model()
model1.gem_compartments["c"] = Compartment("c", "Cytoplasm")
root = Element("Root")
add_compartments(root, model1)
model2 = Model()
parse_compartments(root, model2)
assert model2.gem_compartments == model1.gem_compartments
def test_full_example(self):
""" Test that a minimal evidence example is parsed correctly """
xml_tree = ET.fromstring(full_evidence)
model = Model()
reaction = Reaction("Test")
target_item = Gene("target_id")
reference = Reference("ref_id")
model.add_reaction(reaction)
model.add_gene(target_item)
model.add_reference(reference)
assert len(model.all_evidences) == 0
assert len(reaction.evidences) == 0
parse_evidences_from_xml(xml_tree, model)
assert len(model.all_evidences) == 1
assert len(reaction.evidences) == 1
evidence = list(reaction.evidences)[0]
assert evidence.entity is reaction
assert evidence.target is target_item
assert evidence.assertion == "Catalyzed by"
assert evidence.eco == "ECO:0000000"
assert len(evidence.references) == 1
assert list(evidence.references)[0] is reference
assert evidence.comment == "test comment"
def test_get_item_from_model(self):
model = Model("test id")
reaction = Reaction("r_id")
metabolite = Metabolite("m_id")
gene = Gene("g_id")
# ToDo: Add gene group
model.add_reactions([reaction])
model.add_metabolites([metabolite]),
model.add_gene(gene)
# ToDo: Add gene group
assert get_item_from_model("Model", model.id, model) is model
assert get_item_from_model("Reaction", reaction.id, model) is reaction
assert get_item_from_model("Metabolite", metabolite.id, model) is metabolite
assert get_item_from_model("Gene", gene.id, model) is gene
# Test expected errors
# GeneGroup not implemented
with pytest.raises(NotImplementedError):
get_item_from_model("GeneGroup", "test_id", model)
# ID not in model
with pytest.raises(KeyError):
get_item_from_model("Reaction", "Not in model", model)
with pytest.raises(KeyError):
get_item_from_model("Metabolite", "Not in model", model)
with pytest.raises(KeyError):
get_item_from_model("Gene", "Not in model", model)
def test_close_model_model_cancel(self, mock_close_model):
main_window = mock_close_model
main_window.model = Model()
assert main_window.close_model() is False
assert main_window.save_table_headers.called is False
assert main_window._set_model_loaded.called is False
assert main_window.set_model.called is False
def test_save_state_new_metabolite(self):
metabolite = Metabolite()
model = Model()
widget = MetaboliteAttributesDisplayWidget()
widget.set_item(metabolite, model)
new_id = "New"
new_name = "Name"
new_charge = 2.
new_formula = "H20"
new_compartment = "c"
widget.iDLineEdit.setText(new_id)
widget.nameLineEdit.setText(new_name)
widget.chargeSpinBox.setValue(new_charge)
widget.formulaLineEdit.setText(new_formula)
widget.compartmentComboBox.addItem(new_compartment)
widget.compartmentComboBox.setCurrentText(new_compartment)
widget.save_state()
assert metabolite.id == new_id
assert metabolite.name == new_name
assert metabolite.charge == new_charge
assert metabolite.formula == new_formula
assert metabolite.compartment == new_compartment
assert metabolite in model.metabolites
assert metabolite in model.QtMetaboliteTable.get_items()
def setup_items(self):
self.model = Model()
self.testcase = ModelTest(description="test_description")
self.reaction1 = Reaction(id="r1")
self.testsetting1 = ReactionSetting(self.reaction1,
upper_bound=1000.,
lower_bound=0.,
objective_coefficient=0.)
self.testcase.add_setting(self.testsetting1)
self.reaction3 = Reaction(id="r3")
self.outcome = Outcome(self.reaction3, value=100., operator="greater")
self.testcase.add_outcome(self.outcome)
self.reference = Reference(id="test_refid")
self.testcase.add_reference(self.reference)
self.model.add_reactions([self.reaction1, self.reaction3])
self.model.references[self.reference.id] = self.reference
self.model.tests.append(self.testcase)
self.model.setup_tests_table()
self.root = Element("root", nsmap={None: ge_ns})
add_tests_to_xml(self.root, self.model)
def test_map_metabolite_by_formula(self, database, progress):
model = Model()
met1 = Metabolite("m1", formula="H2O")
model.add_metabolites([met1])
update_metabolite_database_mapping(database, model, progress)
assert model.database_mapping[met1] == 1
def test_not_mapped_for_name_substring(self, database, progress):
model = Model()
met1 = Metabolite("m1", name="ater")
model.add_metabolites([met1])
update_metabolite_database_mapping(database, model, progress)
assert model.database_mapping[met1] is None
def test_setting_reaction(self):
widget = ReactionAttributesDisplayWidget()
reaction = Reaction(id="id",
name="name",
subsystem="subsystem",
lower_bound=-1000.,
upper_bound=1000.)
model = Model()
model.add_reactions((reaction, ))
reaction.objective_coefficient = 1.
assert widget.idLineEdit.text() == ""
assert widget.nameLineEdit.text() == ""
assert widget.subsystemLineEdit.text() == ""
assert widget.lowerBoundInput.value() == 0.
assert widget.upperBoundInput.value() == 0.
assert widget.objectiveCoefficientInput.value() == 0.
assert widget.content_changed is False
assert widget.valid_inputs() is False
widget.set_item(reaction, model)
assert widget.idLineEdit.text() == reaction.id
assert widget.nameLineEdit.text() == reaction.name
assert widget.subsystemLineEdit.text() == reaction.subsystem
assert widget.lowerBoundInput.value() == reaction.lower_bound
assert widget.upperBoundInput.value() == reaction.upper_bound
assert widget.objectiveCoefficientInput.value(
) == reaction.objective_coefficient
assert widget.content_changed is False
assert widget.valid_inputs() is True
def test_deletion(self, user_response):
tab = MetaboliteTab()
model = Model()
metabolite1 = Metabolite("m1")
metabolite2 = Metabolite("m2")
metabolite3 = Metabolite("m3")
model.add_metabolites([metabolite1, metabolite2, metabolite3])
model.setup_metabolite_table()
assert len(
model.metabolites) == model.QtMetaboliteTable.rowCount() == 3
tab.set_model(model)
tab.confirmDeletion = Mock(return_value=user_response)
item = tab.dataTable.item(1, 0)
selected_metabolite = item.link
source_index = tab.dataTable.indexFromItem(item)
view_index = tab.proxyModel.mapFromSource(source_index)
tab.dataView.selectRow(view_index.row())
assert tab.confirmDeletion.called is False
tab.deleteItemSlot()
assert tab.confirmDeletion.called is True
assert (selected_metabolite in model.metabolites) is not user_response
assert tab.dataTable.findItems(
selected_metabolite.id) is not user_response
if user_response:
assert len(
model.metabolites) == model.QtMetaboliteTable.rowCount() == 2
def test_close_model_model_accept(self, mock_close_model):
main_window = mock_close_model
main_window.model = Model()
assert main_window.close_model() is True
assert main_window.save_table_headers.call_count == 1
main_window._set_model_loaded.assert_called_once_with(False)
main_window.set_model.assert_called_once_with(None, None)
def setup_items(self):
self.first_author = Author(lastname="FirstLastname",
firstname="FirstFirstname",
initials="FirstInitials")
self.second_author = Author(lastname="SecondLastname",
firstname="SecondFirstname",
initials="SecondInitials")
self.authors = [self.first_author, self.second_author]
self.test_pmid = "123456"
self.test_pmc = "PMC12345"
self.test_doi = "10.1016/j.chemosphere.2016.03.102"
self.test_url = "http://google.com"
self.test_year = "1999"
self.test_title = "Test title"
self.test_journal = "Test journal"
self.test_ref_id = "Test_id"
self.reference = Reference(id=self.test_ref_id,
pmid=self.test_pmid,
pmc=self.test_pmc,
doi=self.test_doi,
url=self.test_url,
year=self.test_year,
title=self.test_title,
journal=self.test_journal,
authors=self.authors)
self.model = Model("Test")
self.model.references[self.reference.id] = self.reference
def test_writing_empty_model(self):
root = Element("root")
model = Model()
add_tests_to_xml(root, model)
assert len(root) == 0
def test_map_metabolite_by_name(self, database, progress):
model = Model()
met1 = Metabolite("m1", name="Water")
model.add_metabolites([met1])
update_metabolite_database_mapping(database, model, progress)
assert model.database_mapping[met1] == 1
def test_save_state_existing_metabolite(self):
metabolite = Metabolite(id="m1",
charge=1,
name="old name",
formula="O2",
compartment="c")
model = Model()
model.gem_add_metabolites((metabolite, ))
widget = MetaboliteAttributesDisplayWidget()
widget.set_item(metabolite, model)
new_id = "New_id"
new_name = "New name"
new_charge = 3.
new_compartment = "m"
new_formula = "H2O"
widget.iDLineEdit.setText(new_id)
widget.nameLineEdit.setText(new_name)
widget.chargeSpinBox.setValue(new_charge)
widget.compartmentComboBox.addItem(new_compartment)
widget.compartmentComboBox.setCurrentIndex(
widget.compartmentComboBox.count() - 1)
widget.formulaLineEdit.setText(new_formula)
widget.save_state()
assert metabolite.id == new_id
assert metabolite.name == new_name
assert metabolite.charge == new_charge
assert metabolite.compartment == new_compartment
assert metabolite.formula == new_formula
assert model.metabolites.has_id(new_id)
def test_setting_item(self):
metabolite = Metabolite("test_id", "H2O", "Test metabolie", -5, "m")
model = Model()
widget = MetaboliteAttributesDisplayWidget()
# Test prestate
assert widget.iDLineEdit.text() == ""
assert widget.nameLineEdit.text() == ""
assert widget.compartmentComboBox.currentText() == ""
assert widget.chargeSpinBox.value() == 0
assert widget.formulaLineEdit.text() == ""
widget.set_item(metabolite, model)
assert widget.iDLineEdit.text() == metabolite.id
assert widget.nameLineEdit.text() == metabolite.name
assert widget.compartmentComboBox.currentText(
) == metabolite.compartment
assert widget.chargeSpinBox.value() == metabolite.charge
assert widget.formulaLineEdit.text() == metabolite.formula
assert widget.valid_inputs() is True
assert widget.content_changed is False
widget.set_item(None, model)
assert widget.iDLineEdit.text() == ""
assert widget.nameLineEdit.text() == ""
assert widget.compartmentComboBox.currentText() == ""
assert widget.chargeSpinBox.value() == 0.
assert widget.formulaLineEdit.text() == ""
assert widget.valid_inputs() is False
assert widget.content_changed is False
def test_saving_changes(self):
widget = ReactionAttributesDisplayWidget()
reaction = Reaction("r1")
model = Model("id")
model.add_reactions((reaction, ))
widget.set_item(reaction, model)
new_id = "New id"
new_name = "New name"
new_subsytem = "New Subsystem"
new_upper_bound = 200.5
new_lower_bound = -300.5
new_obj_coefficient = 20.4
widget.idLineEdit.setText(new_id)
widget.nameLineEdit.setText(new_name)
widget.subsystemLineEdit.setText(new_subsytem)
widget.upperBoundInput.setValue(new_upper_bound)
widget.lowerBoundInput.setValue(new_lower_bound)
widget.objectiveCoefficientInput.setValue(new_obj_coefficient)
# Action
widget.save_state()
# Check that inputs are saved
assert reaction.id == new_id
assert reaction.name == new_name
assert reaction.subsystem == new_subsytem
assert reaction.lower_bound == new_lower_bound
assert reaction.upper_bound == new_upper_bound
assert reaction.objective_coefficient == new_obj_coefficient
def test_deletion(self, user_response):
tab = ReferenceTab()
model = Model()
reference1 = Reference("r1")
reference2 = Reference("r2")
reference3 = Reference("r3")
model.add_reference(reference1)
model.add_reference(reference2)
model.add_reference(reference3)
model.setup_reference_table()
assert len(model.references) == model.QtReferenceTable.rowCount() == 3
tab.set_model(model)
tab.confirmDeletion = Mock(return_value=user_response)
item = tab.dataTable.item(1, 0)
selected_reference = item.link
source_index = tab.dataTable.indexFromItem(item)
view_index = tab.proxyModel.mapFromSource(source_index)
tab.dataView.selectRow(view_index.row())
assert tab.confirmDeletion.called is False
tab.deleteItemSlot()
assert tab.confirmDeletion.called is True
assert (selected_reference.id in model.references) is not user_response
if user_response:
assert len(
model.references) == model.QtReferenceTable.rowCount() == 2
def test_setting_item(self):
gene = Gene("test_id", "name", "genome")
model = Model()
widget = GeneAttributesDisplayWidget()
# Test prestate
assert widget.iDLineEdit.text() == ""
assert widget.nameLineEdit.text() == ""
assert widget.genomeLineEdit.text() == ""
widget.set_item(gene, model)
assert widget.iDLineEdit.text() == gene.id
assert widget.nameLineEdit.text() == gene.name
assert widget.genomeLineEdit.text() == gene.genome
assert widget.valid_inputs() is True
assert widget.content_changed is False
widget.set_item(None, model)
assert widget.iDLineEdit.text() == ""
assert widget.nameLineEdit.text() == ""
assert widget.genomeLineEdit.text() == ""
assert widget.valid_inputs() is False
assert widget.content_changed is False
def test_run_test_false_outcome2(self, progress):
model_test = ModelTest()
model_test.outcomes = [self.true_outcome1, self.false_outcome1]
results = run_tests((model_test, ), Model(), progress)
status, _ = results[model_test]
assert status is False
def test_do_nothing_if_no_ambiguous_maps(self):
model = Model()
metabolite = Metabolite()
model.database_mapping[metabolite] = 1
check_ambiguous_mappings(model, None)
assert model.database_mapping[metabolite] == 1
def setup_items(self):
self.model = Model("Test")
self.c1 = Compartment(id="c", name="Cytoplasm")
self.c2 = Compartment(id="e", name="Extracellular")
self.model.gem_compartments[self.c1.id] = self.c1
self.compartment_table = CompartmentTable()
self.compartment_table.populate_table(self.model.gem_compartments.values())
self.wrong_format_abbreviation = "ca"
def test_description_loaded(self):
test = ModelTest(description="Test description")
model = Model()
self.dialog.set_test(test, model)
assert self.dialog.nameLineEdit.text() == test.description
def test_parse_compartments():
parent_node = ET.fromstring(valid_compartment_list)
model = Model()
parse_compartments(parent_node, model)
assert model.gem_compartments["p"] == Compartment("p", "Periplasm")
assert model.gem_compartments["c"] == Compartment("c", "Cytoplasm")
assert model.gem_compartments["e"] == Compartment("e", "Extracellular")
def test_add_compartment_empty_model():
model = Model()
root = Element("root")
add_compartments(root, model)
compartment_list = root.find(sbml3_listOfCompartments)
assert compartment_list is None
def test_add_metabolites(self):
model = Model()
metabolite = Metabolite("m1", compartment="c")
model.gem_add_metabolites((metabolite,))
assert metabolite in model.metabolites
assert metabolite in model.QtMetaboliteTable.get_items()
assert "c" in model.gem_compartments
def test_get_selected_item_none_selected(self):
reaction = Reaction()
model = Model()
self.widget.set_item(reaction, model)
assert self.widget.geneTable.rowCount() == 0
table_item, linked_item = self.widget.get_selected_item()
assert table_item is self.widget.geneTable
assert linked_item is reaction
def new_model(self):
if self.close_model():
model = Model()
dialog = EditModelDialog(model)
status = dialog.exec_()
if status:
self.set_model(model, None)
self._set_model_loaded(True)
def test_run_test_infeasible_solution(self, mock_optimize_infeasible,
progress):
model_test = ModelTest()
model_test.outcomes = [self.true_outcome1, self.false_outcome1]
results = run_tests((model_test, ), Model(), progress)
status, solution = results[model_test]
assert solution is mock_optimize_infeasible
assert status is False
def setup_items(self):
self.test_id = "test.id"
self.test_name = "test_name"
self.test_genome = "test_genome"
self.gene = Gene(id=self.test_id,
name=self.test_name,
genome=self.test_genome)
self.model = Model("Test_model")
self.model.genes.append(self.gene)