def test_setting_resetting_boundaries(self):
gene = Gene()
reaction = Reaction(lower_bound=-1000., upper_bound=1000.)
reaction.add_child(gene)
gene.functional = True
condition = GeneSetting(gene, False)
assert gene.functional is True
assert reaction.upper_bound == 1000.
assert reaction.lower_bound == -1000.
condition.do()
assert gene.functional is False
assert reaction.upper_bound == 0.
assert reaction.lower_bound == 0.
condition.undo()
assert gene.functional is True
assert reaction.upper_bound == 1000.
assert reaction.lower_bound == -1000.
# Check that calling undo second time does not change value
condition.undo()
assert gene.functional is True
assert reaction.upper_bound == 1000.
assert reaction.lower_bound == -1000.
def test_addition_emits_changed(self):
parent = QWidget()
widget = GeneSettingDisplayWidget(parent)
test = ModelTest()
gene = Gene()
setting = GeneSetting(gene, False)
model = Model()
test.add_setting(setting)
widget.set_item(test, model)
detector = Mock()
widget.changed.connect(detector.test)
widget.dataTable.update_row_from_item(GeneSetting(Gene(), True))
assert detector.test.called is True
assert widget.content_changed is True
def item_from_row(self, row_idx):
""" Return the setting object as represented in a table row """
choice = self.item(row_idx, 1).text()
if choice == "active":
functional = True
elif choice == "inactive":
functional = False
else:
raise ValueError(
"Unknown state '{}' for gene activity.".format(choice))
return GeneSetting(gene=self.item(row_idx, 0).link,
activity=functional)
def test_modification_emits_changed(self):
parent = QWidget()
widget = GeneSettingDisplayWidget(parent)
test = ModelTest()
gene = Gene()
setting = GeneSetting(gene, True)
model = Model()
test.add_setting(setting)
widget.set_item(test, model)
detector = Mock()
widget.changed.connect(detector.test)
widget.dataTable.item(0, 1).setText("inactive")
assert detector.test.called is True
assert widget.content_changed is 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_setting_item(self):
parent = QWidget()
widget = GeneSettingDisplayWidget(parent)
test = ModelTest()
gene = Gene()
setting = GeneSetting(gene, False)
model = Model()
test.add_setting(setting)
widget.dataTable.populate_table = Mock()
widget.set_item(test, model)
widget.dataTable.populate_table.assert_called_once_with(
test.gene_settings)
assert widget.model is model
assert widget.model_test is test
def test_deletion_emits_changed(self):
parent = QWidget()
widget = GeneSettingDisplayWidget(parent)
test = ModelTest()
gene = Gene()
setting = GeneSetting(gene, False)
model = Model()
test.add_setting(setting)
widget.set_item(test, model)
detector = Mock()
widget.changed.connect(detector.test)
widget.tableView.selectRow(0)
QtTest.QTest.mouseClick(widget.button_del_item, QtCore.Qt.LeftButton)
assert widget.dataTable.rowCount() == 0
assert detector.test.called is True
assert widget.content_changed is True
def test_saving_items(self):
parent = QWidget()
widget = GeneSettingDisplayWidget(parent)
test = ModelTest()
gene = Gene()
setting = GeneSetting(gene, False)
model = Model()
test.add_setting(setting)
widget.set_item(test, model)
new_test = ModelTest()
widget.model_test = new_test
assert len(new_test.gene_settings) == 0
widget.save_state()
assert len(new_test.gene_settings) == 1
new_setting = list(new_test.gene_settings)[0]
assert new_setting == setting
assert new_setting is not setting
def parse_test_from_xml(model_node, model, progress=None):
list_of_tests_node = model_node.find(ge_listOfTests)
if list_of_tests_node is None:
return
elif progress is None:
pass
elif not progress.wasCanceled():
progress.setLabelText("Reading test cases...")
progress.setRange(0, len(list_of_tests_node))
else:
return
for i, test_node in enumerate(list_of_tests_node.iterfind(ge_testCase)):
if progress is None:
pass
elif not progress.wasCanceled():
progress.setValue(i)
QApplication.processEvents()
else:
return
new_test = ModelTest(description=test_node.get("description"),
comment=test_node.get("comment"))
settings_list_node = test_node.find(ge_listOfSettings)
outcomes_list_node = test_node.find(ge_listOfOutcomes)
reference_list_node = test_node.find(ge_listOfReferenceLinks)
# Add settings
if settings_list_node is not None:
for setting_node in settings_list_node.iterfind(
ge_reactionSetting):
reaction = model.reactions.get_by_id(
clip(setting_node.get("reactionId"), "R_"))
new_setting = ReactionSetting(
reaction=reaction,
upper_bound=float(setting_node.get("upperBound")),
lower_bound=float(setting_node.get("lowerBound")),
objective_coefficient=float(
setting_node.get("objectiveCoefficient")))
new_test.add_setting(new_setting)
for gene_setting_node in settings_list_node.iterfind(
ge_geneSetting):
gene = model.genes.get_by_id(
clip(gene_setting_node.get("geneId"), "G_"))
new_setting = GeneSetting(gene)
if gene_setting_node.get("active") == "True":
new_setting.activity = True
elif gene_setting_node.get("active") == "False":
new_setting.activity = False
else:
raise ValueError(
"Unexpected value for activity in gene setting.")
new_test.add_setting(new_setting)
# Add outcomes
if outcomes_list_node is not None:
for outcome_node in outcomes_list_node.iterfind(ge_outcome):
reaction = model.reactions.get_by_id(
clip(outcome_node.get("reactionId"), "R_"))
new_outcome = Outcome(reaction=reaction,
value=float(outcome_node.get("value")),
operator=outcome_node.get("operator"))
new_test.add_outcome(new_outcome)
# Add references
if reference_list_node is not None:
for refLink_node in reference_list_node.iterfind(ge_referenceLink):
new_test.add_reference(
model.references[refLink_node.get("id")])
model.tests.append(new_test)
def setup_items(self):
self.test = ModelTest()
self.outcome1 = Outcome()
self.reaction_setting = ReactionSetting()
self.gene_setting = GeneSetting()
self.reference1 = Reference()