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_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_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_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_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_map_metabolite_by_annotation(self, database, progress):
model = Model()
met1 = Metabolite("m1")
model.add_metabolites([met1])
met1.annotation.add(
Annotation(identifier="MNXM2", collection="metanetx.chemical"))
update_metabolite_database_mapping(database, model, progress)
assert model.database_mapping[met1] == 1
def test_edit_item_dialog_reject(self):
tab = MetaboliteTab()
model = Model()
metabolite1 = Metabolite("m1")
model.add_metabolites([metabolite1])
model.setup_metabolite_table()
model.QtMetaboliteTable.update_row_from_link = Mock()
tab.set_model(model)
tab.dataView.selectRow(0)
assert model.QtMetaboliteTable.update_row_from_link.called is False
tab.editItemSlot()
assert model.QtMetaboliteTable.update_row_from_link.called is False
def test_addition_of_attributes_only_when_set(self):
model = Model("Test")
metabolite = Metabolite(id="test")
model.add_metabolites([metabolite])
add_metabolites(self.root, model)
metabolite_node = self.root.find(sbml3_listOfSpecies+"/"+sbml3_species)
assert metabolite_node is not None
assert metabolite_node.get(fbc_charge) is None
assert metabolite_node.get(fbc_chemicalFormula) is None
assert metabolite_node.get("name") is None
assert metabolite_node.get("compartment") is None
def test_no_map_by_stoichiometry_if_any_metabolite_not_mapped(
self, database, progress):
model = Model()
met1 = Metabolite("m1")
met2 = Metabolite("m2")
model.add_metabolites((met1, met2))
model.database_mapping.update({met1: 1})
reaction = Reaction("r1")
reaction.add_metabolites({met1: -1, met2: -1})
model.add_reactions([reaction])
update_reaction_database_mapping(database, model, progress)
assert reaction not in model.database_mapping
def test_map_reaction_by_stoichiometry(self, database, progress):
model = Model()
met1 = Metabolite("m1")
met2 = Metabolite("m2")
met3 = Metabolite("m3")
met4 = Metabolite("m4")
model.add_metabolites((met1, met2, met3, met4))
model.database_mapping.update({met1: 1, met2: 2, met3: 3, met4: 4})
reaction = Reaction("r1")
reaction.add_metabolites({met1: -1, met2: -1, met3: 1, met4: 1})
model.add_reactions([reaction])
update_reaction_database_mapping(database, model, progress)
assert model.database_mapping[reaction] == 1
def test_map_reaction_by_annotation(self, database, progress):
model = Model()
met1 = Metabolite("m1")
met2 = Metabolite("m2")
model.add_metabolites([met1, met2])
reaction = Reaction("r1")
reaction.add_metabolites({met1: -1, met2: 1})
reaction.annotation.add(
Annotation(identifier="MNXR14892", collection="metanetx.reaction"))
model.add_reactions([reaction])
update_reaction_database_mapping(database, model, progress)
assert model.database_mapping[reaction] == 1
def test_add_compartments_defined_in_metabolite():
model = Model()
metabolite = Metabolite(id="test", compartment="c")
model.add_metabolites([metabolite])
root = Element("Root")
add_compartments(root, model)
compartment_list = root.find(sbml3_listOfCompartments)
assert compartment_list is not None
compartment = compartment_list.find(sbml3_compartment)
assert compartment is not None
assert compartment.get("id") == "c"
assert compartment.get("name") is None
def test_updating(self):
model = Model()
met1 = Metabolite(id="met1", formula="H2O", name="Water", charge=0., compartment="c")
react1 = Reaction(id="react1", name="test2", subsystem="test2", lower_bound=0., upper_bound=1000.)
react1.add_metabolites({met1: -1})
model.add_metabolites([met1])
model.add_reactions([react1])
model.setup_tables()
assert model.QtReactionTable.rowCount() == 1
assert model.QtMetaboliteTable.rowCount() == 1
# Check that content is right
for i, element in enumerate(model.QtMetaboliteTable.header):
assert str(getattr(met1, element.lower())) == model.QtMetaboliteTable.item(0, i).text()
# Check that metabolite id is in table
assert met1.id in model.QtReactionTable.item(0, 2).text()
# Change metabolite
met1.id = "new_id"
met1.name = "new_name"
met1.formula = "H2O2"
met1.name = "None"
met1.charge = 1.
met1.compartment = "e"
# Tables are out of sync
for i, element in enumerate(model.QtMetaboliteTable.header):
assert str(getattr(met1, element.lower())) != model.QtMetaboliteTable.item(0, i).text()
# Check reaction table out of sync
assert react1.id not in model.QtReactionTable.item(0, 2).text()
model.gem_update_metabolites([met1])
# Metabolite table updated
for i, element in enumerate(model.QtMetaboliteTable.header):
assert str(getattr(met1, element.lower())) == model.QtMetaboliteTable.item(0, i).text()
# Reaction table updated
assert met1.id in model.QtReactionTable.item(0, 2).text()
def test_add_item_dialog_reject(self):
tab = MetaboliteTab()
model = Model()
model.add_metabolites = Mock()
model.QtMetaboliteTable.update_row_from_item = Mock()
tab.set_model(model)
assert model.add_metabolites.called is False
assert model.QtMetaboliteTable.update_row_from_item.called is False
tab.addItemSlot()
assert model.add_metabolites.called is False
assert model.QtMetaboliteTable.update_row_from_item.called is False
def test_update_iteratively(self):
""" Check that metabolite are successfully
updated one after another """
react = Reaction("rea")
met1 = Metabolite("met1", formula="C7H8O2")
met2 = Metabolite("met2")
met3 = Metabolite("met3") # Update to CO2 in second iteration
react.add_metabolites({met1: 1, met3: 1, met2: -1})
react1 = Reaction("rea2") # Transfer C8H8O4
met4 = Metabolite("met4", formula="C8H8O4")
react1.add_metabolites({met2: -1, met4: 1})
# Setup model
model = Model("id")
model.add_metabolites([met1, met2, met3, met4])
model.add_reactions([react, react1])
return_value = update_formulae_iteratively(model)
assert met2.formula == met4.formula
assert met3.formula == "CO2"
assert set(return_value) == set([met2, met3])
class TestEditModelSettings:
@pytest.fixture(autouse=True)
def setup_items(self):
self.test_id = "Test_id"
self.test_name = "Test_name"
self.model = Model(self.test_id, self.test_name)
self.parent = QWidget()
self.comp1_name = "Cytoplasm"
self.comp1_id = "c"
self.new_comp_id = "n"
self.new_comp_name = "Nucleus"
self.new_comp = Compartment(self.new_comp_id, self.new_comp_name)
self.comp1 = Compartment(self.comp1_id, self.comp1_name)
self.model.gem_compartments[self.comp1_id] = self.comp1
self.metabolite = Metabolite("test", compartment=self.comp1_id)
self.model.add_metabolites([self.metabolite])
self.model.setup_tables()
self.dialog = EditModelDialog(model=self.model)
@pytest.fixture()
def patch_progress(self, monkeypatch):
monkeypatch.setattr("PyQt5.QtWidgets.QProgressDialog", Mock())
monkeypatch.setattr("PyQt5.QtWidgets.QApplication.processEvents", Mock())
def test_setup(self):
assert self.model.name == self.test_name
assert self.model.id == self.test_id
assert self.comp1_id in self.model.gem_compartments
assert self.model.gem_compartments[self.comp1_id] == self.comp1
assert self.dialog.buttonBox.button(QDialogButtonBox.Save).isEnabled() is False
assert self.dialog.input_name.text() == self.test_name
assert self.dialog.input_id.text() == self.test_id
assert self.dialog.compartmentTable.rowCount() == 1
assert self.metabolite in self.model.metabolites
def test_change_in_id_enables_button(self):
model = Model()
model.gem_compartments["c"] = Compartment("c", "Cytoplasm")
dialog = EditModelDialog(model=model)
save_button = dialog.buttonBox.button(QDialogButtonBox.Save)
# Change id
assert save_button.isEnabled() is False
QtTest.QTest.keyClick(dialog.input_id, "M")
assert save_button.isEnabled() is True
# Undo change
QtTest.QTest.keyClick(dialog.input_id, QtCore.Qt.Key_Backspace)
assert save_button.isEnabled() is False
def test_change_in_name_enables_button(self):
model = Model()
model.gem_compartments["c"] = Compartment("c", "Cytoplasm")
dialog = EditModelDialog(model=model)
save_button = dialog.buttonBox.button(QDialogButtonBox.Save)
# Change id
assert save_button.isEnabled() is False
QtTest.QTest.keyClicks(dialog.input_name, "M")
assert save_button.isEnabled() is True
# Undo change
QtTest.QTest.keyClick(dialog.input_name, QtCore.Qt.Key_Backspace)
assert save_button.isEnabled() is False
def test_add_compartment(self):
row_count = self.dialog.compartmentTable.rowCount()
self.dialog._add_new_compartment_to_table(self.new_comp)
assert self.dialog.compartmentTable.rowCount() == row_count + 1
assert self.dialog.buttonBox.button(QDialogButtonBox.Save).isEnabled() is True
assert self.dialog.input_changed() is True
def test_compartment_deletion(self):
assert self.dialog.compartmentTable.rowCount() == 1
self.dialog.compartmentTableView.selectRow(0)
QtTest.QTest.mouseClick(self.dialog.button_del_compartment, QtCore.Qt.LeftButton)
assert self.dialog.compartmentTable.rowCount() == 0
def test_change_compartment_name(self):
assert self.dialog.buttonBox.button(QDialogButtonBox.Save).isEnabled() is False
self.dialog.compartmentTable.item(0, 1).setText(self.new_comp_name)
assert self.dialog.buttonBox.button(QDialogButtonBox.Save).isEnabled() is True
def test_save_changes_id(self):
QtTest.QTest.keyClicks(self.dialog.input_id, self.test_id)
self.dialog.save_changes()
assert self.model.id == self.test_id + self.test_id
def test_save_changes_name(self):
QtTest.QTest.keyClicks(self.dialog.input_name, self.test_name)
self.dialog.save_changes()
assert self.model.name == self.test_name + self.test_name
def test_save_changes_compartment_addition(self):
self.dialog._add_new_compartment_to_table(self.new_comp)
assert self.dialog.compartmentTable.rowCount() == 2
self.dialog.save_changes()
assert self.model.gem_compartments == {self.comp1_id: self.comp1,
self.new_comp_id: self.new_comp}
assert self.metabolite in self.model.metabolites
def test_save_changes_compartment_deletion(self):
self.dialog.compartmentTable.setRowCount(0)
assert self.metabolite in self.model.metabolites
self.dialog.save_changes()
assert self.model.gem_compartments == {}
assert self.metabolite not in self.model.metabolites
def test_save_changed_compartment_name(self):
self.dialog.compartmentTable.item(0, 1).setText(self.new_comp_name)
assert self.dialog.buttonBox.button(QDialogButtonBox.Save).isEnabled() is True
self.dialog.save_changes()
assert self.model.gem_compartments[self.comp1_id].name == self.new_comp_name
def test_save_changed_compartment_id(self):
new_id = "z"
self.dialog.compartmentTable.item(0, 0).setText(new_id)
self.dialog.save_changes()
assert "z" in self.model.gem_compartments
assert self.metabolite.compartment == new_id
assert self.model.gem_compartments[new_id] is self.comp1
assert self.comp1.name == self.comp1_name
class TestModelDisplayWidget:
@pytest.fixture(autouse=True)
def setup_items(self):
self.parent = QWidget()
self.widget = ModelDisplayWidget(self.parent)
self.test_id = "Test_model"
self.test_name = "Test name"
self.model = Model(self.test_id, name=self.test_name)
self.comp1_abbrev = "c"
self.comp1_name = "Cytoplasm"
self.comp1 = Compartment(self.comp1_abbrev, self.comp1_name)
self.model.gem_compartments[self.comp1_abbrev] = self.comp1
self.gene = Gene(id="test_id", name="test_name")
self.metabolite = Metabolite(id="test_id", compartment="c")
self.reaction = Reaction(id="test_id")
self.model.add_metabolites([self.metabolite])
self.model.add_reactions([self.reaction])
self.model.genes.append(self.gene)
def test_setup(self):
assert len(self.model.metabolites) == 1
assert len(self.model.reactions) == 1
assert len(self.model.genes) == 1
assert self.model.id == self.test_id
assert self.model.name == self.test_name
assert self.model.gem_compartments[self.comp1_abbrev] == self.comp1
def test_model_addition(self):
path = "Test_path"
self.widget.set_model(self.model, path=path)
assert self.widget.label_model_id.text() == self.test_id
assert self.widget.label_model_name.text() == self.test_name
assert self.widget.label_number_genes.text() == str(
len(self.model.genes))
assert self.widget.label_number_reactions.text() == str(
len(self.model.reactions))
assert self.widget.label_number_metabolites.text() == str(
len(self.model.metabolites))
assert self.widget.label_model_path.text() == path
def test_clear_information(self):
path = "Test_path"
self.widget.set_model(self.model, path=path)
self.widget.clear_information()
assert self.widget.label_model_name.text() == ""
assert self.widget.label_model_id.text() == ""
assert self.widget.label_number_reactions.text() == ""
assert self.widget.label_number_metabolites.text() == ""
assert self.widget.label_number_genes.text() == ""
assert self.widget.label_model_path.text() == path
def test_setting_empty_model(self):
path = "Test_path"
self.widget.set_model(self.model, path=path)
self.widget.set_model(None)
assert self.widget.label_model_name.text() == ""
assert self.widget.label_model_id.text() == ""
assert self.widget.label_number_reactions.text() == ""
assert self.widget.label_number_metabolites.text() == ""
assert self.widget.label_number_genes.text() == ""
assert self.widget.label_model_path.text() == ""
class TestMetaboliteIO:
@pytest.fixture(autouse=True)
def setup_items(self):
self.test_id = "test_id"
self.test_name = "test_name"
self.test_formula = "H2O"
self.test_charge = 0
self.test_compartment = "t"
self.metabolite = Metabolite(id=self.test_id,
name=self.test_name,
formula=self.test_formula,
charge=self.test_charge,
compartment=self.test_compartment)
self.annotation1 = Annotation("chebi", "CHEBI:37671")
self.metabolite.annotation.add(self.annotation1)
self.model = Model("Test")
self.model.add_metabolites([self.metabolite])
self.root = Element("root")
def test_setup(self):
assert self.metabolite.id == self.test_id
assert self.metabolite.name == self.test_name
assert self.metabolite.formula == self.test_formula
assert self.metabolite.compartment == self.test_compartment
assert self.metabolite.charge == self.test_charge
assert len(self.model.metabolites) == 1
assert len(self.metabolite.annotation) == 1
assert isinstance(self.metabolite.annotation, set)
assert self.annotation1 in self.metabolite.annotation
def test_adding_metabolites_to_xml(self):
add_metabolites(self.root, self.model)
assert len(self.root) == 1
metabolite_list_node = self.root.find(sbml3_listOfSpecies)
assert metabolite_list_node is not None
assert len(metabolite_list_node) == 1
metabolite = metabolite_list_node.find(sbml3_species)
assert metabolite is not None
assert metabolite.get(fbc_charge) is None
assert metabolite.get("compartment") == self.test_compartment
assert metabolite.get(fbc_chemicalFormula) == self.test_formula
assert metabolite.get("id") == cobra_metabolite_prefix + self.test_id
assert metabolite.get("name") == self.test_name
annotation_node = metabolite.find("/".join([sbml3_annotation, rdf_RDF, rdf_description,
bqbiol_is, rdf_bag, rdf_li]))
assert annotation_node is not None
assert annotation_node.get(rdf_resource) == "http://identifiers.org/chebi/CHEBI:37671"
def test_addition_of_attributes_only_when_set(self):
model = Model("Test")
metabolite = Metabolite(id="test")
model.add_metabolites([metabolite])
add_metabolites(self.root, model)
metabolite_node = self.root.find(sbml3_listOfSpecies+"/"+sbml3_species)
assert metabolite_node is not None
assert metabolite_node.get(fbc_charge) is None
assert metabolite_node.get(fbc_chemicalFormula) is None
assert metabolite_node.get("name") is None
assert metabolite_node.get("compartment") is None
def test_parsing_of_valid_metabolite(self):
parent_node = ET.fromstring(valid_metabolite_with_annotation)
metabolites = parse_metabolites(parent_node)
assert len(metabolites) == 1
metabolite = metabolites[0]
assert metabolite.id == "13GLUCAN"
assert metabolite.name == "1,3-beta-D-Glucan"
assert metabolite.compartment == "c"
assert metabolite.formula == "C18H32O16"
assert metabolite.charge == 0
assert len(metabolite.annotation) == 3
assert Annotation("inchi", "InChI=1S/C18H32O16/c19-1-4-7(22)10(25)11(26)17(31-4)34-15-9(24)6(3-21)32-18(13(15)28)33-14-8(23)5(2-20)30-16(29)12(14)27/h4-29H,1-3H2/t4-,5-,6-,7-,8-,9-,10+,11-,12-,13-,14+,15+,16-,17+,18+/m1/s1") in metabolite.annotation
assert Annotation("chebi", "CHEBI:37671") in metabolite.annotation
assert Annotation("kegg.compound", "C00965") in metabolite.annotation
def test_parsing_of_valid_metabolite_wo_annotation(self):
parent_node = ET.fromstring(valid_metabolite_wo_annotation)
metabolites = parse_metabolites(parent_node)
assert len(metabolites) == 1
metabolite = metabolites[0]
assert metabolite.id == "13GLUCAN"
assert metabolite.name == "1,3-beta-D-Glucan"
assert metabolite.compartment == "c"
assert metabolite.formula == ""
assert metabolite.charge == 0
def test_read_write_consistency(self):
root = Element("root")
add_metabolites(root, self.model)
metabolites = parse_metabolites(root)
assert len(metabolites) == 1
metabolite = metabolites[0]
assert metabolite.id == self.test_id
assert metabolite.name == self.test_name
assert metabolite.charge == self.test_charge
assert metabolite.formula == self.test_formula
assert isinstance(metabolite.annotation, set)
assert self.annotation1 in metabolite.annotation
