def add_item(self):
new_evidence = Evidence()
# Set base_item externally in order to avoid linkage from base_item to
# evidence
new_evidence.entity = self.item
dialog = EditEvidenceDialog(self.window(),
self.model,
evidence=new_evidence)
if dialog.exec_():
self.dataTable.update_row_from_item(new_evidence)
def test_saving_changes(self):
reaction = Reaction()
reference = Reference()
model = Model()
evidence = Evidence(entity=reaction)
evidence.add_reference(reference)
widget = EvidenceDisplayWidget()
model.all_evidences[evidence.internal_id] = evidence
assert evidence in reaction.evidences
assert evidence.internal_id in model.all_evidences
assert reference in evidence.references
# Set reaction and model to widget
widget.set_item(reaction, model)
assert widget.dataTable.rowCount() == 1
# Remove evidence copy from data table
widget.dataTable.setRowCount(0)
# Setup new evidence item
new_evidence = Evidence()
new_evidence.assertion = "Catalyzed by"
new_evidence.entity = reaction
reference = Reference()
new_evidence.add_reference(reference, reciprocal=False)
# Test the setup i.e. that items are only linked in a one way (evidence -> item) fashion
assert new_evidence not in reaction.evidences
assert new_evidence not in reference.linked_items
# Add new reference to widget table
widget.dataTable.update_row_from_item(new_evidence)
assert widget.dataTable.rowCount() == 1
assert widget.dataTable.item(0).link is new_evidence
# Action - Save evidences
widget.save_state()
# Check that old instance is detached from all links
assert evidence not in reaction.evidences
assert len(evidence.references) == 0
# Old evidence still kept alive by this test
old_id = evidence.internal_id
assert old_id in model.all_evidences
evidence = None
gc.collect()
assert old_id not in model.all_evidences
# Check that new evidence is linked properly
assert new_evidence in reaction.evidences
assert new_evidence.internal_id in model.all_evidences
def test_setup_links(self):
entity = Reaction()
target = Gene()
eco = "ECO:000000"
assertion = "Presence"
comment = "test comment"
reference = Reference()
evidence = Evidence()
evidence.entity = entity
evidence.target = target
evidence.eco = eco
evidence.assertion = assertion
evidence.comment = comment
evidence.add_reference(reference, reciprocal=False)
assert evidence not in entity.evidences
assert evidence not in reference.linked_items
assert evidence not in target.evidences
evidence.setup_links()
assert evidence in entity.evidences
assert evidence in reference.linked_items
assert evidence in target.evidences
