def test_sbol_role(self, nm_url, cell_val, raising_err, roles, expected,
sbol_component, sbol_doc):
x = cf.sbol_methods(nm_url, sbol_component, sbol_doc, cell_val)
if len(roles) > 0:
for role in roles:
sbol_component.roles = sbol_component.roles + [
f'http://purl.obolibrary.org/obo/SO_{role}'
]
if raising_err:
with pytest.raises(expected):
x.sbol_role()
else:
expected = [
f'http://purl.obolibrary.org/obo/SO_{role}'
for role in expected
]
x.sbol_role()
sbol_doc.addComponentDefinition(sbol_component)
comp = sbol_doc.componentDefinitions[
'http://examples.org/test_comp_name/1']
assert set(comp.roles) == set(expected)
def test_sbol_displayId(self, nm_url, cell_val, raising_err, expected1,
expected2, sbol_component, sbol_doc):
x = cf.sbol_methods(nm_url, sbol_component, sbol_doc, cell_val)
if raising_err:
with pytest.raises(expected1):
x.sbol_displayId()
else:
x.sbol_displayId()
sbol_doc.addComponentDefinition(sbol_component)
comp = sbol_doc.componentDefinitions[
'http://examples.org/test_comp_name/1']
assert comp.name == expected1 and comp.displayId == expected2
def test_dcterms_description(self, nm_url, cell_val, raising_err, expected,
sbol_component, sbol_doc):
x = cf.sbol_methods(nm_url, sbol_component, sbol_doc, cell_val)
if raising_err:
with pytest.raises(expected):
x.dcterms_description()
else:
x.dcterms_description()
sbol_doc.addComponentDefinition(sbol_component)
comp = sbol_doc.componentDefinitions[
f'http://examples.org/{sbol_component.name}/1']
assert comp.description == expected
def test_sbh_alteredSequence(self, nm_url, cell_val, raising_err, expected,
sbol_component, sbol_doc):
x = cf.sbol_methods(nm_url, sbol_component, sbol_doc, cell_val)
if raising_err:
with pytest.raises(expected):
x.sbh_alteredSequence()
else:
x.sbh_alteredSequence()
sbol_doc.addComponentDefinition(sbol_component)
comp = sbol_doc.componentDefinitions[
'http://examples.org/test_comp_name/1']
assert comp.wasGeneratedBy[0] == expected
def test_sbh_sourceOrganism(self, nm_url, cell_val, raising_err, expected,
sbol_component, sbol_doc):
x = cf.sbol_methods(nm_url, sbol_component, sbol_doc, cell_val)
if raising_err:
with pytest.raises(expected):
x.sbh_sourceOrganism()
else:
x.sbh_sourceOrganism()
sbol_doc.addComponentDefinition(sbol_component)
comp = sbol_doc.componentDefinitions[
'http://examples.org/test_comp_name/1']
assert comp.sourceOrganism == expected
def test_switch(self, sbol_term, nm_url, cell_val, raising_err, expected,
sbol_component, sbol_doc, monkeypatch):
def fake_NA(self):
return "fake_NA"
def fake_add_new(self):
return "fake_add_new"
monkeypatch.setattr(cf.sbol_methods, 'Not_applicable', fake_NA)
monkeypatch.setattr(cf.sbol_methods, 'add_new', fake_add_new)
x = cf.sbol_methods(nm_url, sbol_component, sbol_doc, cell_val)
if raising_err:
with pytest.raises(expected):
x.switch(sbol_term)
else:
assert x.switch(sbol_term) == expected
def test_add_new(self, nm_url, sbol_term, cell_val, raising_err, expected,
sbol_component, sbol_doc):
x = cf.sbol_methods(nm_url, sbol_component, sbol_doc, cell_val)
x.sbol_term = sbol_term
if raising_err:
with pytest.raises(expected):
x.add_new()
else:
x.add_new()
sbol_doc.addComponentDefinition(sbol_component)
sbol_term_sfx = sbol_term.split("_", 1)[1]
comp = sbol_doc.componentDefinitions[
'http://examples.org/test_comp_name/1']
comp_attr = getattr(comp, sbol_term_sfx)
assert comp_attr == expected
def test_sbol_sequence(self, nm_url, cell_val, raising_err, expected,
sbol_component, sbol_doc):
x = cf.sbol_methods(nm_url, sbol_component, sbol_doc, cell_val)
if raising_err:
with pytest.raises(expected):
x.sbol_sequence()
else:
x.sbol_sequence()
sbol_doc.addComponentDefinition(sbol_component)
comp = sbol_doc.componentDefinitions[
f'http://examples.org/{sbol_component.name}/1']
seq = sbol_doc.sequences[
f'http://examples.org/{sbol_component.name}_sequence/1']
assert seq.elements == expected and str(
comp.sequence
) == f'http://examples.org/{sbol_component.name}_sequence/1'
def test_sbh_dataSource(self, nm_url, cell_val, raising_err,
pubmedExpected, expected, sbol_component,
sbol_doc):
x = cf.sbol_methods(nm_url, sbol_component, sbol_doc, cell_val)
if raising_err:
with pytest.raises(expected):
x.sbh_dataSource()
else:
x.sbh_dataSource()
sbol_doc.addComponentDefinition(sbol_component)
comp = sbol_doc.componentDefinitions[
'http://examples.org/test_comp_name/1']
if pubmedExpected:
identi = os.path.split(expected)[1]
assert comp.wasDerivedFrom[
0] == expected and comp.OBI_0001617 == identi
else:
assert comp.wasDerivedFrom[0] == expected