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