class DocumentTestCase(unittest.TestCase):
def setUp(self):
self.document = Document('http://example.org/sbol/')
def test_create_invalid_url(self):
with self.assertRaises(Exception) as context:
doc = Document('example.org')
self.assertTrue('Invalid namespace URI' in str(context.exception))
def test_create_example_document(self):
gene = ComponentDefinition("BB0001")
promoter_seq = Sequence("R0010_seq", "ggctgca")
RBS_seq = Sequence("B0032_seq", "aattatataaa")
CDS_seq = Sequence("E0040_seq", "atgtaa")
terminator_seq = Sequence("B0012_seq", "attcga")
promoter = ComponentDefinition("R0010", roles=['Promoter'], sequences=[promoter_seq])
CDS = ComponentDefinition("B0032", roles=['CDS'], sequences=[CDS_seq])
RBS = ComponentDefinition("E0040", roles=['RBS'], sequences=[RBS_seq])
terminator = ComponentDefinition("B0012", roles=['Terminator'], sequences=[terminator_seq])
self.document.add_component_definition(gene)
self.document.add_component_definition(promoter)
self.document.add_component_definition(CDS)
self.document.add_component_definition(RBS)
self.document.add_component_definition(terminator)
self.assertTrue(len(self.document._sequences) == 0)
self.document.assemble_component(gene, [promoter, RBS, CDS, terminator])
self.assertTrue(len(self.document._components) == 5)
self.assertTrue(len(self.document._sequences) == 5)
def test_read_valid(self):
for file_path in os.listdir('./snekbol/tests/valid'):
if file_path.endswith('xml'):
with open('./snekbol/tests/valid/'+file_path) as rf:
doc = Document('https://example.org/sbol/')
doc.read(rf)
from snekbol.document import Document
doc = Document('https://genemill.liv.ac.uk/sbol/')
with open('tests/AnnotationOutput.xml', 'r') as f:
doc.read(f)
with open('tests/AnnotationOutput_rewrite.xml', 'wb') as fw:
doc.write(fw)
def setUp(self):
self.document = Document('http://example.org/sbol/')
def test_read_valid(self):
for file_path in os.listdir('./snekbol/tests/valid'):
if file_path.endswith('xml'):
with open('./snekbol/tests/valid/'+file_path) as rf:
doc = Document('https://example.org/sbol/')
doc.read(rf)
def test_create_invalid_url(self):
with self.assertRaises(Exception) as context:
doc = Document('example.org')
self.assertTrue('Invalid namespace URI' in str(context.exception))