def test_normalize(self):
filename_core_1 = path.join(self.tempdir, 'model-1.xlsx')
filename_seq_1 = path.join(self.tempdir, 'seq-1.fna')
filename_core_2 = path.join(self.tempdir, 'model-2.xlsx')
filename_seq_2 = path.join(self.tempdir, 'seq-2.fna')
kb = wc_kb.KnowledgeBase(id='kb',
name='KB',
version='0.0.1a',
wc_kb_version='0.0.0')
io.Writer().run(kb,
filename_core_1,
filename_seq_1,
set_repo_metadata_from_path=False)
# with same dest
with __main__.App(
argv=['normalize', filename_core_1, filename_seq_1]) as app:
app.run()
kb2 = io.Reader().run(filename_core_1, filename_seq_1)
self.assertTrue(kb2.is_equal(kb))
# with different dest
with __main__.App(argv=[
'normalize', filename_core_1, filename_seq_1, '--dest-core',
filename_core_2, '--dest-seq', filename_seq_2
]) as app:
app.run()
kb2 = io.Reader().run(filename_core_2, filename_seq_2)
self.assertTrue(kb2.is_equal(kb))
def test_get_version(self):
with CaptureOutput() as capturer:
with __main__.App(argv=['-v']) as app:
with self.assertRaises(SystemExit):
app.run()
self.assertEqual(capturer.get_text(), wc_kb.__version__)
with CaptureOutput() as capturer:
with __main__.App(argv=['--version']) as app:
with self.assertRaises(SystemExit):
app.run()
self.assertEqual(capturer.get_text(), wc_kb.__version__)
def test_convert(self):
filename_in_core = path.join(self.tempdir, 'in.core.xlsx')
filename_in_seq = path.join(self.tempdir, 'in.seq.fna')
filename_out_core = path.join(self.tempdir, 'out.core-*.csv')
filename_out_seq = path.join(self.tempdir, 'out.seq.fna')
kb = wc_kb.KnowledgeBase(id='kb',
name='KB',
version='0.0.1a',
wc_kb_version='0.0.0')
io.Writer().run(kb,
filename_in_core,
filename_in_seq,
set_repo_metadata_from_path=False)
with __main__.App(argv=[
'convert',
filename_in_core,
filename_in_seq,
filename_out_core,
filename_out_seq,
]) as app:
app.run()
self.assertTrue(
path.isfile(path.join(self.tempdir,
'out.core-Knowledge base.csv')))
def test_create_template(self):
filename_core = path.join(self.tempdir, 'core.xlsx')
filename_seq = path.join(self.tempdir, 'seq.fna')
with __main__.App(argv=[
'create-template', filename_core, filename_seq,
'--ignore-repo-metadata'
]) as app:
app.run()
self.assertTrue(path.isfile(filename_core))
self.assertTrue(path.isfile(filename_seq))
def test_validate(self):
kb = wc_kb.KnowledgeBase(id='kb',
name='KB',
version='0.0.1a',
wc_kb_version='0.0.1')
self.assertEqual(Validator().run(kb, get_related=True), None)
filename_core = path.join(self.tempdir, 'core.xlsx')
filename_seq = path.join(self.tempdir, 'seq.fna')
io.Writer().run(kb,
filename_core,
filename_seq,
set_repo_metadata_from_path=False)
with CaptureOutput() as capturer:
with __main__.App(
argv=['validate', filename_core, filename_seq]) as app:
app.run()
self.assertEqual(capturer.get_text(), 'Knowledge base is valid')
def test_validate_exception(self):
kb = wc_kb.KnowledgeBase(id='kb',
name='KB',
version='0.0.1a',
wc_kb_version='0.0.1')
kb.cell = wc_kb.Cell(id='cell')
kb.cell.compartments.create(id='c')
kb.cell.compartments.create(id='c')
self.assertNotEqual(Validator().run(kb, get_related=True), None)
filename_core = path.join(self.tempdir, 'core.xlsx')
filename_seq = path.join(self.tempdir, 'seq.fna')
io.Writer().run(kb,
filename_core,
filename_seq,
set_repo_metadata_from_path=False)
with self.assertRaisesRegex(SystemExit,
'^Knowledge base is invalid: '):
with __main__.App(
argv=['validate', filename_core, filename_seq]) as app:
app.run()
def test_update_version_metadata(self):
filename_core = path.join(self.tempdir, 'core.xlsx')
filename_seq = path.join(self.tempdir, 'seq.fna')
kb = wc_kb.KnowledgeBase(id='kb',
name='KB',
version='0.0.1a',
wc_kb_version='0.0.0')
self.assertNotEqual(kb.wc_kb_version, wc_kb.__version__)
io.Writer().run(kb,
filename_core,
filename_seq,
set_repo_metadata_from_path=False)
with __main__.App(argv=[
'update-version-metadata', filename_core, filename_seq,
'--ignore-repo-metadata'
]) as app:
app.run()
kb = io.Reader().run(filename_core, filename_seq)
self.assertEqual(kb.wc_kb_version, wc_kb.__version__)
def test_difference(self):
kb1 = wc_kb.KnowledgeBase(id='kb',
name='KB',
version='0.0.1a',
wc_kb_version='0.0.0')
filename_core_1 = path.join(self.tempdir, 'core1.xlsx')
filename_seq_1 = path.join(self.tempdir, 'seq1.fna')
io.Writer().run(kb1,
filename_core_1,
filename_seq_1,
set_repo_metadata_from_path=False)
kb2 = wc_kb.KnowledgeBase(id='kb',
name='KB',
version='0.0.1a',
wc_kb_version='0.0.0')
filename_core_2 = path.join(self.tempdir, 'core2.xlsx')
filename_seq_2 = path.join(self.tempdir, 'seq2.fna')
io.Writer().run(kb2,
filename_core_2,
filename_seq_2,
set_repo_metadata_from_path=False)
kb3 = wc_kb.KnowledgeBase(id='kb',
name='KB',
version='0.0.1a',
wc_kb_version='0.0.1')
filename_core_3 = path.join(self.tempdir, 'core3.xlsx')
filename_seq_3 = path.join(self.tempdir, 'seq3.fna')
io.Writer().run(kb3,
filename_core_3,
filename_seq_3,
set_repo_metadata_from_path=False)
with CaptureOutput() as capturer:
with __main__.App(argv=[
'difference',
filename_core_1,
filename_seq_1,
filename_core_2,
filename_seq_2,
]) as app:
app.run()
self.assertEqual(capturer.get_text(),
'Knowledge bases are identical')
with CaptureOutput() as capturer:
with __main__.App(argv=[
'difference', filename_core_1, filename_seq_1,
filename_core_2, filename_seq_2, '--compare-files'
]) as app:
app.run()
self.assertEqual(capturer.get_text(),
'Knowledge bases are identical')
with CaptureOutput() as capturer:
with __main__.App(argv=[
'difference',
filename_core_1,
filename_seq_1,
filename_core_3,
filename_seq_3,
]) as app:
app.run()
diff = (
'Objects (KnowledgeBase: "kb", KnowledgeBase: "kb") have different attribute values:\n '
'`wc_kb_version` are not equal:\n 0.0.0 != 0.0.1')
self.assertEqual(capturer.get_text(), diff)
with CaptureOutput() as capturer:
with __main__.App(argv=[
'difference', filename_core_1, filename_seq_1,
filename_core_3, filename_seq_3, '--compare-files'
]) as app:
app.run()
diff = 'Sheet Knowledge base:\n Row 8:\n Cell B: 0.0.0 != 0.0.1'
self.assertEqual(capturer.get_text(), diff)