def test_parse_and_validate_manifest_expand_vars(self):
expected_fp = os.path.join(self.temp_dir.name, 'manifest.txt')
# touch the file - the valdiator will fail if it doesn't exist
open(expected_fp, 'w')
os.environ['TESTENVGWAR'] = self.temp_dir.name
manifest = io.StringIO(
'sample-id,absolute-filepath,direction\n'
'abc,$TESTENVGWAR/manifest.txt,forward')
manifest = _parse_and_validate_manifest(manifest, single_end=True)
del os.environ['TESTENVGWAR']
self.assertEqual(manifest.iloc[0]['absolute-filepath'], expected_fp)
def test_parse_and_validate_manifest_expand_vars(self):
expected_fp = os.path.join(self.temp_dir.name, 'manifest.txt')
# touch the file - the valdiator will fail if it doesn't exist
open(expected_fp, 'w')
os.environ['TESTENVGWAR'] = self.temp_dir.name
manifest = io.StringIO(
'sample-id,absolute-filepath,direction\n'
'abc,$TESTENVGWAR/manifest.txt,forward')
manifest = _parse_and_validate_manifest(manifest, single_end=True,
absolute=True)
del os.environ['TESTENVGWAR']
self.assertEqual(manifest.iloc[0]['absolute-filepath'], expected_fp)
def test_parse_and_validate_manifest_invalid(self):
manifest = io.StringIO(
'sample-id,absolute-filepath\n'
'abc,/hello/world,forward\n')
with self.assertRaisesRegex(ValueError, "header must contain"):
_parse_and_validate_manifest(manifest, single_end=True)
manifest = io.StringIO(
'sample-id,absolute-filepath,direction\n'
'abc,/hello/world\n'
'abc,/hello/world,forward\n')
with self.assertRaisesRegex(ValueError, 'contains fewer'):
_parse_and_validate_manifest(manifest, single_end=True)
manifest = io.StringIO(
'sample-id,absolute-filepath,direction\n'
'abc,/hello/world,forward\n'
'xyz,/hello/world,forward,extra-field')
with self.assertRaisesRegex(ValueError, 'contains more'):
_parse_and_validate_manifest(manifest, single_end=True)
def test_parse_and_validate_manifest_invalid(self):
manifest = io.StringIO('sample-id,absolute-filepath\n'
'abc,/hello/world,forward\n')
with self.assertRaisesRegex(
ValueError, "Expected.*absolute-filepath.*found "
"'sample-id,absolute-filepath'.$"):
_parse_and_validate_manifest(manifest,
single_end=True,
absolute=True)
manifest = io.StringIO('sample-id,absolute-filepath,direction\n'
'abc,/hello/world\n'
'abc,/hello/world,forward\n')
with self.assertRaisesRegex(ValueError, 'Empty cells'):
_parse_and_validate_manifest(manifest,
single_end=True,
absolute=True)
manifest = io.StringIO('sample-id,absolute-filepath,direction\n'
'abc,/hello/world,forward\n'
'xyz,/hello/world,forward,extra-field')
with self.assertRaisesRegex(ValueError, 'issue parsing the manifest'):
_parse_and_validate_manifest(manifest,
single_end=True,
absolute=True)
manifest = io.StringIO('sample-id,absolute-filepath,direction\n'
'abc,world,forward\n'
'xyz,world,forward')
with self.assertRaisesRegex(ValueError,
'absolute but found relative path'):
_parse_and_validate_manifest(manifest,
single_end=True,
absolute=True)
manifest = io.StringIO('sample-id,absolute-filepath,direction\n'
'abc,world,forward\n'
'abc,world,reverse')
with self.assertRaisesRegex(ValueError,
'absolute but found relative path'):
_parse_and_validate_manifest(manifest,
single_end=False,
absolute=True)
manifest = io.StringIO('sample-id,filename,direction\n'
'abc,/snap/crackle/pop/world,forward\n'
'xyz,/snap/crackle/pop/world,forward')
with self.assertRaisesRegex(ValueError,
'relative but found absolute path'):
_parse_and_validate_manifest(manifest,
single_end=True,
absolute=False)
manifest = io.StringIO('sample-id,filename,direction\n'
'abc,/snap/crackle/pop/world,forward\n'
'abc,/snap/crackle/pop/world,reverse')
with self.assertRaisesRegex(ValueError,
'relative but found absolute path'):
_parse_and_validate_manifest(manifest,
single_end=False,
absolute=False)
def test_parse_and_validate_manifest_invalid(self):
manifest = io.StringIO(
'sample-id,absolute-filepath\n'
'abc,/hello/world,forward\n')
with self.assertRaisesRegex(
ValueError, "Expected.*absolute-filepath.*found "
"'sample-id,absolute-filepath'.$"):
_parse_and_validate_manifest(manifest, single_end=True,
absolute=True)
manifest = io.StringIO(
'sample-id,absolute-filepath,direction\n'
'abc,/hello/world\n'
'abc,/hello/world,forward\n')
with self.assertRaisesRegex(ValueError, 'Empty cells'):
_parse_and_validate_manifest(manifest, single_end=True,
absolute=True)
manifest = io.StringIO(
'sample-id,absolute-filepath,direction\n'
'abc,/hello/world,forward\n'
'xyz,/hello/world,forward,extra-field')
with self.assertRaisesRegex(ValueError, 'issue parsing the manifest'):
_parse_and_validate_manifest(manifest, single_end=True,
absolute=True)
manifest = io.StringIO(
'sample-id,absolute-filepath,direction\n'
'abc,world,forward\n'
'xyz,world,forward')
with self.assertRaisesRegex(ValueError,
'absolute but found relative path'):
_parse_and_validate_manifest(manifest, single_end=True,
absolute=True)
manifest = io.StringIO(
'sample-id,absolute-filepath,direction\n'
'abc,world,forward\n'
'abc,world,reverse')
with self.assertRaisesRegex(ValueError,
'absolute but found relative path'):
_parse_and_validate_manifest(manifest, single_end=False,
absolute=True)
manifest = io.StringIO(
'sample-id,filename,direction\n'
'abc,/snap/crackle/pop/world,forward\n'
'xyz,/snap/crackle/pop/world,forward')
with self.assertRaisesRegex(ValueError,
'relative but found absolute path'):
_parse_and_validate_manifest(manifest, single_end=True,
absolute=False)
manifest = io.StringIO(
'sample-id,filename,direction\n'
'abc,/snap/crackle/pop/world,forward\n'
'abc,/snap/crackle/pop/world,reverse')
with self.assertRaisesRegex(ValueError,
'relative but found absolute path'):
_parse_and_validate_manifest(manifest, single_end=False,
absolute=False)
