def test_fail_bad_type():
clis = _client_mocks()
clis.dfu().get_objects.return_value = {
'data': [{
'info': [
3, 'myobj', 'KBaseGenomes.GenomeComparison-2.1',
'ignored time', 7, 'someuser', 34567, 'some_workspace',
'md5 here', 416467216, {}
],
'data': {
'items': [{
'ref': '1/2/3'
}, {
'ref': '4/5/6'
}]
}
}]
}
with raises(Exception) as got:
download_sequence('34567/3/7', Path('somepath/or/other'), clis)
assert_exception_correct(
got.value,
ValueError('KBaseGenomes.GenomeComparison type is not supported'))
def test_upa_init_fail():
with raises(Exception) as got:
UPA()
assert_exception_correct(got.value, IllegalParameterError('Illegal workspace ID: None'))
_upa_init_str_fail('1', IllegalParameterError('1 is not a valid UPA'))
_upa_init_str_fail('1/2', IllegalParameterError('1/2 is not a valid UPA'))
_upa_init_str_fail('1/2/3/5', IllegalParameterError('1/2/3/5 is not a valid UPA'))
_upa_init_str_fail('1/2/3/', IllegalParameterError('1/2/3/ is not a valid UPA'))
_upa_init_str_fail('/1/2/3', IllegalParameterError('/1/2/3 is not a valid UPA'))
_upa_init_str_fail('f/2/3', IllegalParameterError('f/2/3 is not a valid UPA'))
_upa_init_str_fail('1/f/3', IllegalParameterError('1/f/3 is not a valid UPA'))
_upa_init_str_fail('1/2/f', IllegalParameterError('1/2/f is not a valid UPA'))
_upa_init_str_fail('0/2/3', IllegalParameterError('0/2/3 is not a valid UPA'))
_upa_init_str_fail('1/0/3', IllegalParameterError('1/0/3 is not a valid UPA'))
_upa_init_str_fail('1/2/0', IllegalParameterError('1/2/0 is not a valid UPA'))
_upa_init_str_fail('-24/2/3', IllegalParameterError('-24/2/3 is not a valid UPA'))
_upa_init_str_fail('1/-42/3', IllegalParameterError('1/-42/3 is not a valid UPA'))
_upa_init_str_fail('1/2/-10677810', IllegalParameterError('1/2/-10677810 is not a valid UPA'))
_upa_init_int_fail(None, 2, 3, IllegalParameterError('Illegal workspace ID: None'))
_upa_init_int_fail(1, None, 3, IllegalParameterError('Illegal object ID: None'))
_upa_init_int_fail(1, 2, None, IllegalParameterError('Illegal object version: None'))
_upa_init_int_fail(0, 2, 3, IllegalParameterError('Illegal workspace ID: 0'))
_upa_init_int_fail(1, 0, 3, IllegalParameterError('Illegal object ID: 0'))
_upa_init_int_fail(1, 2, 0, IllegalParameterError('Illegal object version: 0'))
_upa_init_int_fail(-98, 2, 3, IllegalParameterError('Illegal workspace ID: -98'))
_upa_init_int_fail(1, -6, 3, IllegalParameterError('Illegal object ID: -6'))
_upa_init_int_fail(1, 2, -87501, IllegalParameterError('Illegal object version: -87501'))
def _sample_node_build_fail_metadata(meta, expected):
with raises(Exception) as got:
SampleNode('n', SubSampleType.BIOLOGICAL_REPLICATE, controlled_metadata=meta)
assert_exception_correct(got.value, IllegalParameterError(expected.format('Controlled')))
with raises(Exception) as got:
SampleNode('n', SubSampleType.BIOLOGICAL_REPLICATE, user_metadata=meta)
assert_exception_correct(got.value, IllegalParameterError(expected.format('User')))
def test_check_string_control_characters():
for string in ['foo \b bar', 'foo\u200bbar', 'foo\0bar', 'foo\bbar']:
with raises(Exception) as got:
check_string(string, 'var name')
assert_exception_correct(
got.value,
IllegalParameterError('var name contains control characters'))
def test_falsy_fail():
for f in ['', 0, False, [], dict(), {}]:
with raises(Exception) as got:
not_falsy(f, 'my name')
assert_exception_correct(
got.value,
ValueError('my name cannot be a value that evaluates to false'))
def test_check_string_long_fail():
for string, length in {'123456789': 8, 'ab': 1, 'a' * 100: 99}.items():
with raises(Exception) as got:
check_string(string, 'var name', max_len=length)
assert_exception_correct(
got.value,
IllegalParameterError(
f'var name exceeds maximum length of {length}'))
def _prefix_key_metadata_fail_(vals, keys, expected):
mv = MetadataValidatorSet(vals)
with raises(Exception) as got:
mv.prefix_key_metadata(keys)
assert_exception_correct(got.value, expected)
with raises(Exception) as got:
mv.prefix_key_metadata(keys, exact_match=True)
assert_exception_correct(got.value, expected)
def _sample_build_fail(nodes, name, expected):
with raises(Exception) as got:
Sample(nodes, name)
assert_exception_correct(got.value, expected)
id_ = uuid.UUID('1234567890abcdef1234567890abcdef')
with raises(Exception) as got:
SavedSample(id_, UserID('u'), nodes, dt(8), name)
assert_exception_correct(got.value, expected)
def _get_user_workspaces_fail(user, expected):
wsc = create_autospec(Workspace, spec_set=True, instance=True)
ws = WS(wsc)
wsc.administer.assert_called_once_with({'command': 'listModRequests'})
with raises(Exception) as got:
ws.get_user_workspaces(user)
assert_exception_correct(got.value, expected)
def test_duid_init_fail():
with raises(Exception) as got:
DataUnitID(None)
assert_exception_correct(got.value, ValueError(
'upa cannot be a value that evaluates to false'))
with raises(Exception) as got:
DataUnitID(UPA('1/1/1'), 'a' * 257)
assert_exception_correct(got.value, IllegalParameterError(
'dataid exceeds maximum length of 256'))
def test_config_get_validators_fail_bad_file(temp_dir):
tf = _write_validator_config({}, temp_dir)
os.remove(tf)
with raises(Exception) as got:
get_validators('file://' + tf)
assert_exception_correct(
got.value,
ValueError(
f"Failed to open validator configuration file at file://{tf}: " +
f"[Errno 2] No such file or directory: '{tf}'"))
def _sample_node_build_fail_source_metadata(meta, expected, cmeta=None):
if cmeta is None:
cmeta = {sm.key: {'x': 'y'} for sm in meta if sm is not None}
with raises(Exception) as got:
SampleNode(
'n',
SubSampleType.BIOLOGICAL_REPLICATE,
controlled_metadata=cmeta,
source_metadata=meta)
assert_exception_correct(got.value, expected)
def test_is_equivalent_fail():
sid = uuid.UUID('1234567890abcdef1234567890abcdef')
dl1 = DataLink(uuid.UUID('1234567890abcdef1234567890abcdee'),
DataUnitID(UPA('2/6/4'), 'whee'),
SampleNodeAddress(SampleAddress(sid, 8), 'bar'), dt(400),
UserID('myuserᚥnameisHank'), dt(400), UserID('yay'))
with raises(Exception) as got:
dl1.is_equivalent(None)
assert_exception_correct(
got.value,
ValueError('link cannot be a value that evaluates to false'))
def test_falsy_in_iterable_false_insides():
for item, pos in [[['', 'bar'], 0], [['foo', 0], 1],
[[True, True, False, True], 2], [[[]], 0], [[dict()], 0],
[[{}], 0]]:
with raises(Exception) as got:
not_falsy_in_iterable(item, 'my name')
assert_exception_correct(
got.value,
ValueError(
f'Index {pos} of iterable my name cannot be a value that evaluates to false'
))
def _has_permission_fail_ws_exception(ws_exception, expected):
wsc = create_autospec(Workspace, spec_set=True, instance=True)
ws = WS(wsc)
wsc.administer.assert_called_once_with({'command': 'listModRequests'})
wsc.administer.side_effect = ws_exception
with raises(Exception) as got:
ws.has_permission('foo', WorkspaceAccessType.READ, 22)
assert_exception_correct(got.value, expected)
def test_has_permission_fail_on_get_info_server_error():
wsc = create_autospec(Workspace, spec_set=True, instance=True)
ws = WS(wsc)
wsc.administer.assert_called_once_with({'command': 'listModRequests'})
wsc.administer.side_effect = [
{'perms': [{'a': 'w', 'b': 'r', 'c': 'a'}]},
ServerError('JSONRPCError', -32500, 'Thanks Obama')]
with raises(Exception) as got:
ws.has_permission(UserID('b'), WorkspaceAccessType.READ, upa=UPA('67/8/90'))
assert_exception_correct(got.value, ServerError('JSONRPCError', -32500, 'Thanks Obama'))
def test_has_permission_fail_no_object():
wsc = create_autospec(Workspace, spec_set=True, instance=True)
ws = WS(wsc)
wsc.administer.assert_called_once_with({'command': 'listModRequests'})
wsc.administer.side_effect = [
{'perms': [{'a': 'w', 'b': 'r', 'c': 'a'}]},
{'infos': [None]}]
with raises(Exception) as got:
ws.has_permission(UserID('b'), WorkspaceAccessType.READ, upa=UPA('67/8/90'))
assert_exception_correct(got.value, NoSuchWorkspaceDataError('Object 67/8/90 does not exist'))
def _get_user_workspaces_anonymous_fail_ws_exception(ws_exception, expected):
wsc = create_autospec(Workspace, spec_set=True, instance=True)
ws = WS(wsc)
wsc.administer.assert_called_once_with({'command': 'listModRequests'})
wsc.list_workspace_ids.side_effect = ws_exception
wsc.administer.side_effect = ws_exception
with raises(Exception) as got:
ws.get_user_workspaces(None)
assert_exception_correct(got.value, expected)
def test_config_get_validators_fail_bad_yaml(temp_dir):
# calling str() on ValidationErrors returns more detailed into about the error
tf = tempfile.mkstemp('.tmp.cfg', 'config_test_bad_yaml', dir=temp_dir)
os.close(tf[0])
with open(tf[1], 'w') as temp:
temp.write('[bad yaml')
with raises(Exception) as got:
get_validators('file://' + tf[1])
assert_exception_correct(
got.value,
ValueError(
f'Failed to open validator configuration file at file://{tf[1]}: while parsing a '
+
'flow sequence\n in "<urllib response>", line 1, column 1\nexpected \',\' or \']\', '
+
'but got \'<stream end>\'\n in "<urllib response>", line 1, column 10'
))
def test_prefix_key_metadata_fail_prefix_match():
mv = MetadataValidatorSet([
MetadataValidator('abcdef',
prefix_validators=[_noop],
metadata={'f': 'g'}),
MetadataValidator('abcdefhi',
prefix_validators=[_noop],
metadata={'f': 'g'})
])
with raises(Exception) as got:
mv.prefix_key_metadata(None, exact_match=False)
assert_exception_correct(got.value, ValueError('keys cannot be None'))
with raises(Exception) as got:
mv.prefix_key_metadata(['abcde'], exact_match=False)
assert_exception_correct(
got.value,
IllegalParameterError('No prefix metadata keys matching key abcde'))
def _ontology_has_ancestor_build_fail(cfg, expected):
with raises(Exception) as got:
builtin.ontology_has_ancestor(cfg)
assert_exception_correct(got.value, expected)
def _number_build_fail(cfg, expected):
with raises(Exception) as got:
builtin.number(cfg)
assert_exception_correct(got.value, expected)
def _units_build_fail(cfg, expected):
with raises(Exception) as got:
builtin.units(cfg)
assert_exception_correct(got.value, expected)
def _noop_fail_build(cfg, expected):
with raises(Exception) as got:
builtin.noop(cfg)
assert_exception_correct(got.value, expected)
def _string_fail_construct(d, expected):
with raises(Exception) as got:
builtin.string(d)
assert_exception_correct(got.value, expected)
def _init_fail(lid, duid, sna, cr, cru, ex, eu, expected):
with raises(Exception) as got:
DataLink(lid, duid, sna, cr, cru, ex, eu)
assert_exception_correct(got.value, expected)
def _split_value_fail(d, k, expected):
with raises(Exception) as got:
split_value(d, k)
assert_exception_correct(got.value, expected)
def _config_get_validators_fail(cfg, temp_dir, expected):
tf = _write_validator_config(cfg, temp_dir)
with raises(Exception) as got:
get_validators('file://' + tf)
assert_exception_correct(got.value, expected)
def _upa_init_int_fail(wsid, objid, ver, expected):
with raises(Exception) as got:
UPA(wsid=wsid, objid=objid, version=ver)
assert_exception_correct(got.value, expected)
def test_error_root_no_error_type():
with raises(Exception) as got:
SampleError(None)
assert_exception_correct(
got.value, TypeError('error_type cannot be None'))
