class NarrativeExporter():
def __init__(self):
c = Config()
c.HTMLExporter.preprocessors = [NarrativePreprocessor]
c.TemplateExporter.template_path = ['.', self._narrative_template_path()]
c.CSSHTMLHeaderPreprocessor.enabled = True
self.html_exporter = HTMLExporter(config=c)
self.html_exporter.template_file = 'narrative'
self.ws_client = Workspace(URLS.workspace)
self.narr_fetcher = NarrativeIO()
def _narrative_template_path(self):
return os.path.join(os.environ.get('NARRATIVE_DIR', '.'), 'src', 'biokbase', 'narrative', 'exporter', 'templates')
def export_narrative(self, narrative_ref, output_file):
nar = self.narr_fetcher.read_narrative(narrative_ref)
nar = nar['data']
# # 1. Get the narrative object
# # (put in try/except)
# # (should also raise an error if narrative is not public)
# nar = self.ws_client.get_objects([{'ref': narrative_ref}])
# # put in separate try/except
# nar = nar[0]['data']
# 2. Convert to a notebook object
kb_notebook = nbformat.reads(json.dumps(nar), as_version=4)
# 3. make the thing
(body, resources) = self.html_exporter.from_notebook_node(kb_notebook)
with open(output_file, 'w') as output_html:
output_html.write(body)
def __init__(self):
c = Config()
c.HTMLExporter.preprocessors = [NarrativePreprocessor]
c.TemplateExporter.template_path = ['.', self._narrative_template_path()]
c.CSSHTMLHeaderPreprocessor.enabled = True
self.html_exporter = HTMLExporter(config=c)
self.html_exporter.template_file = 'narrative'
self.ws_client = Workspace(URLS.workspace)
self.narr_fetcher = NarrativeIO()
def __init__(self):
c = Config()
c.HTMLExporter.preprocessors = [NarrativePreprocessor]
c.TemplateExporter.template_path = [
'.', self._narrative_template_path()
]
c.CSSHTMLHeaderPreprocessor.enabled = True
self.html_exporter = HTMLExporter(config=c)
self.html_exporter.template_file = 'narrative'
self.ws_client = Workspace(URLS.workspace)
self.narr_fetcher = NarrativeIO()
class NarrativeExporter():
def __init__(self):
c = Config()
c.HTMLExporter.preprocessors = [NarrativePreprocessor]
c.TemplateExporter.template_path = [
'.', self._narrative_template_path()
]
c.CSSHTMLHeaderPreprocessor.enabled = True
self.html_exporter = HTMLExporter(config=c)
self.html_exporter.template_file = 'narrative'
self.ws_client = Workspace(URLS.workspace)
self.narr_fetcher = NarrativeIO()
def _narrative_template_path(self):
return os.path.join(os.environ.get('NARRATIVE_DIR', '.'), 'src',
'biokbase', 'narrative', 'exporter', 'templates')
def export_narrative(self, narrative_ref, output_file):
nar = self.narr_fetcher.read_narrative(narrative_ref)
nar = nar['data']
# # 1. Get the narrative object
# # (put in try/except)
# # (should also raise an error if narrative is not public)
# nar = self.ws_client.get_objects([{'ref': narrative_ref}])
# # put in separate try/except
# nar = nar[0]['data']
# 2. Convert to a notebook object
kb_notebook = nbformat.reads(json.dumps(nar), as_version=4)
# 3. make the thing
(body, resources) = self.html_exporter.from_notebook_node(kb_notebook)
with open(output_file, 'w') as output_html:
output_html.write(body)
class NarrIOTestCase(unittest.TestCase):
# Before test:
# - Log in (for tests that need a valid login)
# also sets the token in the environment variable.
test_token = None
private_token = None
@classmethod
def setUpClass(self):
config = util.TestConfig()
self.test_user = config.get('users', 'test_user')
self.private_user = config.get('users', 'private_user')
self.test_token = util.read_token_file(
config.get_path('token_files', 'test_user', from_root=True))
self.private_token = util.read_token_file(
config.get_path('token_files', 'private_user', from_root=True))
if self.test_token is None or self.private_token is None:
print("Skipping most narrativeio.py tests due to missing tokens.")
print(
"To enable these, place a valid auth token in files\n{}\nand\n{}"
.format(config.get_path('token_files', 'test_user'),
config.get_path('token_files', 'private_user')))
print("Note that these should belong to different users.")
if self.test_token is not None:
global HAS_TEST_TOKEN
HAS_TEST_TOKEN = True
self.ws_uri = URLS.workspace
self.invalid_nar_ref_str = config.get('strings', 'invalid_nar_ref')
self.invalid_nar_ref = str_to_ref(self.invalid_nar_ref_str)
self.bad_nar_ref = config.get('strings', 'bad_nar_ref')
self.invalid_ws_id = config.get('strings', 'invalid_ws_id')
self.bad_ws_id = config.get('strings', 'bad_ws_id')
if self.test_token is not None:
# Now we need to inject some data!
# To avoid cross-contamination (we're testing the new_narrative() code here,
# so we shouldn't use it, right?) this will be done manually using the Workspace
# client.
self.public_nar = util.upload_narrative(config.get_path(
'narratives', 'public_file'),
self.test_token,
self.test_user,
set_public=True,
url=self.ws_uri)
self.private_nar = util.upload_narrative(config.get_path(
'narratives', 'private_file'),
self.test_token,
self.test_user,
url=self.ws_uri)
if self.private_token is not None:
self.unauth_nar = util.upload_narrative(config.get_path(
'narratives', 'unauth_file'),
self.private_token,
self.private_user,
url=self.ws_uri)
@classmethod
def tearDownClass(self):
if self.test_token is not None:
util.delete_narrative(self.public_nar['ws'],
self.test_token,
url=self.ws_uri)
util.delete_narrative(self.private_nar['ws'],
self.test_token,
url=self.ws_uri)
if self.private_token is not None:
util.delete_narrative(self.unauth_nar['ws'],
self.private_token,
url=self.ws_uri)
@classmethod
def setUp(self):
self.mixin = KBaseWSManagerMixin()
# monkeypatch the ws url so it doesn't go to the auto-configured one
self.mixin.ws_uri = self.ws_uri
@classmethod
def login(self, token=None):
if token is None:
token = self.test_token
biokbase.auth.set_environ_token(token)
@classmethod
def logout(self):
biokbase.auth.set_environ_token(None)
def test_mixin_instantiated(self):
self.assertIsInstance(
self.mixin,
biokbase.narrative.contents.narrativeio.KBaseWSManagerMixin)
##### test KBaseWSManagerMixin.narrative_exists #####
def test_narrative_exists_valid(self):
if self.test_token is None:
self.skipTest("No auth token")
self.assertTrue(self.mixin.narrative_exists(self.public_nar['ref']))
def test_narrative_exists_invalid(self):
self.assertFalse(self.mixin.narrative_exists(self.invalid_nar_ref))
def test_narrative_exists_bad(self):
with self.assertRaises(AssertionError) as err:
self.mixin.narrative_exists(self.bad_nar_ref)
self.assertEqual("read_narrative must use a NarrativeRef as input!",
str(err.exception))
def test_narrative_exists_noauth(self):
if self.test_token is None:
self.skipTest("No auth token")
with self.assertRaises(WorkspaceError) as err:
self.mixin.narrative_exists(self.private_nar['ref'])
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.read_narrative #####
def validate_narrative(self, nar, with_content, with_meta):
"""
Validates a narrative object's overall structure.
We're just making sure that the right elements are expected
to be here - we leave the Jupyter Notebook validation part to
the Jupyter test suite.
"""
if nar is None:
return "Unable to validate null Narrative!"
if not isinstance(nar, dict):
return "Narrative needs to be a dict to be valid."
# expected keys:
exp_keys = set(['info'])
if with_content:
exp_keys.update([
'created', 'refs', 'provenance', 'creator',
'copy_source_inaccessible', 'data', 'extracted_ids'
])
missing_keys = exp_keys - set(nar.keys())
if missing_keys:
return "Narrative object is missing the following keys: {}".format(
', '.join(missing_keys))
if len(nar['info']) != 11:
return "Narrative info is incorrect: expected 11 elements, saw {}".format(
len(nar['info']))
if with_meta:
if not nar['info'][10]:
return "Narrative metadata not returned when expected"
meta_keys = set([
'creator', 'data_dependencies', 'description', 'format',
'job_info', 'name', 'type', 'ws_name'
])
missing_keys = meta_keys - set(nar['info'][10])
if missing_keys:
return "Narrative metadata is missing the following keys: {}".format(
', '.join(missing_keys))
return None
def validate_metadata(self, std_meta, meta):
"""
Validates a Narrative's typed object metadata.
"""
pass
def test_read_narrative_valid_content_metadata(self):
if self.test_token is None:
self.skipTest("No auth token")
nar = self.mixin.read_narrative(self.public_nar['ref'],
content=True,
include_metadata=False)
self.assertIsNone(self.validate_narrative(nar, True, True))
def test_read_narrative_valid_content_no_metadata(self):
if self.test_token is None:
self.skipTest("No auth token")
nar = self.mixin.read_narrative(self.public_nar['ref'],
content=True,
include_metadata=True)
self.assertIsNone(self.validate_narrative(nar, True, False))
def test_read_narrative_valid_no_content_metadata(self):
if self.test_token is None:
self.skipTest("No auth token")
nar = self.mixin.read_narrative(self.public_nar['ref'],
content=False,
include_metadata=True)
self.assertIsNone(self.validate_narrative(nar, False, True))
def test_read_narrative_valid_no_content_no_metadata(self):
if self.test_token is None:
self.skipTest("No auth token")
nar = self.mixin.read_narrative(self.public_nar['ref'],
content=False,
include_metadata=False)
self.assertIsNone(self.validate_narrative(nar, False, False))
def test_read_narrative_private_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
with self.assertRaises(WorkspaceError) as err:
self.mixin.read_narrative(self.private_nar['ref'])
self.assertIsNotNone(err)
def test_read_narrative_unauth_login(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(WorkspaceError) as err:
self.mixin.read_narrative(self.unauth_nar['ref'])
self.assertIsNotNone(err)
self.logout()
def test_read_narrative_invalid(self):
with self.assertRaises(WorkspaceError) as err:
self.mixin.read_narrative(self.invalid_nar_ref)
self.assertIsNotNone(err)
def test_read_narrative_bad(self):
with self.assertRaises(AssertionError) as err:
self.mixin.read_narrative(self.bad_nar_ref)
self.assertEqual("read_narrative must use a NarrativeRef as input!",
str(err.exception))
##### test KBaseWSManagerMixin.write_narrative #####
def test_write_narrative_valid_auth(self):
if self.test_token is None:
self.skipTest("No auth token")
# fetch a narrative and just write it back again.
# should return (nar, wsid, objid)
self.login()
nar = self.mixin.read_narrative(self.private_nar['ref'])['data']
result = self.mixin.write_narrative(self.private_nar['ref'], nar,
self.test_user)
self.assertTrue(result[1] == self.private_nar['ws']
and result[2] == self.private_nar['obj'])
self.assertEquals(result[0]['metadata']['is_temporary'], 'false')
ws = clients.get("workspace")
ws_info = ws.get_workspace_info({'id': result[1]})
self.assertEquals(ws_info[8]['searchtags'], 'narrative')
self.logout()
def test_write_narrative_valid_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(WorkspaceError) as err:
self.mixin.write_narrative(self.public_nar['ref'], nar,
'Anonymous')
self.assertIsNotNone(err)
def test_write_narrative_valid_unauth(self):
pass
def test_write_narrative_invalid_ref(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(WorkspaceError) as err:
self.mixin.write_narrative(self.invalid_nar_ref, nar,
self.test_user)
self.assertIsNotNone(err)
self.logout()
def test_write_narrative_shared_write_access(self):
if self.test_token is None or self.private_token is None:
self.skipTest("Missing auth token(s)")
# login as private_user
# set unauth_nar perms to allow test_user w access
# logout
self.login(token=self.private_token)
ws_client = clients.get('workspace')
ws_client.set_permissions({
'id': self.unauth_nar['ws'],
'new_permission': 'w',
'users': [self.test_user]
})
self.logout()
# login as test_user
# re-save unauth_nar
# should succeed
# logout
self.login(token=self.test_token)
nar = self.mixin.read_narrative(self.unauth_nar['ref'])['data']
self.mixin.write_narrative(self.unauth_nar['ref'], nar, self.test_user)
self.logout()
# log back in as private_user
# remove perms from test_user
# log back out
self.login(token=self.private_token)
ws_client = clients.get('workspace')
ws_client.set_permissions({
'id': self.unauth_nar['ws'],
'new_permission': 'n',
'users': [self.test_user]
})
self.logout()
# @unittest.skipIf(test_token is None, "No test user credentials available")
def test_write_narrative_bad_ref(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(AssertionError) as err:
self.mixin.write_narrative(self.bad_nar_ref, nar, self.test_user)
self.assertEqual("write_narrative must use a NarrativeRef as input!",
str(err.exception))
self.logout()
def test_write_narrative_bad_file(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(HTTPError) as err:
self.mixin.write_narrative(self.private_nar['ref'],
{'not': 'a narrative'}, self.test_user)
self.assertEqual(err.exception.status_code, 400)
self.logout()
##### test KBaseWSManagerMixin.rename_narrative #####
def test_rename_narrative_valid_auth(self):
if self.test_token is None:
self.skipTest("No auth token")
new_name = "new_narrative_name"
self.login()
nar = self.mixin.read_narrative(self.private_nar['ref'],
content=False,
include_metadata=True)
cur_name = nar['info'][10]['name']
self.mixin.rename_narrative(self.private_nar['ref'], self.test_user,
new_name)
nar = self.mixin.read_narrative(self.private_nar['ref'],
content=False,
include_metadata=True)
self.assertEqual(new_name, nar['info'][10]['name'])
### now, put it back to the old name, so it doesn't break other tests...
self.mixin.rename_narrative(self.private_nar['ref'], self.test_user,
cur_name)
self.logout()
def test_rename_narrative_valid_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
with self.assertRaises(WorkspaceError) as err:
self.mixin.rename_narrative(self.public_nar['ref'], self.test_user,
'new_name')
self.assertIsNotNone(err)
def test_rename_narrative_unauth(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(WorkspaceError) as err:
self.mixin.rename_narrative(self.unauth_nar['ref'], self.test_user,
'new_name')
self.assertIsNotNone(err)
self.logout()
def test_rename_narrative_invalid(self):
with self.assertRaises(WorkspaceError) as err:
self.mixin.rename_narrative(self.invalid_nar_ref, self.test_user,
'new_name')
self.assertIsNotNone(err)
def test_rename_narrative_bad(self):
with self.assertRaises(AssertionError) as err:
self.mixin.rename_narrative(self.bad_nar_ref, self.test_user,
'new_name')
self.assertEqual("read_narrative must use a NarrativeRef as input!",
str(err.exception))
##### test KBaseWSManagerMixin.copy_narrative #####
def test_copy_narrative_valid(self):
# no op for now
pass
def test_copy_narrative_invalid(self):
# no op for now
pass
##### test KBaseWSManagerMixin.list_narratives #####
def validate_narrative_list(self, nar_list):
self.assertIsInstance(nar_list, list)
for nar in nar_list:
self.assertIsInstance(nar, dict)
self.assertTrue(set(nar.keys()).issubset(metadata_fields))
def test_list_all_narratives_anon(self):
res = self.mixin.list_narratives()
self.validate_narrative_list(res)
def test_list_all_narratives_auth(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
res = self.mixin.list_narratives()
self.validate_narrative_list(res)
self.logout()
def test_list_narrative_ws_valid_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
res = self.mixin.list_narratives(ws_id=self.public_nar['ws'])
self.validate_narrative_list(res)
def test_list_narrative_ws_valid_noperm_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
with self.assertRaises(WorkspaceError) as err:
self.mixin.list_narratives(ws_id=self.private_nar['ws'])
self.assertIsNotNone(err)
def test_list_narrative_ws_valid_login(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
res = self.mixin.list_narratives(ws_id=self.private_nar['ws'])
self.validate_narrative_list(res)
self.logout()
def test_list_narrative_ws_invalid(self):
with self.assertRaises(WorkspaceError) as err:
self.mixin.list_narratives(ws_id=self.invalid_ws_id)
self.assertIsNotNone(err)
def test_list_narrative_ws_valid_noperm_auth(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(WorkspaceError) as err:
self.mixin.list_narratives(ws_id=self.unauth_nar['ws'])
self.assertIsNotNone(err)
self.logout()
def test_list_narrative_ws_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.list_narratives(ws_id=self.bad_nar_ref)
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.narrative_permissions #####
# params:
# narrative ref == valid, invalid, bad/malformed
# user:
# None, specific
# login state
def test_narrative_permissions_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
ret = self.mixin.narrative_permissions(self.public_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret['*'] == 'r')
def test_narrative_permissions_valid_login(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
ret = self.mixin.narrative_permissions(self.public_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret['*'] == 'r')
self.logout()
def test_narrative_permissions_invalid_login(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(WorkspaceError) as err:
self.mixin.narrative_permissions(self.invalid_nar_ref)
self.logout()
def test_narrative_permissions_inaccessible_login(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
ret = self.mixin.narrative_permissions(self.unauth_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret[self.test_user] == 'n')
self.logout()
def test_narrative_permissions_bad(self):
with self.assertRaises(AssertionError) as err:
self.mixin.narrative_permissions(self.bad_nar_ref)
self.assertEqual(
"narrative_permissions must use a NarrativeRef as input!",
str(err.exception))
##### test KBaseWSManagerMixin.narrative_writable #####
def test_narrative_writable_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
ret = self.mixin.narrative_writable(self.public_nar['ref'],
self.test_user)
self.assertFalse(ret)
def test_narrative_writable_valid_login_nouser(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(ValueError) as err:
self.mixin.narrative_writable(self.public_nar['ref'], None)
self.assertIsNotNone(err)
self.logout()
def test_narrative_writable_valid_login_user(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
ret = self.mixin.narrative_writable(self.public_nar['ref'],
self.test_user)
self.assertTrue(ret)
self.logout()
def test_narrative_writable_invalid_login_user(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(WorkspaceError) as err:
self.mixin.narrative_writable(self.invalid_nar_ref, self.test_user)
self.assertIsNotNone(err)
self.logout()
def test_narrative_writable_inaccessible_login_user(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
ret = self.mixin.narrative_writable(self.unauth_nar['ref'],
self.test_user)
self.assertFalse(ret)
self.logout()
def test_narrative_writable_bad_login_user(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(AssertionError) as err:
self.mixin.narrative_writable(self.bad_nar_ref, self.test_user)
self.assertEqual(
"narrative_permissions must use a NarrativeRef as input!",
str(err.exception))
self.logout()
##### test KBaseWSManagerMixin._validate_nar_type #####
def test__validate_nar_type_ok(self):
self.assertIsNone(
self.mixin._validate_nar_type("KBaseNarrative.Narrative-123.45",
None))
self.assertIsNone(
self.mixin._validate_nar_type("KBaseNarrative.Narrative", None))
def test__validate_nar_type_fail(self):
bad_type = "NotANarrative"
ref = "123/45"
with self.assertRaises(HTTPError) as err:
self.mixin._validate_nar_type(bad_type, None)
self.assertIn("Expected a Narrative object, got a {}".format(bad_type),
str(err.exception))
with self.assertRaises(HTTPError) as err:
self.mixin._validate_nar_type(bad_type, ref)
self.assertIn(
"Expected a Narrative object with reference {}, got a {}".format(
ref, bad_type), str(err.exception))
def setUp(self):
self.mixin = KBaseWSManagerMixin()
# monkeypatch the ws url so it doesn't go to the auto-configured one
self.mixin.ws_uri = self.ws_uri
def setUp(self):
self.mixin = KBaseWSManagerMixin()
# monkeypatch the ws url so it doesn't go to the auto-configured one
self.mixin.ws_uri = self.ws_uri
class NarrIOTestCase(unittest.TestCase):
# Before test:
# - Log in (for tests that need a valid login)
# also sets the token in the environment variable.
@classmethod
def setUpClass(self):
config = ConfigParser.ConfigParser()
config.read('test.cfg')
self.test_user = config.get('users', 'test_user')
self.test_pwd = getpass('Password for {}: '.format(self.test_user))
self.test_token = biokbase.auth.Token(user_id=self.test_user, password=self.test_pwd)
self.private_user = config.get('users', 'private_user')
self.private_pwd = getpass('Password for {}: '.format(self.private_user))
self.private_token = biokbase.auth.Token(user_id=self.private_user, password=self.private_pwd)
self.ws_uri = config.get('urls', 'workspace')
self.invalid_nar_ref = config.get('strings', 'invalid_nar_ref')
self.bad_nar_ref = config.get('strings', 'bad_nar_ref')
self.invalid_ws_id = config.get('strings', 'invalid_ws_id')
self.bad_ws_id = config.get('strings', 'bad_ws_id')
# Now we need to inject some data!
# To avoid cross-contamination (we're testing the new_narrative() code here,
# so we shouldn't use it, right?) this will be done manually using the Workspace
# client.
self.public_nar = test_util.upload_narrative(config.get('narratives', 'public_file'), self.test_token, set_public=True, url=self.ws_uri)
self.private_nar = test_util.upload_narrative(config.get('narratives', 'private_file'), self.test_token, url=self.ws_uri)
self.unauth_nar = test_util.upload_narrative(config.get('narratives', 'unauth_file'), self.private_token, url=self.ws_uri)
@classmethod
def tearDownClass(self):
test_util.delete_narrative(self.public_nar['ws'], self.test_token, url=self.ws_uri)
test_util.delete_narrative(self.private_nar['ws'], self.test_token, url=self.ws_uri)
test_util.delete_narrative(self.unauth_nar['ws'], self.private_token, url=self.ws_uri)
@classmethod
def setUp(self):
self.mixin = KBaseWSManagerMixin()
# monkeypatch the ws url so it doesn't go to the auto-configured one
self.mixin.ws_uri = self.ws_uri
@classmethod
def login(self):
biokbase.auth.set_environ_token(self.test_token.token)
@classmethod
def logout(self):
biokbase.auth.set_environ_token(None)
def test_mixin_instantiated(self):
self.assertIsInstance(self.mixin, biokbase.narrative.narrativeio.KBaseWSManagerMixin)
# test we can get a workspace client while logged out, and it's anonymous
def test_get_wsclient_anon(self):
ws_client = self.mixin.ws_client()
# it's anon if the header doesn't have an AUTHORIZATION field, or
# that has a None value
self.assertTrue('AUTHORIZATION' not in ws_client._headers or
ws_client._headers['AUTHORIZATION'] is None)
# test we get a ws client when logged in, and it's authorized
def test_get_wsclient_auth(self):
self.login()
ws_client = self.mixin.ws_client()
self.assertTrue('AUTHORIZATION' in ws_client._headers and
ws_client._headers['AUTHORIZATION'] is not None)
self.logout()
# test we know what a narrative ref looks like with ws and obj ids
def test_obj_ref_ws_obj(self):
self.mixin._test_obj_ref(self.public_nar['ref'])
# test as above, but include version
def test_obj_ref_ws_obj_ver(self):
ref = self.public_nar['ref'] + '/1'
self.mixin._test_obj_ref(ref) # this can ONLY fail, has no return value
# test as above, but make sure it fails right
def test_obj_ref_fail(self):
with self.assertRaises(ValueError) as err:
self.mixin._test_obj_ref(self.bad_nar_ref)
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.narrative_exists #####
def test_narrative_exists_valid(self):
self.assertTrue(self.mixin.narrative_exists(self.public_nar['ref']))
def test_narrative_exists_invalid(self):
self.assertFalse(self.mixin.narrative_exists(self.invalid_nar_ref))
def test_narrative_exists_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.narrative_exists(self.bad_nar_ref)
self.assertIsNotNone(err)
def test_narrative_exists_noauth(self):
with self.assertRaises(PermissionsError) as err:
self.mixin.narrative_exists(self.private_nar['ref'])
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.read_narrative #####
def validate_narrative(self, nar, with_content, with_meta):
"""
Validates a narrative object's overall structure.
We're just making sure that the right elements are expected
to be here - we leave the Jupyter Notebook validation part to
the Jupyter test suite.
"""
if nar is None:
return "Unable to validate null Narrative!"
if not isinstance(nar, dict):
return "Narrative needs to be a dict to be valid."
# expected keys:
exp_keys = set(['info'])
if with_content:
exp_keys.update(['created', 'refs', 'provenance', 'creator',
'copy_source_inaccessible', 'data', 'extracted_ids'])
missing_keys = exp_keys - set(nar.keys())
if missing_keys:
return "Narrative object is missing the following keys: {}".format(', '.join(missing_keys))
if len(nar['info']) != 11:
return "Narrative info is incorrect: expected 11 elements, saw {}".format(len(nar['info']))
if with_meta:
if not nar['info'][10]:
return "Narrative metadata not returned when expected"
meta_keys = set(['creator', 'data_dependencies', 'description', 'format', 'job_info', 'methods', 'name', 'type', 'ws_name'])
missing_keys = meta_keys - set(nar['info'][10])
if missing_keys:
return "Narrative metadata is missing the following keys: {}".format(', '.join(missing_keys))
return None
def validate_metadata(self, std_meta, meta):
"""
Validates a Narrative's typed object metadata.
"""
pass
def test_read_narrative_valid_content_metadata(self):
nar = self.mixin.read_narrative(self.public_nar['ref'], content=True, include_metadata=False)
self.assertIsNone(self.validate_narrative(nar, True, True))
def test_read_narrative_valid_content_no_metadata(self):
nar = self.mixin.read_narrative(self.public_nar['ref'], content=True, include_metadata=True)
self.assertIsNone(self.validate_narrative(nar, True, False))
def test_read_narrative_valid_no_content_metadata(self):
nar = self.mixin.read_narrative(self.public_nar['ref'], content=False, include_metadata=True)
self.assertIsNone(self.validate_narrative(nar, False, True))
def test_read_narrative_valid_no_content_no_metadata(self):
nar = self.mixin.read_narrative(self.public_nar['ref'], content=False, include_metadata=False)
self.assertIsNone(self.validate_narrative(nar, False, False))
def test_read_narrative_private_anon(self):
with self.assertRaises(PermissionsError) as err:
self.mixin.read_narrative(self.private_nar['ref'])
self.assertIsNotNone(err)
def test_read_narrative_unauth_login(self):
self.login()
with self.assertRaises(PermissionsError) as err:
self.mixin.read_narrative(self.unauth_nar['ref'])
self.assertIsNotNone(err)
self.logout()
def test_read_narrative_invalid(self):
with self.assertRaises(ServerError) as err:
self.mixin.read_narrative(self.invalid_nar_ref)
self.assertIsNotNone(err)
def test_read_narrative_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.read_narrative(self.bad_nar_ref)
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.write_narrative #####
def test_write_narrative_valid_auth(self):
# fetch a narrative and just write it back again.
# should return (nar, wsid, objid)
self.login()
nar = self.mixin.read_narrative(self.private_nar['ref'])['data']
result = self.mixin.write_narrative(self.private_nar['ref'], nar, self.test_user)
self.assertTrue(result[1] == self.private_nar['ws'] and result[2] == self.private_nar['obj'])
self.logout()
def test_write_narrative_valid_anon(self):
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(PermissionsError) as err:
self.mixin.write_narrative(self.public_nar['ref'], nar, 'Anonymous')
self.assertIsNotNone(err)
def test_write_narrative_valid_unauth(self):
pass
def test_write_narrative_invalid_ref(self):
self.login()
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(ServerError) as err:
self.mixin.write_narrative(self.invalid_nar_ref, nar, self.test_user)
self.assertIsNotNone(err)
self.logout()
def test_write_narrative_bad_ref(self):
self.login()
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(HTTPError) as err:
self.mixin.write_narrative(self.bad_nar_ref, nar, self.test_user)
self.assertEquals(err.exception.status_code, 500)
self.logout()
def test_write_narrative_bad_file(self):
self.login()
with self.assertRaises(HTTPError) as err:
self.mixin.write_narrative(self.private_nar['ref'], {'not':'a narrative'}, self.test_user)
self.assertEquals(err.exception.status_code, 400)
self.logout()
##### test KBaseWSManagerMixin.rename_narrative #####
def test_rename_narrative_valid_auth(self):
new_name = "new_narrative_name"
self.login()
nar = self.mixin.read_narrative(self.private_nar['ref'], content=False, include_metadata=True)
cur_name = nar['info'][10]['name']
self.mixin.rename_narrative(self.private_nar['ref'], self.test_user, new_name)
nar = self.mixin.read_narrative(self.private_nar['ref'], content=False, include_metadata=True)
self.assertEquals(new_name, nar['info'][10]['name'])
### now, put it back to the old name, so it doesn't break other tests...
self.mixin.rename_narrative(self.private_nar['ref'], self.test_user, cur_name)
self.logout()
def test_rename_narrative_valid_anon(self):
with self.assertRaises(PermissionsError) as err:
self.mixin.rename_narrative(self.public_nar['ref'], self.test_user, 'new_name')
self.assertIsNotNone(err)
def test_rename_narrative_unauth(self):
self.login()
with self.assertRaises(PermissionsError) as err:
self.mixin.rename_narrative(self.unauth_nar['ref'], self.test_user, 'new_name')
self.assertIsNotNone(err)
self.logout()
def test_rename_narrative_invalid(self):
with self.assertRaises(ServerError) as err:
self.mixin.rename_narrative(self.invalid_nar_ref, self.test_user, 'new_name')
self.assertIsNotNone(err)
def test_rename_narrative_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.rename_narrative(self.bad_nar_ref, self.test_user, 'new_name')
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.copy_narrative #####
def test_copy_narrative_valid(self):
# no op for now
pass
def test_copy_narrative_invalid(self):
# no op for now
pass
##### test KBaseWSManagerMixin.list_narratives #####
def validate_narrative_list(self, nar_list):
self.assertIsInstance(nar_list, list)
for nar in nar_list:
self.assertIsInstance(nar, dict)
self.assertTrue(set(nar.keys()).issubset(metadata_fields))
def test_list_all_narratives_anon(self):
res = self.mixin.list_narratives()
self.validate_narrative_list(res)
def test_list_all_narratives_auth(self):
self.login()
res = self.mixin.list_narratives()
self.validate_narrative_list(res)
self.logout()
def test_list_narrative_ws_valid_anon(self):
res = self.mixin.list_narratives(ws_id=self.public_nar['ws'])
self.validate_narrative_list(res)
def test_list_narrative_ws_valid_noperm_anon(self):
with self.assertRaises(PermissionsError) as err:
self.mixin.list_narratives(ws_id=self.private_nar['ws'])
self.assertIsNotNone(err)
def test_list_narrative_ws_valid_login(self):
self.login()
res = self.mixin.list_narratives(ws_id=self.private_nar['ws'])
self.validate_narrative_list(res)
self.logout()
def test_list_narrative_ws_invalid(self):
with self.assertRaises(ServerError) as err:
self.mixin.list_narratives(ws_id=self.invalid_ws_id)
self.assertIsNotNone(err)
def test_list_narrative_ws_valid_noperm_auth(self):
self.login()
with self.assertRaises(PermissionsError) as err:
self.mixin.list_narratives(ws_id=self.unauth_nar['ws'])
self.assertIsNotNone(err)
self.logout()
def test_list_narrative_ws_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.list_narratives(ws_id=self.bad_nar_ref)
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.narrative_permissions #####
# params:
# narrative ref == valid, invalid, bad/malformed
# user:
# None, specific
# login state
def test_narrative_permissions_anon(self):
ret = self.mixin.narrative_permissions(self.public_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret['*'] == 'r')
def test_narrative_permissions_valid_login(self):
self.login()
ret = self.mixin.narrative_permissions(self.public_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret['*'] == 'r')
self.logout()
def test_narrative_permissions_invalid_login(self):
self.login()
with self.assertRaises(ServerError) as err:
self.mixin.narrative_permissions(self.invalid_nar_ref)
self.logout()
def test_narrative_permissions_inaccessible_login(self):
self.login()
ret = self.mixin.narrative_permissions(self.unauth_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret[self.test_user] == 'n')
self.logout()
def test_narrative_permissions_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.narrative_permissions(self.bad_nar_ref)
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.narrative_writable #####
def test_narrative_writable_anon(self):
ret = self.mixin.narrative_writable(self.public_nar['ref'], self.test_user)
self.assertFalse(ret)
def test_narrative_writable_valid_login_nouser(self):
self.login()
with self.assertRaises(ValueError) as err:
self.mixin.narrative_writable(self.public_nar['ref'], None)
self.assertIsNotNone(err)
self.logout()
def test_narrative_writable_valid_login_user(self):
self.login()
ret = self.mixin.narrative_writable(self.public_nar['ref'], self.test_user)
self.assertTrue(ret)
self.logout()
def test_narrative_writable_invalid_login_user(self):
self.login()
with self.assertRaises(ServerError) as err:
self.mixin.narrative_writable(self.invalid_nar_ref, self.test_user)
self.assertIsNotNone(err)
self.logout()
def test_narrative_writable_inaccessible_login_user(self):
self.login()
ret = self.mixin.narrative_writable(self.unauth_nar['ref'], self.test_user)
self.assertFalse(ret)
self.logout()
def test_narrative_writable_bad_login_user(self):
self.login()
with self.assertRaises(ValueError) as err:
self.mixin.narrative_writable(self.bad_nar_ref, self.test_user)
self.assertIsNotNone(err)
self.logout()
class NarrIOTestCase(unittest.TestCase):
# Before test:
# - Log in (for tests that need a valid login)
# also sets the token in the environment variable.
test_token = None
private_token = None
@classmethod
def setUpClass(self):
config = util.TestConfig()
self.test_user = config.get('users', 'test_user')
self.private_user = config.get('users', 'private_user')
self.test_token = util.read_token_file(config.get_path('token_files', 'test_user', from_root=True))
self.private_token = util.read_token_file(config.get_path('token_files', 'private_user', from_root=True))
if self.test_token is None or self.private_token is None:
print("Skipping most narrativeio.py tests due to missing tokens.")
print("To enable these, place a valid auth token in files\n{}\nand\n{}".format(
config.get_path('token_files', 'test_user'),
config.get_path('token_files', 'private_user')))
print("Note that these should belong to different users.")
if self.test_token is not None:
global HAS_TEST_TOKEN
HAS_TEST_TOKEN = True
self.ws_uri = URLS.workspace
self.invalid_nar_ref_str = config.get('strings', 'invalid_nar_ref')
self.invalid_nar_ref = str_to_ref(self.invalid_nar_ref_str)
self.bad_nar_ref = config.get('strings', 'bad_nar_ref')
self.invalid_ws_id = config.get('strings', 'invalid_ws_id')
self.bad_ws_id = config.get('strings', 'bad_ws_id')
if self.test_token is not None:
# Now we need to inject some data!
# To avoid cross-contamination (we're testing the new_narrative() code here,
# so we shouldn't use it, right?) this will be done manually using the Workspace
# client.
self.public_nar = util.upload_narrative(
config.get_path('narratives', 'public_file'), self.test_token, self.test_user,
set_public=True, url=self.ws_uri)
self.private_nar = util.upload_narrative(
config.get_path('narratives', 'private_file'), self.test_token, self.test_user,
url=self.ws_uri)
if self.private_token is not None:
self.unauth_nar = util.upload_narrative(
config.get_path('narratives', 'unauth_file'), self.private_token, self.private_user,
url=self.ws_uri)
@classmethod
def tearDownClass(self):
if self.test_token is not None:
util.delete_narrative(self.public_nar['ws'], self.test_token, url=self.ws_uri)
util.delete_narrative(self.private_nar['ws'], self.test_token, url=self.ws_uri)
if self.private_token is not None:
util.delete_narrative(self.unauth_nar['ws'], self.private_token, url=self.ws_uri)
@classmethod
def setUp(self):
self.mixin = KBaseWSManagerMixin()
# monkeypatch the ws url so it doesn't go to the auto-configured one
self.mixin.ws_uri = self.ws_uri
@classmethod
def login(self, token=None):
if token is None:
token = self.test_token
biokbase.auth.set_environ_token(token)
@classmethod
def logout(self):
biokbase.auth.set_environ_token(None)
def test_mixin_instantiated(self):
self.assertIsInstance(self.mixin, biokbase.narrative.contents.narrativeio.KBaseWSManagerMixin)
##### test KBaseWSManagerMixin.narrative_exists #####
def test_narrative_exists_valid(self):
if self.test_token is None:
self.skipTest("No auth token")
self.assertTrue(self.mixin.narrative_exists(self.public_nar['ref']))
def test_narrative_exists_invalid(self):
self.assertFalse(self.mixin.narrative_exists(self.invalid_nar_ref))
def test_narrative_exists_bad(self):
with self.assertRaises(AssertionError) as err:
self.mixin.narrative_exists(self.bad_nar_ref)
self.assertEquals("read_narrative must use a NarrativeRef as input!", str(err.exception))
def test_narrative_exists_noauth(self):
if self.test_token is None:
self.skipTest("No auth token")
with self.assertRaises(WorkspaceError) as err:
self.mixin.narrative_exists(self.private_nar['ref'])
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.read_narrative #####
def validate_narrative(self, nar, with_content, with_meta):
"""
Validates a narrative object's overall structure.
We're just making sure that the right elements are expected
to be here - we leave the Jupyter Notebook validation part to
the Jupyter test suite.
"""
if nar is None:
return "Unable to validate null Narrative!"
if not isinstance(nar, dict):
return "Narrative needs to be a dict to be valid."
# expected keys:
exp_keys = set(['info'])
if with_content:
exp_keys.update(['created', 'refs', 'provenance', 'creator',
'copy_source_inaccessible', 'data', 'extracted_ids'])
missing_keys = exp_keys - set(nar.keys())
if missing_keys:
return "Narrative object is missing the following keys: {}".format(', '.join(missing_keys))
if len(nar['info']) != 11:
return "Narrative info is incorrect: expected 11 elements, saw {}".format(len(nar['info']))
if with_meta:
if not nar['info'][10]:
return "Narrative metadata not returned when expected"
meta_keys = set(['creator', 'data_dependencies', 'description', 'format', 'job_info', 'name', 'type', 'ws_name'])
missing_keys = meta_keys - set(nar['info'][10])
if missing_keys:
return "Narrative metadata is missing the following keys: {}".format(', '.join(missing_keys))
return None
def validate_metadata(self, std_meta, meta):
"""
Validates a Narrative's typed object metadata.
"""
pass
def test_read_narrative_valid_content_metadata(self):
if self.test_token is None:
self.skipTest("No auth token")
nar = self.mixin.read_narrative(self.public_nar['ref'], content=True, include_metadata=False)
self.assertIsNone(self.validate_narrative(nar, True, True))
def test_read_narrative_valid_content_no_metadata(self):
if self.test_token is None:
self.skipTest("No auth token")
nar = self.mixin.read_narrative(self.public_nar['ref'], content=True, include_metadata=True)
self.assertIsNone(self.validate_narrative(nar, True, False))
def test_read_narrative_valid_no_content_metadata(self):
if self.test_token is None:
self.skipTest("No auth token")
nar = self.mixin.read_narrative(self.public_nar['ref'], content=False, include_metadata=True)
self.assertIsNone(self.validate_narrative(nar, False, True))
def test_read_narrative_valid_no_content_no_metadata(self):
if self.test_token is None:
self.skipTest("No auth token")
nar = self.mixin.read_narrative(self.public_nar['ref'], content=False, include_metadata=False)
self.assertIsNone(self.validate_narrative(nar, False, False))
def test_read_narrative_private_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
with self.assertRaises(WorkspaceError) as err:
self.mixin.read_narrative(self.private_nar['ref'])
self.assertIsNotNone(err)
def test_read_narrative_unauth_login(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(WorkspaceError) as err:
self.mixin.read_narrative(self.unauth_nar['ref'])
self.assertIsNotNone(err)
self.logout()
def test_read_narrative_invalid(self):
with self.assertRaises(WorkspaceError) as err:
self.mixin.read_narrative(self.invalid_nar_ref)
self.assertIsNotNone(err)
def test_read_narrative_bad(self):
with self.assertRaises(AssertionError) as err:
self.mixin.read_narrative(self.bad_nar_ref)
self.assertEquals("read_narrative must use a NarrativeRef as input!", str(err.exception))
##### test KBaseWSManagerMixin.write_narrative #####
def test_write_narrative_valid_auth(self):
if self.test_token is None:
self.skipTest("No auth token")
# fetch a narrative and just write it back again.
# should return (nar, wsid, objid)
self.login()
nar = self.mixin.read_narrative(self.private_nar['ref'])['data']
result = self.mixin.write_narrative(self.private_nar['ref'], nar, self.test_user)
self.assertTrue(result[1] == self.private_nar['ws'] and result[2] == self.private_nar['obj'])
self.assertEquals(result[0]['metadata']['is_temporary'], 'false')
self.logout()
def test_write_narrative_valid_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(WorkspaceError) as err:
self.mixin.write_narrative(self.public_nar['ref'], nar, 'Anonymous')
self.assertIsNotNone(err)
def test_write_narrative_valid_unauth(self):
pass
def test_write_narrative_invalid_ref(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(WorkspaceError) as err:
self.mixin.write_narrative(self.invalid_nar_ref, nar, self.test_user)
self.assertIsNotNone(err)
self.logout()
def test_write_narrative_shared_write_access(self):
if self.test_token is None or self.private_token is None:
self.skipTest("Missing auth token(s)")
# login as private_user
# set unauth_nar perms to allow test_user w access
# logout
self.login(token=self.private_token)
ws_client = clients.get('workspace')
ws_client.set_permissions({'id': self.unauth_nar['ws'], 'new_permission': 'w', 'users': [self.test_user]})
self.logout()
# login as test_user
# re-save unauth_nar
# should succeed
# logout
self.login(token=self.test_token)
nar = self.mixin.read_narrative(self.unauth_nar['ref'])['data']
self.mixin.write_narrative(self.unauth_nar['ref'], nar, self.test_user)
self.logout()
# log back in as private_user
# remove perms from test_user
# log back out
self.login(token=self.private_token)
ws_client = clients.get('workspace')
ws_client.set_permissions({'id': self.unauth_nar['ws'], 'new_permission': 'n', 'users': [self.test_user]})
self.logout()
# @unittest.skipIf(test_token is None, "No test user credentials available")
def test_write_narrative_bad_ref(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(AssertionError) as err:
self.mixin.write_narrative(self.bad_nar_ref, nar, self.test_user)
self.assertEquals("write_narrative must use a NarrativeRef as input!", str(err.exception))
self.logout()
def test_write_narrative_bad_file(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(HTTPError) as err:
self.mixin.write_narrative(self.private_nar['ref'], {'not':'a narrative'}, self.test_user)
self.assertEquals(err.exception.status_code, 400)
self.logout()
##### test KBaseWSManagerMixin.rename_narrative #####
def test_rename_narrative_valid_auth(self):
if self.test_token is None:
self.skipTest("No auth token")
new_name = "new_narrative_name"
self.login()
nar = self.mixin.read_narrative(self.private_nar['ref'], content=False, include_metadata=True)
cur_name = nar['info'][10]['name']
self.mixin.rename_narrative(self.private_nar['ref'], self.test_user, new_name)
nar = self.mixin.read_narrative(self.private_nar['ref'], content=False, include_metadata=True)
self.assertEquals(new_name, nar['info'][10]['name'])
### now, put it back to the old name, so it doesn't break other tests...
self.mixin.rename_narrative(self.private_nar['ref'], self.test_user, cur_name)
self.logout()
def test_rename_narrative_valid_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
with self.assertRaises(WorkspaceError) as err:
self.mixin.rename_narrative(self.public_nar['ref'], self.test_user, 'new_name')
self.assertIsNotNone(err)
def test_rename_narrative_unauth(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(WorkspaceError) as err:
self.mixin.rename_narrative(self.unauth_nar['ref'], self.test_user, 'new_name')
self.assertIsNotNone(err)
self.logout()
def test_rename_narrative_invalid(self):
with self.assertRaises(WorkspaceError) as err:
self.mixin.rename_narrative(self.invalid_nar_ref, self.test_user, 'new_name')
self.assertIsNotNone(err)
def test_rename_narrative_bad(self):
with self.assertRaises(AssertionError) as err:
self.mixin.rename_narrative(self.bad_nar_ref, self.test_user, 'new_name')
self.assertEquals("read_narrative must use a NarrativeRef as input!", str(err.exception))
##### test KBaseWSManagerMixin.copy_narrative #####
def test_copy_narrative_valid(self):
# no op for now
pass
def test_copy_narrative_invalid(self):
# no op for now
pass
##### test KBaseWSManagerMixin.list_narratives #####
def validate_narrative_list(self, nar_list):
self.assertIsInstance(nar_list, list)
for nar in nar_list:
self.assertIsInstance(nar, dict)
self.assertTrue(set(nar.keys()).issubset(metadata_fields))
def test_list_all_narratives_anon(self):
res = self.mixin.list_narratives()
self.validate_narrative_list(res)
def test_list_all_narratives_auth(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
res = self.mixin.list_narratives()
self.validate_narrative_list(res)
self.logout()
def test_list_narrative_ws_valid_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
res = self.mixin.list_narratives(ws_id=self.public_nar['ws'])
self.validate_narrative_list(res)
def test_list_narrative_ws_valid_noperm_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
with self.assertRaises(WorkspaceError) as err:
self.mixin.list_narratives(ws_id=self.private_nar['ws'])
self.assertIsNotNone(err)
def test_list_narrative_ws_valid_login(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
res = self.mixin.list_narratives(ws_id=self.private_nar['ws'])
self.validate_narrative_list(res)
self.logout()
def test_list_narrative_ws_invalid(self):
with self.assertRaises(WorkspaceError) as err:
self.mixin.list_narratives(ws_id=self.invalid_ws_id)
self.assertIsNotNone(err)
def test_list_narrative_ws_valid_noperm_auth(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(WorkspaceError) as err:
self.mixin.list_narratives(ws_id=self.unauth_nar['ws'])
self.assertIsNotNone(err)
self.logout()
def test_list_narrative_ws_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.list_narratives(ws_id=self.bad_nar_ref)
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.narrative_permissions #####
# params:
# narrative ref == valid, invalid, bad/malformed
# user:
# None, specific
# login state
def test_narrative_permissions_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
ret = self.mixin.narrative_permissions(self.public_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret['*'] == 'r')
def test_narrative_permissions_valid_login(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
ret = self.mixin.narrative_permissions(self.public_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret['*'] == 'r')
self.logout()
def test_narrative_permissions_invalid_login(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(WorkspaceError) as err:
self.mixin.narrative_permissions(self.invalid_nar_ref)
self.logout()
def test_narrative_permissions_inaccessible_login(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
ret = self.mixin.narrative_permissions(self.unauth_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret[self.test_user] == 'n')
self.logout()
def test_narrative_permissions_bad(self):
with self.assertRaises(AssertionError) as err:
self.mixin.narrative_permissions(self.bad_nar_ref)
self.assertEquals("narrative_permissions must use a NarrativeRef as input!", str(err.exception))
##### test KBaseWSManagerMixin.narrative_writable #####
def test_narrative_writable_anon(self):
if self.test_token is None:
self.skipTest("No auth token")
ret = self.mixin.narrative_writable(self.public_nar['ref'], self.test_user)
self.assertFalse(ret)
def test_narrative_writable_valid_login_nouser(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(ValueError) as err:
self.mixin.narrative_writable(self.public_nar['ref'], None)
self.assertIsNotNone(err)
self.logout()
def test_narrative_writable_valid_login_user(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
ret = self.mixin.narrative_writable(self.public_nar['ref'], self.test_user)
self.assertTrue(ret)
self.logout()
def test_narrative_writable_invalid_login_user(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(WorkspaceError) as err:
self.mixin.narrative_writable(self.invalid_nar_ref, self.test_user)
self.assertIsNotNone(err)
self.logout()
def test_narrative_writable_inaccessible_login_user(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
ret = self.mixin.narrative_writable(self.unauth_nar['ref'], self.test_user)
self.assertFalse(ret)
self.logout()
def test_narrative_writable_bad_login_user(self):
if self.test_token is None:
self.skipTest("No auth token")
self.login()
with self.assertRaises(AssertionError) as err:
self.mixin.narrative_writable(self.bad_nar_ref, self.test_user)
self.assertEquals("narrative_permissions must use a NarrativeRef as input!", str(err.exception))
self.logout()
##### test KBaseWSManagerMixin._validate_nar_type #####
def test__validate_nar_type_ok(self):
self.assertIsNone(self.mixin._validate_nar_type("KBaseNarrative.Narrative-123.45", None))
self.assertIsNone(self.mixin._validate_nar_type("KBaseNarrative.Narrative", None))
def test__validate_nar_type_fail(self):
bad_type = "NotANarrative"
ref = "123/45"
with self.assertRaises(HTTPError) as err:
self.mixin._validate_nar_type(bad_type, None)
self.assertIn("Expected a Narrative object, got a {}".format(bad_type), str(err.exception))
with self.assertRaises(HTTPError) as err:
self.mixin._validate_nar_type(bad_type, ref)
self.assertIn("Expected a Narrative object with reference {}, got a {}".format(ref, bad_type), str(err.exception))
class NarrIOTestCase(unittest.TestCase):
# Before test:
# - Log in (for tests that need a valid login)
# also sets the token in the environment variable.
@classmethod
def setUpClass(self):
config = ConfigParser.ConfigParser()
config.read('test.cfg')
self.test_user = config.get('users', 'test_user')
self.test_pwd = getpass('Password for {}: '.format(self.test_user))
self.test_token = biokbase.auth.Token(user_id=self.test_user,
password=self.test_pwd)
self.private_user = config.get('users', 'private_user')
self.private_pwd = getpass('Password for {}: '.format(
self.private_user))
self.private_token = biokbase.auth.Token(user_id=self.private_user,
password=self.private_pwd)
self.ws_uri = config.get('urls', 'workspace')
self.invalid_nar_ref = config.get('strings', 'invalid_nar_ref')
self.bad_nar_ref = config.get('strings', 'bad_nar_ref')
self.invalid_ws_id = config.get('strings', 'invalid_ws_id')
self.bad_ws_id = config.get('strings', 'bad_ws_id')
# Now we need to inject some data!
# To avoid cross-contamination (we're testing the new_narrative() code here,
# so we shouldn't use it, right?) this will be done manually using the Workspace
# client.
self.public_nar = test_util.upload_narrative(config.get(
'narratives', 'public_file'),
self.test_token,
set_public=True,
url=self.ws_uri)
self.private_nar = test_util.upload_narrative(config.get(
'narratives', 'private_file'),
self.test_token,
url=self.ws_uri)
self.unauth_nar = test_util.upload_narrative(config.get(
'narratives', 'unauth_file'),
self.private_token,
url=self.ws_uri)
@classmethod
def tearDownClass(self):
test_util.delete_narrative(self.public_nar['ws'],
self.test_token,
url=self.ws_uri)
test_util.delete_narrative(self.private_nar['ws'],
self.test_token,
url=self.ws_uri)
test_util.delete_narrative(self.unauth_nar['ws'],
self.private_token,
url=self.ws_uri)
@classmethod
def setUp(self):
self.mixin = KBaseWSManagerMixin()
# monkeypatch the ws url so it doesn't go to the auto-configured one
self.mixin.ws_uri = self.ws_uri
@classmethod
def login(self):
biokbase.auth.set_environ_token(self.test_token.token)
@classmethod
def logout(self):
biokbase.auth.set_environ_token(None)
def test_mixin_instantiated(self):
self.assertIsInstance(
self.mixin,
biokbase.narrative.contents.narrativeio.KBaseWSManagerMixin)
# # test we can get a workspace client while logged out, and it's anonymous
# def test_get_wsclient_anon(self):
# ws_client = self.mixin.ws_client()
# # it's anon if the header doesn't have an AUTHORIZATION field, or
# # that has a None value
# self.assertTrue('AUTHORIZATION' not in ws_client._headers or
# ws_client._headers['AUTHORIZATION'] is None)
# # test we get a ws client when logged in, and it's authorized
# def test_get_wsclient_auth(self):
# self.login()
# ws_client = self.mixin.ws_client()
# self.assertTrue('AUTHORIZATION' in ws_client._headers and
# ws_client._headers['AUTHORIZATION'] is not None)
# self.logout()
# test we know what a narrative ref looks like with ws and obj ids
def test_obj_ref_ws_obj(self):
self.mixin._test_obj_ref(self.public_nar['ref'])
# test as above, but include version
def test_obj_ref_ws_obj_ver(self):
ref = self.public_nar['ref'] + '/1'
self.mixin._test_obj_ref(
ref) # this can ONLY fail, has no return value
# test as above, but make sure it fails right
def test_obj_ref_fail(self):
with self.assertRaises(ValueError) as err:
self.mixin._test_obj_ref(self.bad_nar_ref)
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.narrative_exists #####
def test_narrative_exists_valid(self):
self.assertTrue(self.mixin.narrative_exists(self.public_nar['ref']))
def test_narrative_exists_invalid(self):
self.assertFalse(self.mixin.narrative_exists(self.invalid_nar_ref))
def test_narrative_exists_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.narrative_exists(self.bad_nar_ref)
self.assertIsNotNone(err)
def test_narrative_exists_noauth(self):
with self.assertRaises(PermissionsError) as err:
self.mixin.narrative_exists(self.private_nar['ref'])
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.read_narrative #####
def validate_narrative(self, nar, with_content, with_meta):
"""
Validates a narrative object's overall structure.
We're just making sure that the right elements are expected
to be here - we leave the Jupyter Notebook validation part to
the Jupyter test suite.
"""
if nar is None:
return "Unable to validate null Narrative!"
if not isinstance(nar, dict):
return "Narrative needs to be a dict to be valid."
# expected keys:
exp_keys = set(['info'])
if with_content:
exp_keys.update([
'created', 'refs', 'provenance', 'creator',
'copy_source_inaccessible', 'data', 'extracted_ids'
])
missing_keys = exp_keys - set(nar.keys())
if missing_keys:
return "Narrative object is missing the following keys: {}".format(
', '.join(missing_keys))
if len(nar['info']) != 11:
return "Narrative info is incorrect: expected 11 elements, saw {}".format(
len(nar['info']))
if with_meta:
if not nar['info'][10]:
return "Narrative metadata not returned when expected"
meta_keys = set([
'creator', 'data_dependencies', 'description', 'format',
'job_info', 'name', 'type', 'ws_name'
])
missing_keys = meta_keys - set(nar['info'][10])
if missing_keys:
return "Narrative metadata is missing the following keys: {}".format(
', '.join(missing_keys))
return None
def validate_metadata(self, std_meta, meta):
"""
Validates a Narrative's typed object metadata.
"""
pass
def test_read_narrative_valid_content_metadata(self):
nar = self.mixin.read_narrative(self.public_nar['ref'],
content=True,
include_metadata=False)
self.assertIsNone(self.validate_narrative(nar, True, True))
def test_read_narrative_valid_content_no_metadata(self):
nar = self.mixin.read_narrative(self.public_nar['ref'],
content=True,
include_metadata=True)
self.assertIsNone(self.validate_narrative(nar, True, False))
def test_read_narrative_valid_no_content_metadata(self):
nar = self.mixin.read_narrative(self.public_nar['ref'],
content=False,
include_metadata=True)
self.assertIsNone(self.validate_narrative(nar, False, True))
def test_read_narrative_valid_no_content_no_metadata(self):
nar = self.mixin.read_narrative(self.public_nar['ref'],
content=False,
include_metadata=False)
self.assertIsNone(self.validate_narrative(nar, False, False))
def test_read_narrative_private_anon(self):
with self.assertRaises(PermissionsError) as err:
self.mixin.read_narrative(self.private_nar['ref'])
self.assertIsNotNone(err)
def test_read_narrative_unauth_login(self):
self.login()
with self.assertRaises(PermissionsError) as err:
self.mixin.read_narrative(self.unauth_nar['ref'])
self.assertIsNotNone(err)
self.logout()
def test_read_narrative_invalid(self):
with self.assertRaises(ServerError) as err:
self.mixin.read_narrative(self.invalid_nar_ref)
self.assertIsNotNone(err)
def test_read_narrative_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.read_narrative(self.bad_nar_ref)
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.write_narrative #####
def test_write_narrative_valid_auth(self):
# fetch a narrative and just write it back again.
# should return (nar, wsid, objid)
self.login()
nar = self.mixin.read_narrative(self.private_nar['ref'])['data']
result = self.mixin.write_narrative(self.private_nar['ref'], nar,
self.test_user)
self.assertTrue(result[1] == self.private_nar['ws']
and result[2] == self.private_nar['obj'])
self.logout()
def test_write_narrative_valid_anon(self):
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(PermissionsError) as err:
self.mixin.write_narrative(self.public_nar['ref'], nar,
'Anonymous')
self.assertIsNotNone(err)
def test_write_narrative_valid_unauth(self):
pass
def test_write_narrative_invalid_ref(self):
self.login()
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(ServerError) as err:
self.mixin.write_narrative(self.invalid_nar_ref, nar,
self.test_user)
self.assertIsNotNone(err)
self.logout()
def test_write_narrative_bad_ref(self):
self.login()
nar = self.mixin.read_narrative(self.public_nar['ref'])['data']
with self.assertRaises(HTTPError) as err:
self.mixin.write_narrative(self.bad_nar_ref, nar, self.test_user)
self.assertEquals(err.exception.status_code, 500)
self.logout()
def test_write_narrative_bad_file(self):
self.login()
with self.assertRaises(HTTPError) as err:
self.mixin.write_narrative(self.private_nar['ref'],
{'not': 'a narrative'}, self.test_user)
self.assertEquals(err.exception.status_code, 400)
self.logout()
##### test KBaseWSManagerMixin.rename_narrative #####
def test_rename_narrative_valid_auth(self):
new_name = "new_narrative_name"
self.login()
nar = self.mixin.read_narrative(self.private_nar['ref'],
content=False,
include_metadata=True)
cur_name = nar['info'][10]['name']
self.mixin.rename_narrative(self.private_nar['ref'], self.test_user,
new_name)
nar = self.mixin.read_narrative(self.private_nar['ref'],
content=False,
include_metadata=True)
self.assertEquals(new_name, nar['info'][10]['name'])
### now, put it back to the old name, so it doesn't break other tests...
self.mixin.rename_narrative(self.private_nar['ref'], self.test_user,
cur_name)
self.logout()
def test_rename_narrative_valid_anon(self):
with self.assertRaises(PermissionsError) as err:
self.mixin.rename_narrative(self.public_nar['ref'], self.test_user,
'new_name')
self.assertIsNotNone(err)
def test_rename_narrative_unauth(self):
self.login()
with self.assertRaises(PermissionsError) as err:
self.mixin.rename_narrative(self.unauth_nar['ref'], self.test_user,
'new_name')
self.assertIsNotNone(err)
self.logout()
def test_rename_narrative_invalid(self):
with self.assertRaises(ServerError) as err:
self.mixin.rename_narrative(self.invalid_nar_ref, self.test_user,
'new_name')
self.assertIsNotNone(err)
def test_rename_narrative_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.rename_narrative(self.bad_nar_ref, self.test_user,
'new_name')
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.copy_narrative #####
def test_copy_narrative_valid(self):
# no op for now
pass
def test_copy_narrative_invalid(self):
# no op for now
pass
##### test KBaseWSManagerMixin.list_narratives #####
def validate_narrative_list(self, nar_list):
self.assertIsInstance(nar_list, list)
for nar in nar_list:
self.assertIsInstance(nar, dict)
self.assertTrue(set(nar.keys()).issubset(metadata_fields))
def test_list_all_narratives_anon(self):
res = self.mixin.list_narratives()
self.validate_narrative_list(res)
def test_list_all_narratives_auth(self):
self.login()
res = self.mixin.list_narratives()
self.validate_narrative_list(res)
self.logout()
def test_list_narrative_ws_valid_anon(self):
res = self.mixin.list_narratives(ws_id=self.public_nar['ws'])
self.validate_narrative_list(res)
def test_list_narrative_ws_valid_noperm_anon(self):
with self.assertRaises(PermissionsError) as err:
self.mixin.list_narratives(ws_id=self.private_nar['ws'])
self.assertIsNotNone(err)
def test_list_narrative_ws_valid_login(self):
self.login()
res = self.mixin.list_narratives(ws_id=self.private_nar['ws'])
self.validate_narrative_list(res)
self.logout()
def test_list_narrative_ws_invalid(self):
with self.assertRaises(ServerError) as err:
self.mixin.list_narratives(ws_id=self.invalid_ws_id)
self.assertIsNotNone(err)
def test_list_narrative_ws_valid_noperm_auth(self):
self.login()
with self.assertRaises(PermissionsError) as err:
self.mixin.list_narratives(ws_id=self.unauth_nar['ws'])
self.assertIsNotNone(err)
self.logout()
def test_list_narrative_ws_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.list_narratives(ws_id=self.bad_nar_ref)
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.narrative_permissions #####
# params:
# narrative ref == valid, invalid, bad/malformed
# user:
# None, specific
# login state
def test_narrative_permissions_anon(self):
ret = self.mixin.narrative_permissions(self.public_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret['*'] == 'r')
def test_narrative_permissions_valid_login(self):
self.login()
ret = self.mixin.narrative_permissions(self.public_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret['*'] == 'r')
self.logout()
def test_narrative_permissions_invalid_login(self):
self.login()
with self.assertRaises(ServerError) as err:
self.mixin.narrative_permissions(self.invalid_nar_ref)
self.logout()
def test_narrative_permissions_inaccessible_login(self):
self.login()
ret = self.mixin.narrative_permissions(self.unauth_nar['ref'])
self.assertTrue(isinstance(ret, dict) and ret[self.test_user] == 'n')
self.logout()
def test_narrative_permissions_bad(self):
with self.assertRaises(ValueError) as err:
self.mixin.narrative_permissions(self.bad_nar_ref)
self.assertIsNotNone(err)
##### test KBaseWSManagerMixin.narrative_writable #####
def test_narrative_writable_anon(self):
ret = self.mixin.narrative_writable(self.public_nar['ref'],
self.test_user)
self.assertFalse(ret)
def test_narrative_writable_valid_login_nouser(self):
self.login()
with self.assertRaises(ValueError) as err:
self.mixin.narrative_writable(self.public_nar['ref'], None)
self.assertIsNotNone(err)
self.logout()
def test_narrative_writable_valid_login_user(self):
self.login()
ret = self.mixin.narrative_writable(self.public_nar['ref'],
self.test_user)
self.assertTrue(ret)
self.logout()
def test_narrative_writable_invalid_login_user(self):
self.login()
with self.assertRaises(ServerError) as err:
self.mixin.narrative_writable(self.invalid_nar_ref, self.test_user)
self.assertIsNotNone(err)
self.logout()
def test_narrative_writable_inaccessible_login_user(self):
self.login()
ret = self.mixin.narrative_writable(self.unauth_nar['ref'],
self.test_user)
self.assertFalse(ret)
self.logout()
def test_narrative_writable_bad_login_user(self):
self.login()
with self.assertRaises(ValueError) as err:
self.mixin.narrative_writable(self.bad_nar_ref, self.test_user)
self.assertIsNotNone(err)
self.logout()
def get_notebook(narrative_ref):
# Get the narrative from the workspace and convert it into a notebook obj
narr_fetcher = NIO()
nar = narr_fetcher.read_narrative(narrative_ref)
nar = nar['data']
return (nbformat.reads(json.dumps(nar), as_version=4))
