def setUp(self):
self.schema_url = "http://localhost:3000/api/v1/schema"
self.schema_file = resource_string(__name__,
'data/schema.json').decode('utf-8')
responses.add(responses.GET,
self.schema_url,
json=json.loads(self.schema_file))
self.api = Api(base_url="http://localhost:3000",
api_key='aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa')
self.uuid_one = "4a668ac6daf74364"
self.uuid_two = "d61f459d077d4cd0"
self.classification_one = resource_string(
__name__,
"data/api/{}.json".format(self.uuid_one)).decode('utf-8') # noqa
self.table_one = resource_string(
__name__, "data/api/{}_table.json".format(self.uuid_one)).decode(
'utf-8') # noqa
self.classification_two = resource_string(
__name__,
"data/api/{}.json".format(self.uuid_two)).decode('utf-8') # noqa
self.table_two = resource_string(
__name__, "data/api/{}_table.json".format(self.uuid_two)).decode(
'utf-8') # noqa
self.classification_one_url = "http://localhost:3000/api/v1/classifications/4a668ac6daf74364"
self.classification_one_table_url = "http://localhost:3000/api/v1/classifications/4a668ac6daf74364/results"
self.classification_two_url = "http://localhost:3000/api/v1/classifications/d61f459d077d4cd0"
self.classification_two_table_url = "http://localhost:3000/api/v1/classifications/d61f459d077d4cd0/results"
def from_notebook_node(self, nb, resources=None, **kw):
"""Takes PDF output from PDFExporter and uploads to One Codex Documents portal."""
output, resources = super(OneCodexDocumentExporter, self).from_notebook_node(
nb, resources=resources, **kw
)
from onecodex import Api
from onecodex.lib.upload import _upload_document_fileobj
ocx = Api()
default_filename = "Analysis Report - {dt:%B} {dt.day}, {dt:%Y}".format(
dt=datetime.datetime.now()
)
file_name = resources["metadata"].get("one_codex_doc_portal_filename", default_filename)
try:
document_id = _upload_document_fileobj(
BytesIO(output), file_name, ocx._client.session, ocx.Documents._resource
)
except UploadException as exc:
resp = json.dumps({"status": 500, "message": str(exc)})
return resp, resources
except Exception:
resp = json.dumps(
{
"status": 500,
"message": "Upload failed. Please contact [email protected] for assistance.",
}
)
return resp, resources
resp = json.dumps({"status": 200, "document_id": document_id})
return resp, resources
def ocx():
"""Instantiated API client
"""
with mock_requests(SCHEMA_ROUTES):
return Api(api_key='1eab4217d30d42849dbde0cd1bb94e39',
base_url='http://localhost:3000',
cache_schema=False)
def test_api_creation(api_data):
ocx = Api(
api_key="1eab4217d30d42849dbde0cd1bb94e39",
base_url="http://localhost:3000",
cache_schema=False,
)
assert isinstance(ocx, Api)
assert True
def setUp(self):
self.schema_url = "http://localhost:3000/api/v1/schema"
self.schema_file = resource_string(__name__,
'data/schema.json').decode('utf-8')
responses.add(responses.GET,
self.schema_url,
json=json.loads(self.schema_file))
self.api = Api(base_url="http://localhost:3000",
api_key='aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa')
def ocx_w_raven():
patched_env = {
'ONE_CODEX_API_BASE': 'http://*****:*****@sentry.example.com/1',
}
with mock.patch.dict(os.environ, patched_env):
with mock_requests(SCHEMA_ROUTES):
return Api(cache_schema=False, telemetry=True)
def ocx_w_raven():
patched_env = os.environ.copy()
patch = {
"ONE_CODEX_API_BASE": "http://*****:*****@sentry.example.com/1",
"ONE_CODEX_NO_TELEMETRY": None,
}
patched_env.update(patch)
with mock.patch.object(os, "environ", patched_env):
with mock_requests(SCHEMA_ROUTES):
return Api(cache_schema=False, telemetry=True)
def setUp(self):
self.schema_url = "http://localhost:3000/api/v1/schema"
self.schema_file = resource_string(__name__,
'data/schema.json').decode('utf-8')
responses.add(responses.GET,
self.schema_url,
json=json.loads(self.schema_file))
self.api = Api(base_url="http://localhost:3000",
api_key='aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa')
self.num_complete = 2
self.num_incomplete = 1
self.complete_analyses = resource_string(
__name__, 'data/api/complete_analyses.json').decode('utf-8')
self.incomplete_analyses = resource_string(
__name__, 'data/api/incomplete_analyses.json').decode('utf-8')
self.sample = resource_string(__name__,
'data/api/sample.json').decode('utf-8')
self.metadata = resource_string(
__name__, 'data/api/metadata.json').decode('utf-8')
self.uuid_one = '1'
self.analysis_one = resource_string(
__name__, 'data/api/complete_analysis_one.json').decode('utf-8')
self.uuid_two = '2'
self.analysis_two = resource_string(
__name__, 'data/api/complete_analysis_two.json').decode('utf-8')
self.uuid_three = '3'
self.analysis_three = resource_string(
__name__, 'data/api/incomplete_analysis_one.json').decode('utf-8')
# URLS for responses
self.analysis_one_url = 'http://localhost:3000/api/v1/analyses/1'
self.analysis_two_url = 'http://localhost:3000/api/v1/analyses/2'
self.analysis_three_url = 'http://localhost:3000/api/v1/analyses/3'
self.complete_url = 'http://localhost:3000/api/v1/analyses?per_page=200&where=%7B%22complete%22%3A+true%7D&page=1'
self.complete_url_new = 'http://localhost:3000/api/v1/analyses?sort=%7B%7D&per_page=200&where=%7B%22complete%22%3A+true%7D&page=1'
self.incomplete_url = 'http://localhost:3000/api/v1/analyses?per_page=200&where=%7B%22complete%22%3A+false%7D&page=1'
self.incomplete_url_new = 'http://localhost:3000/api/v1/analyses?sort=%7B%7D&per_page=200&where=%7B%22complete%22%3A+false%7D&page=1'
self.sample_url = 'http://localhost:3000/api/v1/samples/d66e901ea9854f1f'
self.metadata_url = 'http://localhost:3000/api/v1/metadata/50fd2f0513d34372'
def test_bearer_auth_from_env(api_data, monkeypatch):
monkeypatch.setenv("ONE_CODEX_BEARER_TOKEN", "mysecrettoken")
ocx = Api(base_url="http://localhost:3000", cache_schema=True)
assert isinstance(ocx._req_args["auth"], BearerTokenAuth)
sample = ocx.Samples.get("761bc54b97f64980")
assert sample.visibility != "public"
def test_api_key_auth_from_kwargs(api_data):
ocx = Api(api_key="mysecretkey", base_url="http://localhost:3000", cache_schema=True)
assert isinstance(ocx._req_args["auth"], HTTPBasicAuth)
def test_bearer_auth_from_kwargs(api_data):
ocx = Api(bearer_token="mysecrettoken", base_url="http://localhost:3000", cache_schema=True)
assert isinstance(ocx._req_args["auth"], BearerTokenAuth)
def test_api_key_auth_from_env(api_data, monkeypatch):
monkeypatch.setenv("ONE_CODEX_API_KEY", "mysecretkey")
ocx = Api(base_url="http://localhost:3000", cache_schema=True)
assert isinstance(ocx._req_args["auth"], HTTPBasicAuth)
def test_bearer_auth_from_env(api_data, monkeypatch):
monkeypatch.setenv('ONE_CODEX_BEARER_TOKEN', 'mysecrettoken')
ocx = Api(base_url='http://localhost:3000', cache_schema=True)
assert isinstance(ocx._req_args['auth'], BearerTokenAuth)
sample = ocx.Samples.get('761bc54b97f64980')
assert sample.visibility != 'public'
def test_api_key_auth_from_kwargs(api_data):
ocx = Api(api_key='mysecretkey',
base_url='http://localhost:3000',
cache_schema=True)
assert isinstance(ocx._req_args['auth'], HTTPBasicAuth)
def test_api_key_auth_from_env(api_data, monkeypatch):
monkeypatch.setenv('ONE_CODEX_API_KEY', 'mysecretkey')
ocx = Api(base_url='http://localhost:3000', cache_schema=True)
assert isinstance(ocx._req_args['auth'], HTTPBasicAuth)