Open
Description
Step to reproduce:
Run the tool with incorrect environment keyword.
$ analyze-submission -d int 5c9b50a6436bf1000897212c
Expected Behavior:
Let the user know the allowed arguments/parameters
Actual Behavior:
Unhandled exception
Stacktrace:
(metadata-schema) C02X488AJHD2:metadata-schema zina$
Using deployment: int
PHASE 1: Get submission primary bundle list from Ingest:
Retrieving submission...Traceback (most recent call last):
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/urllib3/connection.py", line 141, in _new_conn
(self.host, self.port), self.timeout, **extra_kw)
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/urllib3/util/connection.py", line 60, in create_connection
for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
File "/anaconda3/envs/metadata-schema/lib/python3.6/socket.py", line 745, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno 8] nodename nor servname provided, or not known
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/urllib3/connectionpool.py", line 601, in urlopen
chunked=chunked)
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/urllib3/connectionpool.py", line 346, in _make_request
self._validate_conn(conn)
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/urllib3/connectionpool.py", line 850, in _validate_conn
conn.connect()
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/urllib3/connection.py", line 284, in connect
conn = self._new_conn()
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/urllib3/connection.py", line 150, in _new_conn
self, "Failed to establish a new connection: %s" % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.VerifiedHTTPSConnection object at 0x10f41f320>: Failed to establish a new connection: [Errno 8] nodename nor servname provided, or not known
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/urllib3/connectionpool.py", line 639, in urlopen
_stacktrace=sys.exc_info()[2])
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/urllib3/util/retry.py", line 388, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='api.ingest.int.data.humancellatlas.org', port=443): Max retries exceeded with url: /submissionEnvelopes/5c9b50a6436bf1000897212c (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x10f41f320>: Failed to establish a new connection: [Errno 8] nodename nor servname provided, or not known',))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/anaconda3/envs/metadata-schema/bin/analyze-submission", line 677, in <module>
AnalyzeSubmission()
File "/anaconda3/envs/metadata-schema/bin/analyze-submission", line 592, in __init__
self._get_submission_project_and_primary_bundle_list_from_ingest()
File "/anaconda3/envs/metadata-schema/bin/analyze-submission", line 650, in _get_submission_project_and_primary_bundle_list_from_ingest
submission = finder.find(f"subm_id={self.state.submission_id}")
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/dcp_diag/finders/ingest_finder.py", line 27, in find
return SubmissionEnvelope.load_by_id(submission_id=field_value, ingest_api_agent=self.ingest)
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/dcp_diag/component_entities/ingest_entities.py", line 67, in load_by_id
data = ingest_api_agent.get(f"/submissionEnvelopes/{submission_id}")
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/dcp_diag/component_agents/hateoas_agent.py", line 52, in get
response = requests.get(url, headers=self.headers)
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/requests/api.py", line 75, in get
return request('get', url, params=params, **kwargs)
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/requests/api.py", line 60, in request
return session.request(method=method, url=url, **kwargs)
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/requests/sessions.py", line 533, in request
resp = self.send(prep, **send_kwargs)
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/requests/sessions.py", line 646, in send
r = adapter.send(request, **kwargs)
File "/anaconda3/envs/metadata-schema/lib/python3.6/site-packages/requests/adapters.py", line 516, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='api.ingest.int.data.humancellatlas.org', port=443): Max retries exceeded with url: /submissionEnvelopes/5c9b50a6436bf1000897212c (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x10f41f320>: Failed to establish a new connection: [Errno 8] nodename nor servname provided, or not known',))
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