candig/candig-opa

Developing relevant rego policies for OPA CanDIGv2

candig-opa's Issues

Had to change the version of postgres in docker compose yaml from latest to buster

Had to change the version of postgres in docker compose yaml from latest to buster so that Travis can pass. Not sure what is the issue with the latest postgres docker image. Katsu does not seem to be able to connect to postgres db.

$ python3 tests/create_katsu_test_datasets.py
Traceback (most recent call last):
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/urllib3/connectionpool.py", line 445, in _make_request
six.raise_from(e, None)
File "", line 3, in raise_from
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/urllib3/connectionpool.py", line 440, in _make_request
httplib_response = conn.getresponse()
File "/opt/python/3.6.7/lib/python3.6/http/client.py", line 1331, in getresponse
response.begin()
File "/opt/python/3.6.7/lib/python3.6/http/client.py", line 297, in begin
version, status, reason = self._read_status()
File "/opt/python/3.6.7/lib/python3.6/http/client.py", line 258, in _read_status
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
File "/opt/python/3.6.7/lib/python3.6/socket.py", line 586, in readinto
return self._sock.recv_into(b)
ConnectionResetError: [Errno 104] Connection reset by peer
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/urllib3/util/retry.py", line 532, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/urllib3/packages/six.py", line 769, in reraise
raise value.with_traceback(tb)
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/urllib3/connectionpool.py", line 445, in _make_request
six.raise_from(e, None)
File "", line 3, in raise_from
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/urllib3/connectionpool.py", line 440, in _make_request
httplib_response = conn.getresponse()
File "/opt/python/3.6.7/lib/python3.6/http/client.py", line 1331, in getresponse
response.begin()
File "/opt/python/3.6.7/lib/python3.6/http/client.py", line 297, in begin
version, status, reason = self._read_status()
File "/opt/python/3.6.7/lib/python3.6/http/client.py", line 258, in _read_status
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
File "/opt/python/3.6.7/lib/python3.6/socket.py", line 586, in readinto
return self._sock.recv_into(b)
urllib3.exceptions.ProtocolError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "tests/create_katsu_test_datasets.py", line 348, in
create_project_table_meta_data(title)
File "tests/create_katsu_test_datasets.py", line 336, in create_project_table_meta_data
project_id = get_project_id(project_title)
File "tests/create_katsu_test_datasets.py", line 20, in get_project_id
return post_data(f"{KATSU_URL}/api/projects", {"title": project_title, "description": "Project for tests"})["identifier"]
File "tests/create_katsu_test_datasets.py", line 9, in post_data
response = requests.post(url, json=data)
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/requests/api.py", line 117, in post
return request('post', url, data=data, json=json, **kwargs)
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/requests/api.py", line 61, in request
return session.request(method=method, url=url, **kwargs)
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))

Integrate Dash's GA4GH passport work into this repo

https://github.com/CanDIG/candigv2_opa