fix: using a default mediator

[dbluhm]

This fixes an error in the use of a default mediator in the connections and out of band protocols. The mediation ID was being saved as None instead of the retrieved default mediator value.

[dbluhm]

Unit tests are failing due to JSONLD context resolution errors 🤔

[dbluhm]

I would really like to get this fix into 0.7.2 if possible. @swcurran

[swcurran]

Will do. @ianco , @shaangill025 or @TimoGlastra want to review?

[ianco]

The tests all ran on my local I'll try to re-run. (Probably failed due to solar flares)

Scratch that able to reproduce locally.

[ianco]

The tests all ran on my local I'll try to re-run. (Probably failed due to solar flares)

Scratch that able to reproduce locally.

Hmmm not consistent sometimes it passes, weird

[codecov-commenter]

Codecov Report

Merging #1490 (a3d8a15) into main (e1e95de) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #1490   +/-   ##
=======================================
  Coverage   95.71%   95.71%           
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  Files         489      489           
  Lines       30264    30264           
=======================================
  Hits        28967    28967           
  Misses       1297     1297           

[swcurran]

Any more idea on what is happening? I got a fail on merging this...

[swcurran]

Looked at the error and the JSON-LD for the example is not loading. I tried the document in the JSON-LD Playground and it does indeed give an error.

• Error Message: pyld.jsonld.JsonLdError: ('Dereferencing a URL did not result in a valid JSON-LD object. Possible causes are an inaccessible URL perhaps due to a same-origin policy (ensure the server uses CORS if you are using client-side JavaScript), too many redirects, a non-JSON response, or more than one HTTP Link Header was provided for a remote context.',) Type: jsonld.InvalidUrl Code: loading remote context failed Details: {'url': 'https://fhircat.org/fhir-r5/rdf-r5/contexts/patient.context.jsonld', 'cause': JsonLdError('Could not retrieve a JSON-LD document from the URL.',)} self = <urllib3.connection.HTTPSConnection object at 0x7f45dda01f28>
• Failing URL: https://fhircat.org/fhir-r5/rdf-r5/contexts/patient.context.jsonld
• JSON-LD Playground Error: jsonld.SyntaxError: Invalid JSON-LD syntax; invalid scoped context.

Not much help...from the me or from the error messages.

[swcurran]

@shaangill025 -- looks like this is a consistent problem. I'm guessing something changed in the context. Should we remove this test from the suite for now? Can you please take a look this morning? I'd like this resolved for 0.7.2.

Thanks

[ianco]

Any more idea on what is happening? I got a fail on merging this...

This error was happening sporadically for me, I suspect some external dependency ...

[ianco]

Seems like "connection refused" on urls at https://fhircat.org/:

E               ConnectionRefusedError: [Errno 111] Connection refused

../.pyenv/versions/3.6.13/lib/python3.6/site-packages/urllib3/util/connection.py:86: ConnectionRefusedError

During handling of the above exception, another exception occurred:

self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7fabcda862b0>, method = 'GET', url = '/fhir-r5/rdf-r5/contexts/sampleddata.context.jsonld', body = None
headers = {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': 'application/ld+json;profile=ht...application/ld+json, application/json;q=0.5, text/html;q=0.8, application/xhtml+xml;q=0.8', 'Connection': 'keep-alive'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None), redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None, release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/fhir-r5/rdf-r5/contexts/sampleddata.context.jsonld', query=None, fragment=None)
destination_scheme = None, conn = None, release_this_conn = True, http_tunnel_required = False, err = None, clean_exit = False

The url's work fine for me manually and there are tests that randomly fail (it's not always the same test)

Not sure if we can add a retry? In this case it's getting pulled in through a dependency from http://hl7.org/fhir/Patient I think, so not sure we have direct control of it ...

[ianco]

Error is getting thrown from within the pyld package:

E           pyld.jsonld.JsonLdError: ('Could not retrieve a JSON-LD document from the URL.',)
E           Type: jsonld.LoadDocumentError
E           Code: loading document failed
E           Cause: HTTPSConnectionPool(host='fhircat.org', port=443): Max retries exceeded with url: /fhir-r5/rdf-r5/contexts/sampleddata.context.jsonld (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7fabcda86860>: Failed to establish a new connection: [Errno 111] Connection refused',))  File "/home/indy/.pyenv/versions/3.6.13/lib/python3.6/site-packages/pyld/documentloader/requests.py", line 63, in loader
E               response = requests.get(url, headers=headers, **kwargs)
E             File "/home/indy/.pyenv/versions/3.6.13/lib/python3.6/site-packages/requests/api.py", line 76, in get
E               return request('get', url, params=params, **kwargs)
E             File "/home/indy/.pyenv/versions/3.6.13/lib/python3.6/site-packages/requests/api.py", line 61, in request
E               return session.request(method=method, url=url, **kwargs)
E             File "/home/indy/.pyenv/versions/3.6.13/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
E               resp = self.send(prep, **send_kwargs)
E             File "/home/indy/.pyenv/versions/3.6.13/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
E               r = adapter.send(request, **kwargs)
E             File "/home/indy/.pyenv/versions/3.6.13/lib/python3.6/site-packages/requests/adapters.py", line 516, in send
E               raise ConnectionError(e, request=request)

../.pyenv/versions/3.6.13/lib/python3.6/site-packages/pyld/documentloader/requests.py:103: JsonLdError