def test_parse_matches(case_obj, match_objs):
"""tests that a list of MatchMaker matches returned by the server is interpreted
as it should
"""
case_id = case_obj["_id"]
affected_id = ""
for individual in case_obj["individuals"]:
if individual["phenotype"] == "affected":
affected_id = individual["individual_id"]
assert affected_id
# scout patient's id in matchmaker database is composed like this
# scout_case_id.affected_individual_id
mme_patient_id = ".".join([case_id, affected_id])
# make sure that results are returned by parsing matching object
parsed_obj = parse_matches(mme_patient_id, match_objs)
assert isinstance(parsed_obj, list)
# mme_patient_id has matches in match_objs:
assert len(parsed_obj) == 2
for match in parsed_obj:
# make sure that all important fields are available in match results
assert match["match_oid"]
assert match["match_date"]
matching_patients = match["patients"]
for m_patient in matching_patients:
assert m_patient["patient_id"]
assert m_patient["node"]
assert m_patient["score"]
assert m_patient["patient"]
def test_parse_matches(case_obj, match_objs):
""" tests that a list of MatchMaker matches returned by the server is interpreted
as it should
"""
case_id = case_obj['_id']
affected_id = ''
for individual in case_obj['individuals']:
if individual['phenotype'] == 'affected':
affected_id = individual['individual_id']
assert affected_id
# scout patient's id in matchmaker database is composed like this
# scout_case_id.affected_individual_id
mme_patient_id = '.'.join([case_id, affected_id])
# make sure that results are returned by parsing matching object
parsed_obj = parse_matches(mme_patient_id, match_objs)
assert isinstance(parsed_obj, list)
# mme_patient_id has matches in match_objs:
assert len(parsed_obj) == 2
for match in parsed_obj:
# make sure that all important fields are available in match results
assert match['match_oid']
assert match['match_date']
matching_patients = match['patients']
for m_patient in matching_patients:
assert m_patient['patient_id']
assert m_patient['node']
assert m_patient['score']
assert m_patient['patient']
def matchmaker_matches(request, institute_id, case_name):
"""Show Matchmaker submission data for a sample and eventual matches.
Args:
request(werkzeug.local.LocalProxy)
institute_id(str): _id of an institute
case_name(str): display name of a case
Returns:
data(dict): data to display in the html template
"""
# Check that general MME request requirements are fulfilled
matchmaker_check_requirements(request)
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
data = {
"institute": institute_obj,
"case": case_obj,
"server_errors": [],
"panel": 1,
}
matches = {}
for patient in case_obj.get("mme_submission", {}).get("patients", []):
patient_id = patient["id"]
matches[patient_id] = None
server_resp = matchmaker.patient_matches(patient_id)
if server_resp.get("status_code") != 200: # server returned error
flash(
"MatchMaker server returned error:{}".format(data["server_errors"]),
"danger",
)
return redirect(request.referrer)
# server returned a valid response
pat_matches = []
if server_resp.get("content", {}).get("matches"):
pat_matches = parse_matches(patient_id, server_resp["content"]["matches"])
matches[patient_id] = pat_matches
data["matches"] = matches
return data
def mme_matches(case_obj, institute_obj, mme_base_url, mme_token):
"""Show Matchmaker submission data for a sample and eventual matches.
Args:
case_obj(dict): a scout case object
institute_obj(dict): an institute object
mme_base_url(str) base url of the MME server
mme_token(str) auth token of the MME server
Returns:
data(dict): data to display in the html template
"""
data = {
'institute' : institute_obj,
'case' : case_obj,
'server_errors' : []
}
matches = {}
# loop over the submitted samples and get matches from the MatchMaker server
if not case_obj.get('mme_submission'):
return None
for patient in case_obj['mme_submission']['patients']:
patient_id = patient['id']
matches[patient_id] = None
url = ''.join([ mme_base_url, '/matches/', patient_id])
server_resp = matchmaker_request(url=url, token=mme_token, method='GET')
if 'status_code' in server_resp: # the server returned a valid response
# and this will be a list of match objects sorted by desc date
pat_matches = []
if server_resp.get('matches'):
pat_matches = parse_matches(patient_id, server_resp['matches'])
matches[patient_id] = pat_matches
else:
LOG.warning('Server returned error message: {}'.format(server_resp['message']))
data['server_errors'].append(server_resp['message'])
data['matches'] = matches
return data
def mme_matches(case_obj, institute_obj, mme_base_url, mme_token):
"""Show Matchmaker submission data for a sample and eventual matches.
Args:
case_obj(dict): a scout case object
institute_obj(dict): an institute object
mme_base_url(str) base url of the MME server
mme_token(str) auth token of the MME server
Returns:
data(dict): data to display in the html template
"""
data = {
'institute' : institute_obj,
'case' : case_obj,
'server_errors' : []
}
matches = {}
# loop over the submitted samples and get matches from the MatchMaker server
if not case_obj.get('mme_submission'):
return None
for patient in case_obj['mme_submission']['patients']:
patient_id = patient['id']
matches[patient_id] = None
url = ''.join([ mme_base_url, '/matches/', patient_id])
server_resp = matchmaker_request(url=url, token=mme_token, method='GET')
if 'status_code' in server_resp: # the server returned a valid response
# and this will be a list of match objects sorted by desc date
pat_matches = []
if server_resp.get('matches'):
pat_matches = parse_matches(patient_id, server_resp['matches'])
matches[patient_id] = pat_matches
else:
LOG.warning('Server returned error message: {}'.format(server_resp['message']))
data['server_errors'].append(server_resp['message'])
data['matches'] = matches
return data
def mme_matches(case_obj, institute_obj, mme_base_url, mme_token):
"""Show Matchmaker submission data for a sample and eventual matches.
Args:
case_obj(dict): a scout case object
institute_obj(dict): an institute object
mme_base_url(str) base url of the MME server
mme_token(str) auth token of the MME server
Returns:
data(dict): data to display in the html template
"""
data = {"institute": institute_obj, "case": case_obj, "server_errors": []}
matches = {}
# loop over the submitted samples and get matches from the MatchMaker server
if not case_obj.get("mme_submission"):
return None
for patient in case_obj["mme_submission"]["patients"]:
patient_id = patient["id"]
matches[patient_id] = None
url = "".join([mme_base_url, "/matches/", patient_id])
server_resp = matchmaker_request(url=url,
token=mme_token,
method="GET")
if "status_code" in server_resp: # the server returned a valid response
# and this will be a list of match objects sorted by desc date
pat_matches = []
if server_resp.get("matches"):
pat_matches = parse_matches(patient_id, server_resp["matches"])
matches[patient_id] = pat_matches
else:
LOG.warning("Server returned error message: {}".format(
server_resp["message"]))
data["server_errors"].append(server_resp["message"])
data["matches"] = matches
return data