def _search_external_matches(nodes_to_query, patient_data):
body = {'_disclaimer': MME_DISCLAIMER}
body.update(patient_data)
external_results = []
submission_gene_ids = set()
for feature in patient_data['patient'].get('genomicFeatures', []):
submission_gene_ids.update(get_gene_ids_for_feature(feature, {}))
for node in nodes_to_query:
headers = {
'X-Auth-Token': node['token'],
'Accept': MME_ACCEPT_HEADER,
'Content-Type': MME_ACCEPT_HEADER,
'Content-Language': 'en-US',
}
try:
external_result = requests.post(url=node['url'],
headers=headers,
data=json.dumps(body))
if external_result.status_code != 200:
try:
message = external_result.json().get('message')
except Exception:
message = external_result.content
error_message = '{} ({})'.format(message or 'Error',
external_result.status_code)
raise Exception(error_message)
node_results = external_result.json()['results']
logger.info('Found {} matches from {}'.format(
len(node_results), node['name']))
if node_results:
_, _, gene_symbols_to_ids = get_mme_genes_phenotypes_for_results(
node_results)
invalid_results = []
for result in node_results:
if (not submission_gene_ids) or \
_is_valid_external_match(result, submission_gene_ids, gene_symbols_to_ids):
external_results.append(result)
else:
invalid_results.append(result)
if invalid_results:
error_message = 'Received {} invalid matches from {}'.format(
len(invalid_results), node['name'])
logger.error(error_message)
except Exception as e:
error_message = 'Error searching in {}: {}\n(Patient info: {})'.format(
node['name'], e.message, json.dumps(patient_data))
logger.error(error_message)
post_to_slack(MME_SLACK_ALERT_NOTIFICATION_CHANNEL, error_message)
return external_results
def _is_valid_external_match(result, submission_gene_ids, gene_symbols_to_ids):
for feature in result.get('patient', {}).get('genomicFeatures', []):
if any(gene_id in submission_gene_ids for gene_id in get_gene_ids_for_feature(feature, gene_symbols_to_ids)):
return True
return False
