def test_mme_add(self, populated_database, user_obj, case_obj,
parsed_variant):
"""test calling the controller that submits new patients to Matchmaker"""
session = requests.Session()
adapter = populated_database
# Add an HPO term to this scout case
assert case_obj.get('phenotype_terms') == None
phenotype_term = {
'phenotype_id': 'HP:0011031',
'feature': 'Abnormality of iron homeostasis'
}
updated_case = adapter.case_collection.find_one_and_update(
{'_id': case_obj['_id']},
{'$set': {
'phenotype_terms': [phenotype_term]
}},
return_document=pymongo.ReturnDocument.AFTER)
assert updated_case['phenotype_terms'][0] == phenotype_term
# Check that features (HPO) terms are obtained by MME parser
features = hpo_terms(updated_case)
assert features
# Add a couple of OMIM diagnoses to this case
assert case_obj.get('diagnosis_phenotypes') == None
updated_case = adapter.case_collection.find_one_and_update(
{'_id': case_obj['_id']},
{'$set': {
'diagnosis_phenotypes': [615349, 616833]
}},
return_document=pymongo.ReturnDocument.AFTER)
assert updated_case['diagnosis_phenotypes']
# Check that OMIM terms are obtained by MME parser
diagnoses = omim_terms(updated_case)
assert diagnoses
# Add variant containing a gene to database and pin it for this case
a_gene = adapter.hgnc_collection.find_one()
assert a_gene['hgnc_id']
assert adapter.variant_collection.find_one() is None
parsed_variant['hgnc_ids'] = [a_gene['hgnc_id']]
parsed_variant['samples'] = [
{ # pretend the affected subject has the allele
'sample_id': 'ADM1059A2',
'display_name': 'NA12882',
'genotype_call': '0/1'
}
]
adapter.variant_collection.insert_one(parsed_variant)
assert adapter.variant_collection.find_one()
# pin it
updated_case = adapter.case_collection.find_one_and_update(
{'_id': case_obj['_id']},
{'$set': {
'suspects': [parsed_variant['_id']]
}},
return_document=pymongo.ReturnDocument.AFTER)
assert updated_case['suspects'] == [parsed_variant['_id']]
# Check that genomic features are created correcly by MME parser
g_feat = genomic_features(adapter, updated_case, 'NA12882', 'False')
assert g_feat
# use controller to send request and collect response
mme_base_url = 'http://localhost:{port}'.format(
port=self.mock_server_port)
submitted_info = controllers.mme_add(store=adapter,
user_obj=user_obj,
case_obj=updated_case,
add_gender=True,
add_features=True,
add_disorders=True,
genes_only=False,
mme_base_url=mme_base_url,
mme_accepts=MME_ACCEPTS,
mme_token=MME_TOKEN)
assert submitted_info['server_responses'][0]['patient']
def test_mme_add(self, populated_database, user_obj, case_obj,
parsed_variant):
"""test calling the controller that submits new patients to Matchmaker"""
session = requests.Session()
adapter = populated_database
# Add an HPO term to this scout case
assert len(case_obj.get("phenotype_terms")) == 0
phenotype_term = {
"phenotype_id": "HP:0011031",
"feature": "Abnormality of iron homeostasis",
}
updated_case = adapter.case_collection.find_one_and_update(
{"_id": case_obj["_id"]},
{"$set": {
"phenotype_terms": [phenotype_term]
}},
return_document=pymongo.ReturnDocument.AFTER,
)
assert updated_case["phenotype_terms"][0] == phenotype_term
# Check that features (HPO) terms are obtained by MME parser
features = hpo_terms(updated_case)
assert features
# Add a couple of OMIM diagnoses to this case
assert case_obj.get("diagnosis_phenotypes") is None
updated_case = adapter.case_collection.find_one_and_update(
{"_id": case_obj["_id"]},
{"$set": {
"diagnosis_phenotypes": [615349, 616833]
}},
return_document=pymongo.ReturnDocument.AFTER,
)
assert updated_case["diagnosis_phenotypes"]
# Check that OMIM terms are obtained by MME parser
diagnoses = omim_terms(updated_case)
assert diagnoses
# Add variant containing a gene to database and pin it for this case
a_gene = adapter.hgnc_collection.find_one()
assert a_gene["hgnc_id"]
assert adapter.variant_collection.find_one() is None
parsed_variant["hgnc_ids"] = [a_gene["hgnc_id"]]
parsed_variant["samples"] = [
{ # pretend the affected subject has the allele
"sample_id": "ADM1059A2",
"display_name": "NA12882",
"genotype_call": "0/1",
}
]
adapter.variant_collection.insert_one(parsed_variant)
assert adapter.variant_collection.find_one()
# pin it
updated_case = adapter.case_collection.find_one_and_update(
{"_id": case_obj["_id"]},
{"$set": {
"suspects": [parsed_variant["_id"]]
}},
return_document=pymongo.ReturnDocument.AFTER,
)
assert updated_case["suspects"] == [parsed_variant["_id"]]
# Check that genomic features are created correcly by MME parser
g_feat = genomic_features(adapter, updated_case, "NA12882", "False")
assert g_feat
# use controller to send request and collect response
mme_base_url = "http://localhost:{port}".format(
port=self.mock_server_port)
submitted_info = controllers.mme_add(
store=adapter,
user_obj=user_obj,
case_obj=updated_case,
add_gender=True,
add_features=True,
add_disorders=True,
genes_only=False,
mme_base_url=mme_base_url,
mme_accepts=MME_ACCEPTS,
mme_token=MME_TOKEN,
)
assert submitted_info["server_responses"][0]["patient"]