def matchmaker_add(institute_id, case_name):
"""Add or update a case in MatchMaker"""
# check that only authorized users can add patients to MME
user_obj = store.user(current_user.email)
if "mme_submitter" not in user_obj["roles"]:
flash("unauthorized request", "warning")
return redirect(request.referrer)
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
causatives = False
features = False
if case_obj.get("suspects") and len(case_obj.get("suspects")) > 3:
flash(
"At the moment it is not possible to save to MatchMaker more than 3 pinned variants",
"warning",
)
return redirect(request.referrer)
elif case_obj.get("suspects"):
causatives = True
if case_obj.get("phenotype_terms"):
features = True
mme_save_options = ["sex", "features", "disorders"]
for index, item in enumerate(mme_save_options):
if item in request.form:
LOG.info("item {} is in request form".format(item))
mme_save_options[index] = True
else:
mme_save_options[index] = False
genomic_features = request.form.get("genomicfeatures")
genes_only = True # upload to matchmaker only gene names
if genomic_features == "variants":
genes_only = False # upload to matchmaker both variants and gene names
# If there are no genomic features nor HPO terms to share for this case, abort
if (not case_obj.get("suspects")
and not mme_save_options[1]) or (causatives is False
and features is False):
flash(
"In order to upload a case to MatchMaker you need to pin a variant or at least assign a phenotype (HPO term)",
"danger",
)
return redirect(request.referrer)
user_obj = store.user(current_user.email)
# Required params for sending an add request to MME:
mme_base_url = current_app.config.get("MME_URL")
mme_accepts = current_app.config.get("MME_ACCEPTS")
mme_token = current_app.config.get("MME_TOKEN")
if not mme_base_url or not mme_accepts or not mme_token:
flash(
"An error occurred reading matchmaker connection parameters. Please check config file!",
"danger",
)
return redirect(request.referrer)
add_result = controllers.mme_add(
store=store,
user_obj=user_obj,
case_obj=case_obj,
add_gender=mme_save_options[0],
add_features=mme_save_options[1],
add_disorders=mme_save_options[2],
genes_only=genes_only,
mme_base_url=mme_base_url,
mme_accepts=mme_accepts,
mme_token=mme_token,
)
# flash MME responses (one for each patient posted)
n_succes_response = 0
n_inserted = 0
n_updated = 0
category = "warning"
for resp in add_result["server_responses"]:
message = resp.get("message")
if resp.get("status_code") == 200:
n_succes_response += 1
else:
flash(
"an error occurred while adding patient to matchmaker: {}".
format(message),
"warning",
)
if message == "Patient was successfully updated.":
n_updated += 1
elif message == "Patient was successfully inserted into database.":
n_inserted += 1
# if at least one patient was inserted or updated into matchmaker, save submission at the case level:
if n_inserted or n_updated:
category = "success"
store.case_mme_update(case_obj=case_obj,
user_obj=user_obj,
mme_subm_obj=add_result)
flash(
"Number of new patients in matchmaker:{0}, number of updated records:{1}, number of failed requests:{2}"
.format(
n_inserted,
n_updated,
len(add_result.get("server_responses")) - n_succes_response,
),
category,
)
return redirect(request.referrer)
def matchmaker_add(request, institute_id, case_name):
"""Add all affected individuals from a case to a MatchMaker server
Args:
request(werkzeug.local.LocalProxy)
institute_id(str): _id of an institute
case_name(str): display name of a case
"""
# Check that general MME request requirements are fulfilled
matchmaker_check_requirements(request)
_, case_obj = institute_and_case(store, institute_id, case_name)
candidate_vars = request.form.getlist("selected_var")
if len(candidate_vars) > 3:
flash(
"At the moment it is not possible to save to MatchMaker more than 3 candidate variants / genes",
"warning",
)
return redirect(request.referrer)
save_gender = "sex" in request.form
features = (
hpo_terms(case_obj)
if "features" in request.form and case_obj.get("phenotype_terms")
else []
)
disorders = omim_terms(store, case_obj) if "disorders" in request.form else []
genes_only = request.form.get("genomicfeatures") == "genes"
if not features and not candidate_vars:
flash(
"In order to upload a case to MatchMaker you need to pin a variant or at least assign a phenotype (HPO term)",
"danger",
)
return redirect(request.referrer)
# create contact dictionary
user_obj = store.user(current_user.email)
contact_info = {
"name": user_obj["name"],
"href": "".join(["mailto:", user_obj["email"]]),
"institution": "Scout software user, Science For Life Laboratory, Stockholm, Sweden",
}
submitted_info = {
"contact": contact_info,
"sex": save_gender,
"features": features,
"disorders": disorders,
"genes_only": genes_only,
"patient_id": [],
"server_responses": [],
}
server_responses = []
n_updated = 0
for individual in case_obj.get("individuals"):
if not individual["phenotype"] in [
2,
"affected",
]: # include only affected individuals
continue
patient = {
"contact": contact_info,
"id": ".".join(
[case_obj["_id"], individual.get("individual_id")]
), # This is a required field form MME
"label": ".".join([case_obj["display_name"], individual.get("display_name")]),
"features": features,
"disorders": disorders,
}
if save_gender:
if individual["sex"] == "1":
patient["sex"] = "MALE"
else:
patient["sex"] = "FEMALE"
if candidate_vars:
g_features = genomic_features(
store, case_obj, individual.get("display_name"), candidate_vars, genes_only
)
patient["genomicFeatures"] = g_features
resp = matchmaker.patient_submit(patient)
submitted_info["server_responses"].append(
{
"patient": patient,
"message": resp.get("message"),
"status_code": resp.get("status_code"),
}
)
if resp.get("status_code") != 200:
flash(
"an error occurred while adding patient to matchmaker: {}".format(resp),
"warning",
)
continue
flash(f"Patient {individual.get('display_name')} saved to MatchMaker", "success")
n_updated += 1
if n_updated > 0:
store.case_mme_update(case_obj=case_obj, user_obj=user_obj, mme_subm_obj=submitted_info)
return n_updated
def test_delete_user_mme_submitter(
empty_mock_app, user_obj, case_obj, institute_obj, mme_submission, mme_patient
):
"""Test deleting a user that is a contact for a MatchMaker Exchange case"""
runner = empty_mock_app.test_cli_runner()
user_email = user_obj["email"]
# GIVEN a user in the database
store.user_collection.insert_one(user_obj)
## GIVEN a case with an affected individual saved in MatchMaker
store.institute_collection.insert_one(institute_obj)
case_obj["individuals"] = [
{"phenotype": 2, "individual_id": "ADM1059A2", "display_name": "NA12882"}
]
mme_submission["patients"] = [mme_patient]
case_obj["mme_submission"] = mme_submission
store.case_collection.insert_one(case_obj)
## GIVEN that user_obj is the MME patient's contact
updated_case = store.case_mme_update(case_obj, user_obj, mme_submission)
# Submission contact should contain user's email
assert updated_case["mme_submission"]["subm_user"] == user_email
# And one associated event should be found in database
assert store.event_collection.find_one({"verb": "mme_add", "user_id": user_email})
# WHEN using the CLI command to remove the user, then the function should ask to reassign MME case
result = runner.invoke(cli, ["delete", "user", "-m", user_email], input="n")
# AND user shouldn't be removed if answer is no
assert "Aborted" in result.output
assert store.user_collection.find_one({"email": user_email})
# User should also not be removed if answer provided is yes, but new contact doesn't exist
non_existent_user = "******"
result = runner.invoke(
cli, ["delete", "user", "-m", user_email], input="\n".join(["y", non_existent_user])
)
assert f"User with email '{non_existent_user}' was not found" in result.output
assert store.user_collection.find_one({"email": user_email})
# GIVEN another user with no right over the MME submission
new_users_email = "*****@*****.**"
result = runner.invoke(
cli,
[
"load",
"user",
"-i",
institute_obj["_id"],
"-u",
"Diana Prince",
"-m",
new_users_email,
],
)
assert result.exit_code == 0
# THEN if this user is provided as a new MME contact the remove command should fail again
result = runner.invoke(
cli, ["delete", "user", "-m", user_email], input="\n".join(["y", new_users_email])
)
assert (
f"Scout user with email '{new_users_email}' doesn't have a 'mme_submitter' role"
in result.output
)
assert store.user_collection.find_one({"email": user_email})
# GIVEN that the new user has a "mme_submitter" role
store.user_collection.find_one_and_update(
{"email": new_users_email}, {"$set": {"roles": ["mme_submitter"]}}
)
# THEN the new user can be used as a new MME patient's contact
result = runner.invoke(
cli, ["delete", "user", "-m", user_email], input="\n".join(["y", new_users_email])
)
assert result.exit_code == 0
# AND the old user should be removed
assert store.user_collection.find_one({"email": user_email}) is None
def matchmaker_add(institute_id, case_name):
"""Add or update a case in MatchMaker"""
# check that only authorized users can add patients to MME
user_obj = store.user(current_user.email)
if 'mme_submitter' not in user_obj['roles']:
flash('unauthorized request', 'warning')
return redirect(request.referrer)
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
causatives = False
features = False
if case_obj.get('suspects') and len(case_obj.get('suspects'))>3:
flash('At the moment it is not possible to save to MatchMaker more than 3 pinned variants', 'warning')
return redirect(request.referrer)
elif case_obj.get('suspects'):
causatives = True
if case_obj.get('phenotype_terms'):
features = True
mme_save_options = ['sex', 'features', 'disorders']
for index, item in enumerate(mme_save_options):
if item in request.form:
log.info('item {} is in request form'.format(item))
mme_save_options[index] = True
else:
mme_save_options[index] = False
genomic_features = request.form.get('genomicfeatures')
genes_only = True # upload to matchmaker only gene names
if genomic_features == 'variants':
genes_only = False # upload to matchmaker both variants and gene names
# If there are no genomic features nor HPO terms to share for this case, abort
if (not case_obj.get('suspects') and not mme_save_options[1]) or (causatives is False and features is False):
flash('In order to upload a case to MatchMaker you need to pin a variant or at least assign a phenotype (HPO term)', 'danger')
return redirect(request.referrer)
user_obj = store.user(current_user.email)
# Required params for sending an add request to MME:
mme_base_url = current_app.config.get('MME_URL')
mme_accepts = current_app.config.get('MME_ACCEPTS')
mme_token = current_app.config.get('MME_TOKEN')
if not mme_base_url or not mme_accepts or not mme_token:
flash('An error occurred reading matchmaker connection parameters. Please check config file!', 'danger')
return redirect(request.referrer)
add_result = controllers.mme_add(store=store, user_obj=user_obj, case_obj=case_obj,
add_gender=mme_save_options[0], add_features=mme_save_options[1],
add_disorders=mme_save_options[2], genes_only=genes_only,
mme_base_url = mme_base_url, mme_accepts=mme_accepts, mme_token=mme_token)
# flash MME responses (one for each patient posted)
n_succes_response = 0
n_inserted = 0
n_updated = 0
category = 'warning'
for resp in add_result['server_responses']:
message = resp.get('message')
if resp.get('status_code') == 200:
n_succes_response += 1
else:
flash('an error occurred while adding patient to matchmaker: {}'.format(message), 'warning')
if message == 'Patient was successfully updated.':
n_updated +=1
elif message == 'Patient was successfully inserted into database.':
n_inserted +=1
# if at least one patient was inserted or updated into matchmaker, save submission at the case level:
if n_inserted or n_updated:
category = 'success'
store.case_mme_update(case_obj=case_obj, user_obj=user_obj, mme_subm_obj=add_result)
flash('Number of new patients in matchmaker:{0}, number of updated records:{1}, number of failed requests:{2}'.format(
n_inserted, n_updated, len(add_result.get('server_responses')) - n_succes_response), category)
return redirect(request.referrer)