def test_backend_remove_patient(gpx4_patients, database):
""" Test adding 2 test patients and then removing them using label or ID """
# test conversion to format required for the database:
test_mme_patients = [ mme_patient(json_patient=patient) for patient in gpx4_patients]
# make sure 2 json patient are correctly parsed
assert len(test_mme_patients) == 2
# insert the 2 patients into the database
inserted_ids = [ backend_add_patient(mongo_db=database, patient=mme_patient, match_external=False) for mme_patient in test_mme_patients ]
assert len(inserted_ids) == 2
# make sure that inserted patients contain computed phenotypes from Monarch
a_patient = database['patients'].find_one()
assert a_patient
# test removing a patient by ID:
remove_query = {'_id' : 'P0001058'}
deleted = delete_by_query(remove_query, database, 'patients')
db_patients = database['patients'].find()
assert db_patients.count() == 1
# test removing a patient by label:
remove_query = {'label' : '350_2-test'}
deleted = delete_by_query(remove_query, database, 'patients')
db_patients = database['patients'].find()
assert db_patients.count() == 0
def client(id):
"""Remove a client from database by providing its ID"""
query = {"_id": id}
n_removed = delete_by_query(query=query,
mongo_db=current_app.db,
mongo_collection="clients")
click.echo("Number of clients removed from database:{}".format(n_removed))
def node(id):
"""Remove a node from database by providing its ID"""
query = {'_id': id}
n_removed = delete_by_query(query=query,
mongo_db=current_app.db,
mongo_collection='nodes')
click.echo('Number of nodes removed from database:{}'.format(n_removed))
def delete_patient(database, patient_id):
"""Remove a patient by ID"""
message = ''
# first delete all matches in database for this patient:
query = {'data.patient.id' : patient_id}
deleted = delete_by_query(query, database, 'matches')
LOG.info('deleted {} matche/s triggered by this patient'.format(deleted))
query = {'_id' : patient_id}
deleted = delete_by_query(query, database, 'patients')
message = {}
if deleted == 1:
message['message'] = 'Patient and its matches were successfully deleted from database'
else:
message['message'] = 'ERROR. Could not delete a patient with ID {} from database'.format(patient_id)
return message
def delete_patient(database, patient_id):
"""Remove a patient by ID"""
message = ""
# first delete all matches in database for this patient:
query = {"data.patient.id": patient_id}
deleted = delete_by_query(query, database, "matches")
LOG.info("deleted {} matche/s triggered by this patient".format(deleted))
query = {"_id": patient_id}
deleted = delete_by_query(query, database, "patients")
message = {}
if deleted == 1:
message["message"] = "Patient and its matches were successfully deleted from database"
else:
message["message"] = "ERROR. Could not delete a patient with ID {} from database".format(
patient_id
)
return message
def patient(id, label, remove_matches):
"""Removing a patient from patientMatcher providing its ID"""
if not id and not label:
click.echo(
"Error: either ID and/or label should be provided to delete a patient."
)
raise click.Abort()
if remove_matches and not id:
click.echo(
"Please provide patient ID and not label to remove all its matches."
)
raise click.Abort()
query = {}
if id:
query["_id"] = id
if label:
query["label"] = label
n_removed = delete_by_query(query=query,
mongo_db=current_app.db,
mongo_collection="patients")
click.echo("Number of patients removed from database:{}".format(n_removed))
if remove_matches:
# this will remove ONLY matches where this patient was the query patient
# NOT those where patient was among the matching results
query = {"data.patient.id": id}
n_removed = delete_by_query(query=query,
mongo_db=current_app.db,
mongo_collection="matches")
click.echo(
"Number of matches for this patient removed from database:{}".
format(n_removed))
