def real_database(database_name, institute_obj, user_obj, genes, panel_info):
"""Setup a real database with populated data"""
mongo_client = pymongo.MongoClient()
mongo_client.drop_database(database_name)
database = mongo_client[database_name]
adapter = MongoAdapter(database)
# Populate the database
adapter.add_institute(institute_obj)
adapter.add_user(user_obj)
load_hgnc_genes(adapter, genes)
adapter.hgnc_collection.create_index([('build', pymongo.ASCENDING),
('hgnc_symbol', pymongo.ASCENDING)])
load_panel(adapter=adapter, panel_info=panel_info)
# load_hpo(adapter=gene_database, hpo_lines=hpo_terms_handle, disease_lines=genemap_handle)
# adapter.add_case(case_obj)
# for variant in variant_objs:
# adapter.load_variant(variant)
yield adapter
mongo_client.drop_database(database_name)
def real_database(request, database_name, institute_obj, user_obj, genes,
panel_info):
"""Setup a real database with populated data"""
mongo_client = pymongo.MongoClient()
mongo_client.drop_database(database_name)
database = mongo_client[database_name]
adapter = MongoAdapter(database)
# Populate the database
adapter.add_institute(institute_obj)
adapter.add_user(user_obj)
load_hgnc_genes(adapter, genes)
adapter.hgnc_collection.create_index([('build', pymongo.ASCENDING),
('hgnc_symbol', pymongo.ASCENDING)])
adapter.load_panel(path=panel_info['file'],
institute=panel_info['institute'],
panel_id=panel_info['panel_name'],
date=panel_info['date'],
panel_type=panel_info['type'],
version=panel_info['version'],
display_name=panel_info['full_name'])
# load_hpo(adapter=gene_database, hpo_lines=hpo_terms_handle, disease_lines=genemap_handle)
# adapter.add_case(case_obj)
# for variant in variant_objs:
# adapter.load_variant(variant)
def teardown():
mongo_client.drop_database(database_name)
request.addfinalizer(teardown)
return adapter