def conn():
"""Initialize a memory DB with test data and return a connexion on this DB"""
conn = sql.get_sql_connection(":memory:")
sql.create_project(conn, "test", "hg19")
assert table_exists(conn, "projects"), "cannot create table projects"
sql.create_table_fields(conn)
assert table_exists(conn, "fields"), "cannot create table fields"
sql.insert_many_fields(conn, FIELDS)
assert table_count(conn,
"fields") == len(FIELDS), "cannot insert many fields"
sql.create_table_selections(conn)
assert table_exists(conn, "selections"), "cannot create table selections"
sql.create_table_annotations(
conn, sql.get_field_by_category(conn, "annotations"))
assert table_exists(conn, "annotations"), "cannot create table annotations"
sql.create_table_samples(conn, sql.get_field_by_category(conn, "samples"))
assert table_exists(conn, "samples"), "cannot create table samples"
sql.insert_many_samples(conn, SAMPLES)
sql.create_table_variants(conn,
sql.get_field_by_category(conn, "variants"))
assert table_exists(conn, "variants"), "cannot create table variants"
sql.insert_many_variants(conn, VARIANTS)
sql.create_table_wordsets(conn)
assert table_exists(conn, "wordsets"), "cannot create table sets"
return conn
def test_create_db(reader):
conn = sqlite3.connect(":memory:")
sql.create_table_fields(conn)
sql.insert_many_fields(conn, reader.get_fields())
assert len(list(sql.get_fields(conn))) == len(list(reader.get_fields()))
sql.create_table_samples(conn, reader.get_fields_by_category("samples"))
sql.insert_many_samples(conn, reader.get_samples())
assert len(list(sql.get_samples(conn))) == len(list(reader.get_samples()))
sql.create_table_annotations(conn,
reader.get_fields_by_category("annotations"))
sql.create_table_variants(conn, reader.get_fields_by_category("variants"))
sql.create_table_selections(conn)
sql.insert_many_variants(conn, reader.get_variants())
# count variant with annotation
variant_count = len(list(reader.get_variants()))
assert sql.get_variants_count(conn) == variant_count