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Add search_table_name param to LofMySQLDao for gene alias resolution #655

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Add search_table_name param to LofMySQLDao for gene alias resolution #655

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16 changes: 13 additions & 3 deletions pheweb/serve/data_access/db.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1858,15 +1858,25 @@ def get_by_variant(self, variant):


class LofMySQLDao(LofDB):
def __init__(self, authentication_file, table_name="lof"):
def __init__(self,
authentication_file,
table_name="lof",
search_table_name: Optional[str] = None):
"""
Args:
search_table_name: Table to search for a particular gene. Genes may have aliases
and it is expected to resolve aliases in this search. If None, defaults to
table_name (preserving the old behavior).
"""
self.authentication_file = authentication_file
auth_module = load_source("mysql_auth", self.authentication_file)
self.user = getattr(auth_module, "mysql")["user"]
self.password = getattr(auth_module, "mysql")["password"]
self.host = getattr(auth_module, "mysql")["host"]
self.db = getattr(auth_module, "mysql")["db"]
self.release = getattr(auth_module, "mysql")["release"]
self.table_name=table_name
self.table_name = table_name
self.search_table_name = search_table_name or self.table_name

def get_connection(self):
return pymysql.connect(
Expand All @@ -1888,7 +1898,7 @@ def get_lofs(self, gene):
conn = self.get_connection()
try:
with conn.cursor(pymysql.cursors.DictCursor) as cursori:
sql = f"SELECT * FROM {self.table_name} WHERE rel=%s AND gene=%s"
sql = f"SELECT * FROM {self.search_table_name} WHERE rel=%s AND gene=%s"
cursori.execute(sql, [self.release, gene])
result = [{"gene_data": data} for data in cursori.fetchall()]
finally:
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