diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/traits.py | 26 |
1 files changed, 15 insertions, 11 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 37b111e..fddb8be 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -91,20 +91,24 @@ def insert_publication(pubmed_id: int, publication: Optional[Dict], with conn.cursor() as cursor: cursor.execute(insert_query, tuple(publication.values())) -def retrieve_probeset_trait_name(threshold, name, connection): +def retrieve_type_trait_name(trait_type, threshold, name, connection): """ - Retrieve the name for a Probeset trait + Retrieve the name of a trait given the trait's name - This is extracted from the `webqtlDataset.retrieveName` function, - specifically the section dealing with 'ProbeSet' type traits - https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-154""" + This is extracted from the `webqtlDataset.retrieveName` function as is + implemented at + https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-L169 + """ + columns = "Id, Name, FullName, ShortName{}".format( + ", DataScale" if trait_type == "ProbeSet" else "") query = ( - 'SELECT Id, Name, FullName, ShortName, DataScale ' - 'FROM ProbeSetFreeze ' - 'WHERE ' - 'public > %(threshold)s ' - 'AND ' - '(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)') + "SELECT {columns} " + "FROM {trait_type}Freeze " + "WHERE " + "public > %(threshold)s " + "AND " + "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)").format( + columns=columns, trait_type=trait_type) with connection.cursor() as cursor: cursor.execute(query, {"threshold": threshold, "name": name}) return cursor.fetchone() |