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| author | Frederick Muriuki Muriithi | 2021-11-26 11:44:53 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2021-11-29 12:05:16 +0300 |
| commit | f88d8e4446c8c9d6693197a452669e0e9c8ea812 (patch) | |
| tree | 5a5c9c3c68f8a33efb5c8b2445672fffab4bac32 /gn3/db | |
| parent | 40f264876f2309fcccfcd3d04a2999bdf3fa5d98 (diff) | |
| download | genenetwork3-f88d8e4446c8c9d6693197a452669e0e9c8ea812.tar.gz | |
Fix query parametrisation
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Pass parameters to the query the way the MySQL driver expects.
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/correlations.py | 16 | ||||
| -rw-r--r-- | gn3/db/species.py | 2 |
2 files changed, 11 insertions, 7 deletions
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py index a1daa3c..c838597 100644 --- a/gn3/db/correlations.py +++ b/gn3/db/correlations.py @@ -23,8 +23,8 @@ def get_filename(target_db_name: str, conn: Any) -> str: """ with conn.cursor() as cursor: cursor.execute( - "SELECT Id, FullName from ProbeSetFreeze WHERE Name-%s", - target_db_name) + "SELECT Id, FullName from ProbeSetFreeze WHERE Name=%s", + (target_db_name,)) result = cursor.fetchone() if result: return "ProbeSetFreezeId_{tid}_FullName_{fname}.txt".format( @@ -398,9 +398,12 @@ def fetch_sample_ids( "AND Species.name=%(species_name)s") with conn.cursor() as cursor: cursor.execute( - query, samples_names=tuple(sample_names), - species_name=species_name) return cursor.fetchall() + query, + { + "samples_names": tuple(sample_names), + "species_name": species_name + }) def build_query_sgo_lit_corr( db_type: str, temp_table: str, sample_id_columns: str, @@ -511,8 +514,9 @@ def fetch_all_database_data(# pylint: disable=[R0913, R0914] query, data_start_pos = __build_query__(sample_ids, temp_table) with conn.cursor() as cursor: cursor.execute( - query, db_name=db_name, - **{f"T{item}_sample_id": item for item in sample_ids}) + query, + {"db_name": db_name, + **{f"T{item}_sample_id": item for item in sample_ids}}) return (cursor.fetchall(), data_start_pos) sample_ids = tuple( diff --git a/gn3/db/species.py b/gn3/db/species.py index 20170ba..5b8e096 100644 --- a/gn3/db/species.py +++ b/gn3/db/species.py @@ -71,6 +71,6 @@ def species_name(conn: Any, group: str) -> str: ("SELECT Species.Name FROM Species, InbredSet " "WHERE InbredSet.Name = %(group_name)s " "AND InbredSet.SpeciesId = Species.Id"), - group_name=group_name) + {"group_name": group}) return cursor.fetchone()[0] return None |