diff options
Diffstat (limited to 'gn3/db/traits.py')
| -rw-r--r-- | gn3/db/traits.py | 101 |
1 files changed, 50 insertions, 51 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index a7e7e7c..90d1e9d 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -69,7 +69,7 @@ def export_trait_data( return accumulator + (trait_data["data"][sample]["ndata"], ) if dtype == "all": return accumulator + __export_all_types(trait_data["data"], sample) - raise KeyError("Type `%s` is incorrect" % dtype) + raise KeyError(f"Type `{dtype}` is incorrect") if var_exists and n_exists: return accumulator + (None, None, None) if var_exists or n_exists: @@ -125,9 +125,8 @@ def update_sample_data(conn: Any, #pylint: disable=[R0913] "PublishXRef.Id = %s AND " "PublishXRef.PhenotypeId = %s " "AND PublishData.StrainId = Strain.Id " - "AND Strain.Name = \"%s\"") % (trait_name, - phenotype_id, - str(strain_name))) + "AND Strain.Name = %s"), + (trait_name, phenotype_id, str(strain_name))) strain_id, data_id = cursor.fetchone() updated_published_data: int = 0 updated_se_data: int = 0 @@ -137,8 +136,8 @@ def update_sample_data(conn: Any, #pylint: disable=[R0913] # Update the PublishData table if value == "x": cursor.execute(("DELETE FROM PublishData " - "WHERE StrainId = %s AND Id = %s") - % (strain_id, data_id)) + "WHERE StrainId = %s AND Id = %s"), + (strain_id, data_id)) updated_published_data = cursor.rowcount else: cursor.execute(("UPDATE PublishData SET value = %s " @@ -148,19 +147,20 @@ def update_sample_data(conn: Any, #pylint: disable=[R0913] if not updated_published_data: cursor.execute( - "SELECT * FROM " - "PublishData WHERE StrainId = " - "%s AND Id = %s" % (strain_id, data_id)) + ("SELECT * FROM " + "PublishData WHERE StrainId = " + "%s AND Id = %s"), + (strain_id, data_id)) if not cursor.fetchone(): cursor.execute(("INSERT INTO PublishData (Id, StrainId, " - " value) VALUES (%s, %s, %s)") % + " value) VALUES (%s, %s, %s)"), (data_id, strain_id, value)) updated_published_data = cursor.rowcount # Update the PublishSE table if error == "x": cursor.execute(("DELETE FROM PublishSE " - "WHERE StrainId = %s AND DataId = %s") % + "WHERE StrainId = %s AND DataId = %s"), (strain_id, data_id)) updated_se_data = cursor.rowcount else: @@ -171,21 +171,22 @@ def update_sample_data(conn: Any, #pylint: disable=[R0913] updated_se_data = cursor.rowcount if not updated_se_data: cursor.execute( - "SELECT * FROM " - "PublishSE WHERE StrainId = " - "%s AND DataId = %s" % (strain_id, data_id)) + ("SELECT * FROM " + "PublishSE WHERE StrainId = " + "%s AND DataId = %s"), + (strain_id, data_id)) if not cursor.fetchone(): - cursor.execute(("INSERT INTO PublishSE (StrainId, DataId, " - " error) VALUES (%s, %s, %s)") % - (strain_id, data_id, - None if error == "x" else error)) + cursor.execute( + ("INSERT INTO PublishSE (StrainId, DataId, " + " error) VALUES (%s, %s, %s)"), + (strain_id, data_id, None if error == "x" else error)) updated_se_data = cursor.rowcount # Update the NStrain table if count == "x": cursor.execute(("DELETE FROM NStrain " - "WHERE StrainId = %s AND DataId = %s" % - (strain_id, data_id))) + "WHERE StrainId = %s AND DataId = %s"), + (strain_id, data_id)) updated_n_strains = cursor.rowcount else: cursor.execute(("UPDATE NStrain SET count = %s " @@ -194,13 +195,14 @@ def update_sample_data(conn: Any, #pylint: disable=[R0913] updated_n_strains = cursor.rowcount if not updated_n_strains: cursor.execute( - "SELECT * FROM " - "NStrain WHERE StrainId = " - "%s AND DataId = %s" % (strain_id, data_id)) + ("SELECT * FROM " + "NStrain WHERE StrainId = " + "%s AND DataId = %s"), + (strain_id, data_id)) if not cursor.fetchone(): cursor.execute(("INSERT INTO NStrain " "(StrainId, DataId, count) " - "VALUES (%s, %s, %s)") % + "VALUES (%s, %s, %s)"), (strain_id, data_id, count)) updated_n_strains = cursor.rowcount return (updated_published_data, @@ -237,9 +239,8 @@ def delete_sample_data(conn: Any, "PublishXRef.Id = %s AND " "PublishXRef.PhenotypeId = %s " "AND PublishData.StrainId = Strain.Id " - "AND Strain.Name = \"%s\"") % (trait_name, - phenotype_id, - str(strain_name))) + "AND Strain.Name = %s"), + (trait_name, phenotype_id, str(strain_name))) # Check if it exists if the data was already deleted: if _result := cursor.fetchone(): @@ -248,20 +249,20 @@ def delete_sample_data(conn: Any, # Only run if the strain_id and data_id exist if strain_id and data_id: cursor.execute(("DELETE FROM PublishData " - "WHERE StrainId = %s AND Id = %s") - % (strain_id, data_id)) + "WHERE StrainId = %s AND Id = %s"), + (strain_id, data_id)) deleted_published_data = cursor.rowcount # Delete the PublishSE table cursor.execute(("DELETE FROM PublishSE " - "WHERE StrainId = %s AND DataId = %s") % + "WHERE StrainId = %s AND DataId = %s"), (strain_id, data_id)) deleted_se_data = cursor.rowcount # Delete the NStrain table cursor.execute(("DELETE FROM NStrain " - "WHERE StrainId = %s AND DataId = %s" % - (strain_id, data_id))) + "WHERE StrainId = %s AND DataId = %s"), + (strain_id, data_id)) deleted_n_strains = cursor.rowcount except Exception as e: #pylint: disable=[C0103, W0612] conn.rollback() @@ -312,7 +313,7 @@ def insert_sample_data(conn: Any, #pylint: disable=[R0913] # Insert into the PublishSE table if error is specified if error and error != "x": cursor.execute(("INSERT INTO PublishSE (StrainId, DataId, " - " error) VALUES (%s, %s, %s)") % + " error) VALUES (%s, %s, %s)"), (strain_id, data_id, error)) inserted_se_data = cursor.rowcount @@ -320,7 +321,7 @@ def insert_sample_data(conn: Any, #pylint: disable=[R0913] if count and count != "x": cursor.execute(("INSERT INTO NStrain " "(StrainId, DataId, count) " - "VALUES (%s, %s, %s)") % + "VALUES (%s, %s, %s)"), (strain_id, data_id, count)) inserted_n_strains = cursor.rowcount except Exception as e: #pylint: disable=[C0103, W0612] @@ -356,14 +357,14 @@ def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any): "PublishXRef.comments") query = ( "SELECT " - "{columns} " + f"{columns} " "FROM " "PublishXRef, Publication, Phenotype " "WHERE " "PublishXRef.Id = %(trait_name)s AND " "Phenotype.Id = PublishXRef.PhenotypeId AND " "Publication.Id = PublishXRef.PublicationId AND " - "PublishXRef.InbredSetId = %(trait_dataset_id)s").format(columns=columns) + "PublishXRef.InbredSetId = %(trait_dataset_id)s") with conn.cursor() as cursor: cursor.execute( query, @@ -399,17 +400,16 @@ def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any): "probe_set_specificity", "probe_set_blat_score", "probe_set_blat_mb_start", "probe_set_blat_mb_end", "probe_set_strand", "probe_set_note_by_rw", "flag") + columns = (f"ProbeSet.{x}" for x in keys) query = ( - "SELECT " - "{columns} " + f"SELECT {','.join(columns)} " "FROM " "ProbeSet, ProbeSetFreeze, ProbeSetXRef " "WHERE " "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND " "ProbeSetXRef.ProbeSetId = ProbeSet.Id AND " "ProbeSetFreeze.Name = %(trait_dataset_name)s AND " - "ProbeSet.Name = %(trait_name)s").format( - columns=", ".join(["ProbeSet.{}".format(x) for x in keys])) + "ProbeSet.Name = %(trait_name)s") with conn.cursor() as cursor: cursor.execute( query, @@ -425,16 +425,15 @@ def retrieve_geno_trait_info(trait_data_source: Dict[str, Any], conn: Any): https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L438-L449""" keys = ("name", "chr", "mb", "source2", "sequence") + columns = ", ".join(f"Geno.{x}" for x in keys) query = ( - "SELECT " - "{columns} " + f"SELECT {columns} " "FROM " - "Geno, GenoFreeze, GenoXRef " + "Geno INNER JOIN GenoXRef ON GenoXRef.GenoId = Geno.Id " + "INNER JOIN GenoFreeze ON GenoFreeze.Id = GenoXRef.GenoFreezeId " "WHERE " - "GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND " "GenoFreeze.Name = %(trait_dataset_name)s AND " - "Geno.Name = %(trait_name)s").format( - columns=", ".join(["Geno.{}".format(x) for x in keys])) + "Geno.Name = %(trait_name)s") with conn.cursor() as cursor: cursor.execute( query, @@ -451,8 +450,8 @@ def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any): https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L450-452""" keys = ("name", "description") query = ( - "SELECT {columns} FROM Temp " - "WHERE Name = %(trait_name)s").format(columns=", ".join(keys)) + f"SELECT {', '.join(keys)} FROM Temp " + "WHERE Name = %(trait_name)s") with conn.cursor() as cursor: cursor.execute( query, @@ -577,7 +576,7 @@ def load_qtl_info(qtl, trait_type, trait_info, conn): "Publish": load_publish_qtl_info, "ProbeSet": load_probeset_qtl_info } - if trait_info["name"] not in qtl_info_functions.keys(): + if trait_info["name"] not in qtl_info_functions: return trait_info return qtl_info_functions[trait_type](trait_info, conn) @@ -947,8 +946,8 @@ def retrieve_trait_data(trait: dict, conn: Any, samplelist: Sequence[str] = tupl def generate_traits_filename(base_path: str = TMPDIR): """Generate a unique filename for use with generated traits files.""" - return "{}/traits_test_file_{}.txt".format( - os.path.abspath(base_path), random_string(10)) + return ( + f"{os.path.abspath(base_path)}/traits_test_file_{random_string(10)}.txt") def export_informative(trait_data: dict, inc_var: bool = False) -> tuple: |