diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/correlations.py | 4 | ||||
| -rw-r--r-- | gn3/db/menu.py | 10 | ||||
| -rw-r--r-- | gn3/db/sample_data.py | 24 |
3 files changed, 20 insertions, 18 deletions
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py index aec8eac..5d6cfb3 100644 --- a/gn3/db/correlations.py +++ b/gn3/db/correlations.py @@ -328,7 +328,7 @@ def build_temporary_tissue_correlations_table( return temp_table_name -def fetch_tissue_correlations(# pylint: disable=R0913 +def fetch_tissue_correlations(# pylint: disable=[R0913, too-many-arguments, too-many-positional-arguments] dataset: dict, trait_symbol: str, probeset_freeze_id: int, method: str, return_number: int, conn: Any) -> dict: """ @@ -529,7 +529,7 @@ def __build_query__( f"ORDER BY {db_type}.Id"), 1) -# pylint: disable=too-many-arguments +# pylint: disable=[too-many-arguments, too-many-positional-arguments] def __fetch_data__( conn, sample_ids: tuple, db_name: str, db_type: str, method: str, temp_table: Optional[str]) -> Tuple[Tuple[Any], int]: diff --git a/gn3/db/menu.py b/gn3/db/menu.py index 8dccabf..3fe9062 100644 --- a/gn3/db/menu.py +++ b/gn3/db/menu.py @@ -14,10 +14,12 @@ def gen_dropdown_json(conn): groups = get_groups(conn, tuple(row[0] for row in species)) types = get_types(conn, groups) datasets = get_datasets(conn, types) - return dict(species=species, - groups=groups, - types=types, - datasets=datasets) + return { + "species": species, + "groups": groups, + "types": types, + "datasets": datasets + } def get_groups(conn, species_names: Tuple[str, ...]): """Build groups list""" diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py index 8db40e3..415b0b0 100644 --- a/gn3/db/sample_data.py +++ b/gn3/db/sample_data.py @@ -302,8 +302,8 @@ def update_sample_data( if data_type == "mrna": strain_id, data_id, inbredset_id = get_mrna_sample_data_ids( conn=conn, - probeset_id=int(probeset_id), - dataset_name=dataset_name, + probeset_id=int(probeset_id),# pylint: disable=[possibly-used-before-assignment] + dataset_name=dataset_name,# pylint: disable=[possibly-used-before-assignment] strain_name=extract_strain_name(csv_header, original_data), ) none_case_attrs = { @@ -315,8 +315,8 @@ def update_sample_data( else: strain_id, data_id, inbredset_id = get_pheno_sample_data_ids( conn=conn, - publishxref_id=int(trait_name), - phenotype_id=phenotype_id, + publishxref_id=int(trait_name),# pylint: disable=[possibly-used-before-assignment] + phenotype_id=phenotype_id,# pylint: disable=[possibly-used-before-assignment] strain_name=extract_strain_name(csv_header, original_data), ) none_case_attrs = { @@ -422,8 +422,8 @@ def delete_sample_data( if data_type == "mrna": strain_id, data_id, inbredset_id = get_mrna_sample_data_ids( conn=conn, - probeset_id=int(probeset_id), - dataset_name=dataset_name, + probeset_id=int(probeset_id),# pylint: disable=[possibly-used-before-assignment] + dataset_name=dataset_name,# pylint: disable=[possibly-used-before-assignment] strain_name=extract_strain_name(csv_header, data), ) none_case_attrs: Dict[str, Any] = { @@ -435,8 +435,8 @@ def delete_sample_data( else: strain_id, data_id, inbredset_id = get_pheno_sample_data_ids( conn=conn, - publishxref_id=int(trait_name), - phenotype_id=phenotype_id, + publishxref_id=int(trait_name),# pylint: disable=[possibly-used-before-assignment] + phenotype_id=phenotype_id,# pylint: disable=[possibly-used-before-assignment] strain_name=extract_strain_name(csv_header, data), ) none_case_attrs = { @@ -528,8 +528,8 @@ def insert_sample_data( if data_type == "mrna": strain_id, data_id, inbredset_id = get_mrna_sample_data_ids( conn=conn, - probeset_id=int(probeset_id), - dataset_name=dataset_name, + probeset_id=int(probeset_id),# pylint: disable=[possibly-used-before-assignment] + dataset_name=dataset_name,# pylint: disable=[possibly-used-before-assignment] strain_name=extract_strain_name(csv_header, data), ) none_case_attrs = { @@ -541,8 +541,8 @@ def insert_sample_data( else: strain_id, data_id, inbredset_id = get_pheno_sample_data_ids( conn=conn, - publishxref_id=int(trait_name), - phenotype_id=phenotype_id, + publishxref_id=int(trait_name),# pylint: disable=[possibly-used-before-assignment] + phenotype_id=phenotype_id,# pylint: disable=[possibly-used-before-assignment] strain_name=extract_strain_name(csv_header, data), ) none_case_attrs = { |