diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/correlations.py | 5 | ||||
| -rw-r--r-- | gn3/db/traits.py | 47 |
2 files changed, 30 insertions, 22 deletions
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py index 2a38bae..3d12019 100644 --- a/gn3/db/correlations.py +++ b/gn3/db/correlations.py @@ -29,7 +29,7 @@ def get_filename(conn: Any, target_db_name: str, text_files_dir: str) -> Union[ filename = "ProbeSetFreezeId_{tid}_FullName_{fname}.txt".format( tid=result[0], fname=result[1].replace(' ', '_').replace('/', '_')) - return ((filename in os.listdir(text_file_dir)) + return ((filename in os.listdir(text_files_dir)) and f"{text_files_dir}/{filename}") return False @@ -280,7 +280,8 @@ def build_temporary_tissue_correlations_table( # We should probably pass the `correlations_of_all_tissue_traits` function # as an argument to this function and get rid of the one call immediately # following this comment. - from gn3.computations.partial_correlations import correlations_of_all_tissue_traits + from gn3.computations.partial_correlations import (#pylint: disable=[C0415, R0401] + correlations_of_all_tissue_traits) # This import above is necessary within the function to avoid # circular-imports. # diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 75de4f4..d4a96f0 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -1,9 +1,10 @@ """This class contains functions relating to trait data manipulation""" import os -import MySQLdb from functools import reduce from typing import Any, Dict, Union, Sequence +import MySQLdb + from gn3.settings import TMPDIR from gn3.random import random_string from gn3.function_helpers import compose @@ -81,10 +82,10 @@ def export_trait_data( def get_trait_csv_sample_data(conn: Any, trait_name: int, phenotype_id: int): """Fetch a trait and return it as a csv string""" - def __float_strip(n): - if str(n)[-2:] == ".0": - return str(int(n)) - return str(n) + def __float_strip(num_str): + if str(num_str)[-2:] == ".0": + return str(int(num_str)) + return str(num_str) sql = ("SELECT DISTINCT Strain.Name, PublishData.value, " "PublishSE.error, NStrain.count FROM " "(PublishData, Strain, PublishXRef, PublishFreeze) " @@ -108,7 +109,7 @@ def get_trait_csv_sample_data(conn: Any, return "\n".join(csv_data) -def update_sample_data(conn: Any, +def update_sample_data(conn: Any, #pylint: disable=[R0913] trait_name: str, strain_name: str, phenotype_id: int, @@ -219,7 +220,7 @@ def delete_sample_data(conn: Any, "WHERE StrainId = %s AND DataId = %s" % (strain_id, data_id))) deleted_n_strains = cursor.rowcount - except Exception as e: + except Exception as e: #pylint: disable=[C0103, W0612] conn.rollback() raise MySQLdb.Error conn.commit() @@ -230,7 +231,7 @@ def delete_sample_data(conn: Any, deleted_se_data, deleted_n_strains) -def insert_sample_data(conn: Any, +def insert_sample_data(conn: Any, #pylint: disable=[R0913] trait_name: str, strain_name: str, phenotype_id: int, @@ -272,7 +273,7 @@ def insert_sample_data(conn: Any, "VALUES (%s, %s, %s)") % (strain_id, data_id, count)) inserted_n_strains = cursor.rowcount - except Exception as e: + except Exception as e: #pylint: disable=[C0103, W0612] conn.rollback() raise MySQLdb.Error return (inserted_published_data, @@ -450,7 +451,7 @@ def set_homologene_id_field(trait_type, trait_info, conn): Common postprocessing function for all trait types. Sets the value for the 'homologene' key.""" - def set_to_null(ti): return {**ti, "homologeneid": None} + def set_to_null(ti): return {**ti, "homologeneid": None} # pylint: disable=[C0103, C0321] functions_table = { "Temp": set_to_null, "Geno": set_to_null, @@ -656,8 +657,9 @@ def retrieve_temp_trait_data(trait_info: dict, conn: Any): query, {"trait_name": trait_info["trait_name"]}) return [dict(zip( - ["sample_name", "value", "se_error", "nstrain", "id"], row)) - for row in cursor.fetchall()] + ["sample_name", "value", "se_error", "nstrain", "id"], + row)) + for row in cursor.fetchall()] return [] @@ -696,8 +698,10 @@ def retrieve_geno_trait_data(trait_info: Dict, conn: Any): "dataset_name": trait_info["db"]["dataset_name"], "species_id": retrieve_species_id( trait_info["db"]["group"], conn)}) - return [dict(zip( - ["sample_name", "value", "se_error", "id"], row)) + return [ + dict(zip( + ["sample_name", "value", "se_error", "id"], + row)) for row in cursor.fetchall()] return [] @@ -728,8 +732,9 @@ def retrieve_publish_trait_data(trait_info: Dict, conn: Any): query, {"trait_name": trait_info["trait_name"], "dataset_id": trait_info["db"]["dataset_id"]}) - return [dict(zip( - ["sample_name", "value", "se_error", "nstrain", "id"], row)) + return [ + dict(zip( + ["sample_name", "value", "se_error", "nstrain", "id"], row)) for row in cursor.fetchall()] return [] @@ -762,8 +767,9 @@ def retrieve_cellid_trait_data(trait_info: Dict, conn: Any): {"cellid": trait_info["cellid"], "trait_name": trait_info["trait_name"], "dataset_id": trait_info["db"]["dataset_id"]}) - return [dict(zip( - ["sample_name", "value", "se_error", "id"], row)) + return [ + dict(zip( + ["sample_name", "value", "se_error", "id"], row)) for row in cursor.fetchall()] return [] @@ -792,8 +798,9 @@ def retrieve_probeset_trait_data(trait_info: Dict, conn: Any): query, {"trait_name": trait_info["trait_name"], "dataset_name": trait_info["db"]["dataset_name"]}) - return [dict(zip( - ["sample_name", "value", "se_error", "id"], row)) + return [ + dict(zip( + ["sample_name", "value", "se_error", "id"], row)) for row in cursor.fetchall()] return [] |