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authorFrederick Muriuki Muriithi2021-11-29 14:01:44 +0300
committerFrederick Muriuki Muriithi2021-11-29 14:01:44 +0300
commit99953f6e4a540da41d0517203eb63da4e19405cd (patch)
tree92faedba7770082d95cff3fb0aa7e1a6595c004d /gn3/db
parent6b147173d514093ec4e461f5843170c968290e5e (diff)
downloadgenenetwork3-99953f6e4a540da41d0517203eb63da4e19405cd.tar.gz
Fix linting errors
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
Diffstat (limited to 'gn3/db')
-rw-r--r--gn3/db/correlations.py5
-rw-r--r--gn3/db/traits.py47
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 []