update black version and re-lint

genie/config.py

@@ -1,4 +1,5 @@
 """Configuration to obtain registry classes"""
+
 import importlib
 import logging
 

genie/create_case_lists.py

@@ -1,6 +1,7 @@
 """
 Creates case lists per cancer type
 """
+
 from collections import defaultdict
 import csv
 import os

genie/dashboard_table_updater.py

@@ -1,4 +1,5 @@
 """Updates dashboard tables"""
+
 import argparse
 import datetime
 import logging
@@ -347,9 +348,11 @@ def update_oncotree_code_tables(syn, database_mappingdf):
     oncotree_mapping = process_functions.get_oncotree_code_mappings(oncotree_link)
 
     clinicaldf["PRIMARY_CODES"] = [
-        oncotree_mapping[i.upper()]["ONCOTREE_PRIMARY_NODE"]
-        if i.upper() in oncotree_mapping.keys()
-        else "DEPRECATED_CODE"
+        (
+            oncotree_mapping[i.upper()]["ONCOTREE_PRIMARY_NODE"]
+            if i.upper() in oncotree_mapping.keys()
+            else "DEPRECATED_CODE"
+        )
         for i in clinicaldf.ONCOTREE_CODE
     ]
 
@@ -457,9 +460,9 @@ def update_sample_difference_table(syn, database_mappingdf):
         .applymap(int)
     )
 
-    diff_between_releasesdf[
-        ["Clinical", "Mutation", "CNV", "SEG", "Fusions"]
-    ] = new_values
+    diff_between_releasesdf[["Clinical", "Mutation", "CNV", "SEG", "Fusions"]] = (
+        new_values
+    )
 
     load._update_table(
         syn,

genie/database_to_staging.py

@@ -223,9 +223,7 @@ def remove_maf_samples(mafdf: pd.DataFrame, keep_samples: list) -> pd.DataFrame:
 
     """
     keep_maf = mafdf["Tumor_Sample_Barcode"].isin(keep_samples)
-    mafdf = mafdf.loc[
-        keep_maf,
-    ]
+    mafdf = mafdf.loc[keep_maf,]
     return mafdf
 
 
@@ -1054,30 +1052,38 @@ def store_clinical_files(
     }
 
     clinicaldf["CANCER_TYPE"] = [
-        oncotree_dict[code.upper()]["CANCER_TYPE"]
-        if code.upper() in oncotree_dict.keys()
-        else float("nan")
+        (
+            oncotree_dict[code.upper()]["CANCER_TYPE"]
+            if code.upper() in oncotree_dict.keys()
+            else float("nan")
+        )
         for code in clinicaldf["ONCOTREE_CODE"]
     ]
 
     clinicaldf["CANCER_TYPE_DETAILED"] = [
-        oncotree_dict[code.upper()]["CANCER_TYPE_DETAILED"]
-        if code.upper() in oncotree_dict.keys()
-        else float("nan")
+        (
+            oncotree_dict[code.upper()]["CANCER_TYPE_DETAILED"]
+            if code.upper() in oncotree_dict.keys()
+            else float("nan")
+        )
         for code in clinicaldf["ONCOTREE_CODE"]
     ]
 
     clinicaldf["ONCOTREE_PRIMARY_NODE"] = [
-        oncotree_dict[code.upper()]["ONCOTREE_PRIMARY_NODE"]
-        if code.upper() in oncotree_dict.keys()
-        else float("nan")
+        (
+            oncotree_dict[code.upper()]["ONCOTREE_PRIMARY_NODE"]
+            if code.upper() in oncotree_dict.keys()
+            else float("nan")
+        )
         for code in clinicaldf["ONCOTREE_CODE"]
     ]
 
     clinicaldf["ONCOTREE_SECONDARY_NODE"] = [
-        oncotree_dict[code.upper()]["ONCOTREE_SECONDARY_NODE"]
-        if code.upper() in oncotree_dict.keys()
-        else float("nan")
+        (
+            oncotree_dict[code.upper()]["ONCOTREE_SECONDARY_NODE"]
+            if code.upper() in oncotree_dict.keys()
+            else float("nan")
+        )
         for code in clinicaldf["ONCOTREE_CODE"]
     ]
 
@@ -1088,9 +1094,11 @@ def store_clinical_files(
     # descriptions can match
     clinicaldf["AGE_AT_SEQ_REPORT_DAYS"] = clinicaldf["AGE_AT_SEQ_REPORT"]
     clinicaldf["AGE_AT_SEQ_REPORT"] = [
-        int(math.floor(int(float(age)) / 365.25))
-        if process_functions.checkInt(age)
-        else age
+        (
+            int(math.floor(int(float(age)) / 365.25))
+            if process_functions.checkInt(age)
+            else age
+        )
         for age in clinicaldf["AGE_AT_SEQ_REPORT"]
     ]
     clinicaldf["AGE_AT_SEQ_REPORT"][clinicaldf["AGE_AT_SEQ_REPORT"] == ">32485"] = ">89"

genie/example_filetype_format.py

@@ -1,6 +1,7 @@
 """TODO: Rename this to model.py
 This contains the GENIE model objects
 """
+
 from abc import ABCMeta
 from dataclasses import dataclass
 import logging

genie/load.py

@@ -2,6 +2,7 @@
 This module contains all the functions that stores data
 to Synapse
 """
+
 import logging
 import os
 import time

genie/process_functions.py

@@ -1,4 +1,5 @@
 """Processing functions that are used in the GENIE pipeline"""
+
 import datetime
 import json
 import logging

genie/process_mutation.py

@@ -1,5 +1,6 @@
 """Process mutation files
 TODO deprecate this module and spread functions around"""
+
 from collections import namedtuple
 import logging
 import os

genie/transform.py

@@ -1,5 +1,6 @@
 """This module contains all the transformation functions used throughout the GENIE
 package"""
+
 import warnings
 
 import pandas as pd

genie/write_invalid_reasons.py

@@ -1,4 +1,5 @@
 """Write invalid reasons"""
+
 import logging
 import os
 

genie_registry/__init__.py

@@ -1,4 +1,5 @@
 """Initialize GENIE registry"""
+
 # Import logging last to not take in synapseclient logging
 import logging
 

genie_registry/assay.py

@@ -1,4 +1,5 @@
 """Assay information class"""
+
 import os
 import yaml
 

genie_registry/bed.py

@@ -1,4 +1,5 @@
 """GENIE bed class and functions"""
+
 import os
 import logging
 import subprocess

genie_registry/clinical.py

@@ -1,4 +1,5 @@
 """Clinical file format validation and processing"""
+
 # from __future__ import annotations
 import datetime
 from io import StringIO

setup.py

@@ -1,4 +1,5 @@
 """genie package setup"""
+
 from setuptools import setup
 
 setup()

tests/test_assay.py

@@ -1,4 +1,5 @@
 """Test assay information validation and processing"""
+
 import copy
 from unittest.mock import patch
 

tests/test_bed.py

@@ -1,4 +1,5 @@
 """Test GENIE Bed class"""
+
 import tempfile
 import shutil
 from unittest import mock

tests/test_database_to_staging.py

@@ -1,4 +1,5 @@
 """Tests database to staging functions"""
+
 import os
 from unittest import mock
 from unittest.mock import patch

tests/test_example_filetype_format.py

@@ -76,7 +76,10 @@ def test_that_validate_returns_expected_msg_if__validate_passes(filetype_format_
 
 
 def test_that_validate_throws_exception_if_file_read_error(filetype_format_class):
-    with patch.object(FileTypeFormat, "_validate",) as patch_validate, patch.object(
+    with patch.object(
+        FileTypeFormat,
+        "_validate",
+    ) as patch_validate, patch.object(
         FileTypeFormat,
         "read_file",
         side_effect=Exception("mocked error"),

tests/test_extract.py

@@ -1,4 +1,5 @@
 """Test genie.extract module"""
+
 from unittest.mock import patch
 
 import pandas as pd

tests/test_filters.py

@@ -1,6 +1,7 @@
 """
 Test GENIE filters
 """
+
 import datetime
 import os
 import sys

tests/test_process_mutation.py

@@ -1,4 +1,5 @@
 """Test process mutation functions"""
+
 import os
 from collections import namedtuple
 from pandas.testing import assert_frame_equal

tests/test_transform.py

@@ -1,4 +1,5 @@
 """Test genie.transform module"""
+
 import os
 from io import BytesIO
 from unittest import mock

tests/test_validate.py

@@ -1,4 +1,5 @@
 """Tests validate.py"""
+
 from unittest.mock import Mock, patch
 
 import pandas as pd

tests/test_write_invalid_reasons.py

@@ -1,4 +1,5 @@
 """Test write invalid reasons module"""
+
 from unittest import mock
 from unittest.mock import patch