From 7926afbe13760ff7e0b5bca5de4e2f44277144b2 Mon Sep 17 00:00:00 2001
From: Boris <bio-boris@github.com>
Date: Fri, 26 Apr 2024 15:28:40 -0500
Subject: [PATCH] Updated actions, removed flake8, fixed unused vars

---
 import_specifications/clients/baseclient.py    | 16 ++++------------
 pyproject.toml                                 | 10 +++++-----
 staging_service/autodetect/GenerateMappings.py |  6 +++++-
 3 files changed, 14 insertions(+), 18 deletions(-)

diff --git a/import_specifications/clients/baseclient.py b/import_specifications/clients/baseclient.py
index 77457e2b..8bac630e 100644
--- a/import_specifications/clients/baseclient.py
+++ b/import_specifications/clients/baseclient.py
@@ -52,8 +52,7 @@ def _get_token(user_id, password, auth_svc):
         tok = _json.loads(ret.text)
     elif status == 403:
         raise Exception(
-            "Authentication failed: Bad user_id/password "
-            + "combination for user %s" % (user_id)
+            "Authentication failed: Bad user_id/password " + "combination for user %s" % (user_id)
         )
     else:
         raise Exception(ret.text)
@@ -61,9 +60,7 @@ def _get_token(user_id, password, auth_svc):
 
 
 def _read_inifile(
-    file=_os.environ.get(
-        "KB_DEPLOYMENT_CONFIG", _os.environ["HOME"] + "/.kbase_config"
-    ),
+    file=_os.environ.get("KB_DEPLOYMENT_CONFIG", _os.environ["HOME"] + "/.kbase_config"),
 ):  # @ReservedAssignment
     # Another bandaid to read in the ~/.kbase_config file if one is present
     authdata = None
@@ -102,9 +99,7 @@ def __init__(self, name, code, message, data=None, error=None):
         # data = JSON RPC 2.0, error = 1.1
 
     def __str__(self):
-        return (
-            self.name + ": " + str(self.code) + ". " + self.message + "\n" + self.data
-        )
+        return self.name + ": " + str(self.code) + ". " + self.message + "\n" + self.data
 
 
 class _JSONObjectEncoder(_json.JSONEncoder):
@@ -181,10 +176,7 @@ def __init__(
             if authdata is not None:
                 if authdata.get("token") is not None:
                     self._headers["AUTHORIZATION"] = authdata["token"]
-                elif (
-                    authdata.get("user_id") is not None
-                    and authdata.get("password") is not None
-                ):
+                elif authdata.get("user_id") is not None and authdata.get("password") is not None:
                     self._headers["AUTHORIZATION"] = _get_token(
                         authdata["user_id"], authdata["password"], auth_svc
                     )
diff --git a/pyproject.toml b/pyproject.toml
index f611d1db..38fb2ca3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ line-length = 100
 
 
 [tool.ruff]
-select = [
+lint.select = [
     # core
     "F", # Pyflakes
     "E", # pycodestyle errors
@@ -27,15 +27,15 @@ select = [
 # E203: whitespace before ‘,’, ‘;’, or ‘:’
 # E501: line length
 # W503: line break after binary operator
-ignore = [
+lint.ignore = [
     "E203",
     "E501",
     "S101",
 ]
 
 # Allow autofix for all enabled rules (when `--fix`) is provided.
-fixable = ["ALL"]
-unfixable = []
+lint.fixable = ["ALL"]
+lint.unfixable = []
 
 # Exclude a variety of commonly ignored directories.
 exclude = [
@@ -67,7 +67,7 @@ exclude = [
     "sample_data",
     "venv",
 ]
-per-file-ignores = { }
+lint.per-file-ignores = { }
 
 # Same as Black.
 line-length = 100
diff --git a/staging_service/autodetect/GenerateMappings.py b/staging_service/autodetect/GenerateMappings.py
index d9c34b1c..f5af89d6 100644
--- a/staging_service/autodetect/GenerateMappings.py
+++ b/staging_service/autodetect/GenerateMappings.py
@@ -89,7 +89,11 @@
     fastq_reads_interleaved_id,
     fastq_reads_noninterleaved_id,
 ]
-file_format_to_app_mapping[FASTA] = [assembly_id, gff_genome_id, gff_metagenome_id]
+file_format_to_app_mapping[FASTA] = [
+    assembly_id,
+    gff_genome_id,
+    gff_metagenome_id,
+]
 file_format_to_app_mapping[GENBANK] = [genbank_genome_id]
 file_format_to_app_mapping[GFF] = [gff_genome_id, gff_metagenome_id]
 file_format_to_app_mapping[ZIP] = [decompress_id]