Fix pylint errors.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

8 files changed, 16 insertions, 14 deletions

diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 2dd53ea..abe772c 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -12,7 +12,6 @@ from gn3.commands import run_cmd
 from gn3.fs_helpers import cache_ipfs_file
 from gn3.fs_helpers import jsonfile_to_dict, assert_paths_exist
 from gn3.computations.gemma import generate_gemma_cmd
-from gn3.computations.gemma import assert_paths_exist
 
 
 gemma = Blueprint("gemma", __name__)
diff --git a/gn3/api/metadata_api/wiki.py b/gn3/api/metadata_api/wiki.py
index 9ea0d53..6436f3d 100644
--- a/gn3/api/metadata_api/wiki.py
+++ b/gn3/api/metadata_api/wiki.py
@@ -5,7 +5,6 @@ from typing import Any, Dict
 from flask import Blueprint, request, jsonify, current_app, make_response
 from gn3 import db_utils
 from gn3.db import wiki
-from gn3.db.rdf import query_frame_and_compact
 from gn3.db.rdf.wiki import (get_wiki_entries_by_symbol,
                              get_comment_history)
 
@@ -121,6 +120,7 @@ def get_species():
 
 @wiki_blueprint.route("/<int:comment_id>/history", methods=["GET"])
 def get_history(comment_id):
+    """Fetch all of a given comment's history given it's comment id"""
     status_code = 200
     response = get_comment_history(comment_id=comment_id,
                                    sparql_uri=current_app.config["SPARQL_ENDPOINT"])
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 68299d4..c2d988a 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -6,7 +6,6 @@ from flask import current_app
 from flask import jsonify
 from flask import request
 
-from gn3.debug import __pk__
 from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_mapping, \
                                   process_rqtl_pairscan, process_perm_output
 from gn3.fs_helpers import assert_paths_exist, get_tmpdir
diff --git a/gn3/app.py b/gn3/app.py
index d7fcbea..c8f0c5a 100644
--- a/gn3/app.py
+++ b/gn3/app.py
@@ -28,7 +28,6 @@ from gn3.api.sampledata import sampledata
 from gn3.api.llm import gnqa
 from gn3.auth import oauth2
 from gn3.case_attributes import caseattr
-from gn3.fs_helpers import get_tmpdir
 
 
 def create_app(config: Union[Dict, str, None] = None) -> Flask:
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index 577d8e8..6c53ecc 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -1,14 +1,12 @@
 """Procedures related gemma computations"""
-import errno
 import os
 
 from base64 import b64encode
 from hashlib import md5
 from typing import Optional, Dict
 from typing import List
-from typing import ValuesView
 from gn3.commands import compose_gemma_cmd
-from gn3.fs_helpers import get_hash_of_files, assert_paths_exist
+from gn3.fs_helpers import get_hash_of_files
 
 
 def generate_hash_of_string(unhashed_str: str) -> str:
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 0b8c23d..16f1398 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,7 +1,5 @@
 """Procedures related to R/qtl computations"""
 import os
-import sys
-import logging
 from bisect import bisect
 from typing import Dict, List, Tuple, Union
 
diff --git a/gn3/debug.py b/gn3/debug.py
index 945e237..8b67a92 100644
--- a/gn3/debug.py
+++ b/gn3/debug.py
@@ -4,13 +4,17 @@ from flask import current_app
 
 __this_module_name__ = __name__
 
+
+# pylint: disable=invalid-name
 def getLogger():
+    """Return a logger"""
     return (
         logging.getLogger(__this_module_name__)
         if not bool(current_app)
         else current_app.logger)
 
 def __pk__(*args):
+    """Format log entry"""
     value = args[-1]
     title_vals = " => ".join(args[0:-1])
     logger = getLogger()
diff --git a/gn3/fs_helpers.py b/gn3/fs_helpers.py
index 1b226bc..2ce381e 100644
--- a/gn3/fs_helpers.py
+++ b/gn3/fs_helpers.py
@@ -16,14 +16,20 @@ from werkzeug.utils import secure_filename
 from flask import current_app
 
 def get_tmpdir() -> str:
-    """Get the temp directory from the FLASK tmpdir setting. If it is not set, set it to /tmp. Note
-    that the app should check for environment settings to initialize its TMPDIR.
+    """Get the temp directory from the FLASK tmpdir setting. If it is
+    not set, set it to /tmp. Note that the app should check for
+    environment settings to initialize its TMPDIR.
+
     """
     tmpdir = current_app.config.get("TMPDIR")
     if not tmpdir:
         tmpdir = "/tmp"
     if not os.path.isdir(tmpdir):
-        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), f"TMPDIR {tmpdir} is not a valid directory")
+        raise FileNotFoundError(
+            errno.ENOENT,
+            os.strerror(errno.ENOENT),
+            f"TMPDIR {tmpdir} is not a valid directory"
+        )
 
     return tmpdir
 
@@ -32,8 +38,7 @@ def assert_path_exists(path: str, throw_error: bool = True) -> bool:
     if not os.path.isfile(path):
         if throw_error:
             raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path)
-        else:
-            return False
+        return False
     return True
 
 def assert_paths_exist(paths: ValuesView, throw_error: bool = True) -> bool: