Fix code errors caught by linter.

7 files changed, 40 insertions, 17 deletions

diff --git a/gn_libs/jobs/__init__.py b/gn_libs/jobs/__init__.py
index 6f400ef..d6e4ce3 100644
--- a/gn_libs/jobs/__init__.py
+++ b/gn_libs/jobs/__init__.py
@@ -1,3 +1,4 @@
+"""This package deals with launching and managing background/async jobs."""
 from .migrations import run_migrations
 from .jobs import (job,
                    launch_job,
diff --git a/gn_libs/jobs/jobs.py b/gn_libs/jobs/jobs.py
index 17c1ac6..8d77139 100644
--- a/gn_libs/jobs/jobs.py
+++ b/gn_libs/jobs/jobs.py
@@ -6,7 +6,6 @@ import shlex
 import logging
 import subprocess
 from pathlib import Path
-from functools import reduce
 from functools import partial
 from typing import Union, Optional
 from datetime import datetime, timezone, timedelta
@@ -87,16 +86,18 @@ def __save_job__(conn: DbConnection, the_job: dict, expiry_seconds: int) -> dict
     return the_job
 
 
-def initialise_job(
+def initialise_job(# pylint: disable=[too-many-arguments, too-many-positional-arguments]
         conn: DbConnection,
         job_id: uuid.UUID,
         command: list,
         job_type: str,
-        extra_meta: dict = {},
+        extra_meta: Optional[dict] = None,
         expiry_seconds: Optional[int] = _DEFAULT_EXPIRY_SECONDS_
 ) -> dict:
     """Initialise the job and put the details in a SQLite3 database."""
-    
+    if extra_meta is None:
+        extra_meta = {}
+
     _job = {
         "job_id": job_id,
         "command": shlex.join(command),
@@ -121,7 +122,11 @@ stdout_filename = partial(output_file, stream="stdout")
 stderr_filename = partial(output_file, stream="stderr")
 
 
-def build_environment(extras: dict[str, str] = {}):
+def build_environment(extras: Optional[dict[str, str]] = None) -> dict[str, str]:
+    """Setup the runtime environment variables for the background script."""
+    if extras is None:
+        extras = {}
+
     return {
         **dict(os.environ),
         "PYTHONPATH": ":".join(sys.path),
@@ -180,7 +185,11 @@ def update_metadata(conn: DbConnection, job_id: Union[str, uuid.UUID], key: str,
             })
 
 
-def push_to_stream(conn: DbConnection, job_id: Union[str, uuid.UUID], stream_name: str, content: str):
+def push_to_stream(
+        conn: DbConnection,
+        job_id: Union[str, uuid.UUID],
+        stream_name: str, content: str
+):
     """Initialise, and keep adding content to the stream from the provided content."""
     with _cursor(conn) as cursor:
         cursor.execute("SELECT * FROM jobs_standard_outputs "
diff --git a/gn_libs/jobs/launcher.py b/gn_libs/jobs/launcher.py
index 89884b6..d565f9e 100644
--- a/gn_libs/jobs/launcher.py
+++ b/gn_libs/jobs/launcher.py
@@ -1,3 +1,4 @@
+"""Default launcher/manager script for background jobs."""
 import os
 import sys
 import time
@@ -54,7 +55,7 @@ def run_job(conn, job, outputs_directory: Path):
 
         logger.info("exiting job manager/launcher")
         return exit_status
-    except:
+    except Exception as _exc:# pylint: disable=[broad-exception-caught]
         logger.error("An exception was raised when attempting to run the job",
                      exc_info=True)
         jobs.update_metadata(conn, job_id, "status", "error")
@@ -90,8 +91,7 @@ def main():
     args = parse_args()
     logger.setLevel(args.log_level.upper())
     args.outputs_directory.mkdir(parents=True, exist_ok=True)
-    with (sqlite3.connection(args.jobs_db_uri) as conn,
-          sqlite3.cursor(conn) as cursor):
+    with sqlite3.connection(args.jobs_db_uri) as conn:
         job = jobs.job(conn, args.job_id)
         if job:
             return run_job(conn, job, args.outputs_directory)
diff --git a/gn_libs/jobs/migrations.py b/gn_libs/jobs/migrations.py
index 86fb958..0c9825b 100644
--- a/gn_libs/jobs/migrations.py
+++ b/gn_libs/jobs/migrations.py
@@ -1,6 +1,6 @@
 """Database migrations for the jobs to ensure consistency downstream."""
 from gn_libs.protocols import DbCursor
-from gn_libs.sqlite3 import cursor, connection
+from gn_libs.sqlite3 import connection, cursor as acquire_cursor
 
 def __create_table_jobs__(cursor: DbCursor):
     """Create the jobs table"""
@@ -61,8 +61,9 @@ def __create_table_jobs_output_streams__(cursor: DbCursor):
 
 
 def run_migrations(sqlite_url: str):
+    """Run the migrations to setup the background jobs database."""
     with (connection(sqlite_url) as conn,
-          cursor(conn) as curr):
+          acquire_cursor(conn) as curr):
         __create_table_jobs__(curr)
         __create_table_jobs_metadata__(curr)
         __create_table_jobs_output_streams__(curr)
diff --git a/gn_libs/monadic_requests.py b/gn_libs/monadic_requests.py
index 0a3c282..a09acc5 100644
--- a/gn_libs/monadic_requests.py
+++ b/gn_libs/monadic_requests.py
@@ -19,8 +19,13 @@ def get(url, params=None, **kwargs) -> Either:
 
     :rtype: pymonad.either.Either
     """
+    timeout = kwargs.get("timeout")
+    kwargs = {key: val for key,val in kwargs.items() if key != "timeout"}
+    if timeout is None:
+        timeout = (9.13, 20)
+
     try:
-        resp = requests.get(url, params=params, **kwargs)
+        resp = requests.get(url, params=params, timeout=timeout, **kwargs)
         if resp.status_code in SUCCESS_CODES:
             return Right(resp.json())
         return Left(resp)
@@ -36,8 +41,13 @@ def post(url, data=None, json=None, **kwargs) -> Either:
 
     :rtype: pymonad.either.Either
     """
+    timeout = kwargs.get("timeout")
+    kwargs = {key: val for key,val in kwargs.items() if key != "timeout"}
+    if timeout is None:
+        timeout = (9.13, 20)
+
     try:
-        resp = requests.post(url, data=data, json=json, **kwargs)
+        resp = requests.post(url, data=data, json=json, timeout=timeout, **kwargs)
         if resp.status_code in SUCCESS_CODES:
             return Right(resp.json())
         return Left(resp)
@@ -55,10 +65,10 @@ def make_either_error_handler(msg):
             try:
                 _data = error.json()
             except Exception as _exc:
-                raise Exception(error.content) from _exc
-            raise Exception(_data)
+                raise Exception(error.content) from _exc# pylint: disable=[broad-exception-raised]
+            raise Exception(_data)# pylint: disable=[broad-exception-raised]
 
         logger.debug("\n\n%s\n\n", msg)
-        raise Exception(error)
+        raise Exception(error)# pylint: disable=[broad-exception-raised]
 
     return __fail__
diff --git a/gn_libs/protocols/__init__.py b/gn_libs/protocols/__init__.py
index e71f1ce..83a31a8 100644
--- a/gn_libs/protocols/__init__.py
+++ b/gn_libs/protocols/__init__.py
@@ -1 +1,2 @@
+"""This package is a collection of major Protocols/Interfaces definitions."""
 from .db import DbCursor, DbConnection
diff --git a/gn_libs/sqlite3.py b/gn_libs/sqlite3.py
index 1dcdf29..78e1c41 100644
--- a/gn_libs/sqlite3.py
+++ b/gn_libs/sqlite3.py
@@ -1,7 +1,8 @@
+"""This module deals with connections to a(n) SQLite3 database."""
 import logging
 import traceback
 import contextlib
-from typing import Any, Protocol, Callable, Iterator
+from typing import Callable, Iterator
 
 import sqlite3