Fix linting and type errors

13 files changed, 97 insertions, 94 deletions

diff --git a/README.org b/README.org
index 2897d91..5ec53f0 100644
--- a/README.org
+++ b/README.org
@@ -72,7 +72,7 @@ Run tests with:
 
 To run the linter over the code base, run:
 #+BEGIN_SRC shell
-  pylint tests quality_control qc_app
+  pylint *.py tests quality_control qc_app scripts
 #+END_SRC
 
 To check for correct type usage in the application, run:
diff --git a/mypy.ini b/mypy.ini
index f61431a..74e2d91 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -9,17 +9,14 @@ ignore_missing_imports = True
 [mypy-hypothesis.*]
 ignore_missing_imports = True
 
-[mypy-rq.*]
-ignore_missing_imports = True
-
 [mypy-redis.*]
 ignore_missing_imports = True
 
-[mypy-magic.*]
-ignore_missing_imports = True
-
 [mypy-werkzeug.*]
 ignore_missing_imports = True
 
 [mypy-setuptools.*]
+ignore_missing_imports = True
+
+[mypy-jsonpickle.*]
 ignore_missing_imports = True
\ No newline at end of file
diff --git a/qc_app/__init__.py b/qc_app/__init__.py
index 7f423c2..08b56c9 100644
--- a/qc_app/__init__.py
+++ b/qc_app/__init__.py
@@ -17,10 +17,10 @@ def instance_path():
 
     return path
 
-def create_app(instance_path):
+def create_app(instance_dir):
     """The application factory"""
     app = Flask(
-        __name__, instance_path=instance_path, instance_relative_config=True)
+        __name__, instance_path=instance_dir, instance_relative_config=True)
     app.config.from_pyfile(os.path.join(os.getcwd(), "etc/default_config.py"))
     app.config.from_pyfile("config.py") # Override defaults with instance path
 
diff --git a/qc_app/entry.py b/qc_app/entry.py
index 7f67a33..c53648a 100644
--- a/qc_app/entry.py
+++ b/qc_app/entry.py
@@ -1,7 +1,5 @@
 """Entry-point module"""
 import os
-import random
-import string
 import mimetypes
 from typing import Tuple
 from zipfile import ZipFile, is_zipfile
@@ -18,24 +16,24 @@ from flask import (
 
 entrybp = Blueprint("entry", __name__)
 
-def errors(request) -> Tuple[str, ...]:
-    """Return a tuple of the errors found in the `request`. If no error is
+def errors(rqst) -> Tuple[str, ...]:
+    """Return a tuple of the errors found in the request `rqst`. If no error is
     found, then an empty tuple is returned."""
     def __filetype_error__():
         return (
             ("Invalid file type provided.",)
-            if request.form.get("filetype") not in ("average", "standard-error")
+            if rqst.form.get("filetype") not in ("average", "standard-error")
             else tuple())
 
     def __file_missing_error__():
         return (
             ("No file was uploaded.",)
-            if ("qc_text_file" not in request.files or
-                request.files["qc_text_file"].filename == "")
+            if ("qc_text_file" not in rqst.files or
+                rqst.files["qc_text_file"].filename == "")
             else tuple())
 
     def __file_mimetype_error__():
-        text_file = request.files["qc_text_file"]
+        text_file = rqst.files["qc_text_file"]
         return (
             (
                 ("Invalid file! Expected a tab-separated-values file, or a zip "
@@ -50,26 +48,26 @@ def errors(request) -> Tuple[str, ...]:
 
 def zip_file_errors(filepath, upload_dir) -> Tuple[str, ...]:
     """Check the uploaded zip file for errors."""
-    zfile_errors = tuple()
+    zfile_errors: Tuple[str, ...] = tuple()
     if is_zipfile(filepath):
-        zfile = ZipFile(filepath, "r")
-        infolist = zfile.infolist()
-        if len(infolist) != 1:
-            zfile_errors = zfile_errors + (
-                ("Expected exactly one (1) member file within the uploaded zip "
-                 "file. Got {len(infolist)} member files."))
-        if len(infolist) == 1 and infolist[0].is_dir():
-            zfile_errors = zfile_errors + (
-                ("Expected a member text file in the uploaded zip file. Got a "
-                 "directory/folder."))
-
-        if len(infolist) == 1 and not infolist[0].is_dir():
-            zfile.extract(infolist[0], path=upload_dir)
-            mime = mimetypes.guess_type(f"{upload_dir}/{infolist[0].filename}")
-            if mime[0] != "text/tab-separated-values":
+        with ZipFile(filepath, "r") as zfile:
+            infolist = zfile.infolist()
+            if len(infolist) != 1:
+                zfile_errors = zfile_errors + (
+                    ("Expected exactly one (1) member file within the uploaded zip "
+                     "file. Got {len(infolist)} member files."),)
+            if len(infolist) == 1 and infolist[0].is_dir():
                 zfile_errors = zfile_errors + (
-                    ("Expected the member text file in the uploaded zip file to"
-                     " be a tab-separated file."))
+                    ("Expected a member text file in the uploaded zip file. Got a "
+                     "directory/folder."),)
+
+            if len(infolist) == 1 and not infolist[0].is_dir():
+                zfile.extract(infolist[0], path=upload_dir)
+                mime = mimetypes.guess_type(f"{upload_dir}/{infolist[0].filename}")
+                if mime[0] != "text/tab-separated-values":
+                    zfile_errors = zfile_errors + (
+                        ("Expected the member text file in the uploaded zip file to"
+                         " be a tab-separated file."),)
 
     return zfile_errors
 
diff --git a/qc_app/jobs.py b/qc_app/jobs.py
index e97d175..4e6a11e 100644
--- a/qc_app/jobs.py
+++ b/qc_app/jobs.py
@@ -1,3 +1,4 @@
+"""Handle jobs"""
 import os
 import shlex
 import subprocess
@@ -7,29 +8,32 @@ from datetime import timedelta
 from redis import Redis
 
 def error_filename(job_id, error_dir):
+    "Compute the path of the file where errors will be dumped."
     return f"{error_dir}/job_{job_id}.error"
 
-def launch_job(
+def launch_job(# pylint: disable=[too-many-arguments]
         redis_conn: Redis, filepath: str, filetype, redisurl, error_dir,
         ttl_seconds: int):
     """Launch a job in the background"""
     job_id = str(uuid4())
     command = [
-        "python3", "-m" "scripts.worker", filetype, filepath, redisurl, job_id]
-    job = {
+        "python3", "-m", "scripts.worker", filetype, filepath, redisurl, job_id]
+    the_job = {
         "job_id": job_id, "command": shlex.join(command), "status": "pending",
         "filename": os.path.basename(filepath), "percent": 0
     }
-    redis_conn.hset(name=job["job_id"], mapping=job)
-    redis_conn.expire(name=job["job_id"], time=timedelta(seconds=ttl_seconds))
+    redis_conn.hset(name=the_job["job_id"], mapping=the_job)
+    redis_conn.expire(name=the_job["job_id"], time=timedelta(seconds=ttl_seconds))
 
     if not os.path.exists(error_dir):
         os.mkdir(error_dir)
 
-    with open(error_filename(job_id, error_dir), "w") as errorfile:
-        subprocess.Popen(command, stderr=errorfile)
+    with open(error_filename(job_id, error_dir),
+              "w",
+              encoding="utf-8") as errorfile:
+        subprocess.Popen(command, stderr=errorfile) # pylint: disable=[consider-using-with]
 
-    return job
+    return the_job
 
 def job(redis_conn, job_id: str):
     "Retrieve the job"
diff --git a/qc_app/parse.py b/qc_app/parse.py
index b2a0156..e72a163 100644
--- a/qc_app/parse.py
+++ b/qc_app/parse.py
@@ -1,23 +1,13 @@
 """File parsing module"""
 import os
-from functools import reduce
 
 import jsonpickle
 from redis import Redis
-from flask import (
-    flash,
-    request,
-    url_for,
-    redirect,
-    Blueprint,
-    render_template,
-    current_app as app)
+from flask import flash, request, url_for, redirect, Blueprint, render_template
+from flask import current_app as app
 
-from . import jobs
 from quality_control.errors import InvalidValue
-from quality_control.parsing import (
-    FileType,
-    strain_names)
+from . import jobs
 
 parsebp = Blueprint("parse", __name__)
 isinvalidvalue = lambda item: isinstance(item, InvalidValue)
@@ -25,7 +15,6 @@ isinvalidvalue = lambda item: isinstance(item, InvalidValue)
 @parsebp.route("/parse", methods=["GET"])
 def parse():
     """Trigger file parsing"""
-    # TODO: Maybe implement external process to parse the files
     errors = False
     filename = request.args.get("filename")
     filetype = request.args.get("filetype")
@@ -59,6 +48,7 @@ def parse():
 
 @parsebp.route("/status/<job_id>", methods=["GET"])
 def parse_status(job_id: str):
+    "Retrieve the status of the job"
     with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
         job = jobs.job(rconn, job_id)
 
@@ -76,7 +66,7 @@ def parse_status(job_id: str):
         filename = job.get("filename", "uploaded file")
         errors = jsonpickle.decode(
             job.get("errors", jsonpickle.encode(tuple())))
-        if status == "success" or status == "aborted":
+        if status in ("success", "aborted"):
             return redirect(url_for("parse.results", job_id=job_id))
 
         if status == "parse-error":
@@ -133,6 +123,7 @@ def fail(job_id: str):
 
 @parsebp.route("/abort", methods=["POST"])
 def abort():
+    """Handle user request to abort file processing"""
     job_id = request.form["job_id"]
 
     with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
diff --git a/quality_control/average.py b/quality_control/average.py
index 06b0a47..2b098db 100644
--- a/quality_control/average.py
+++ b/quality_control/average.py
@@ -1,19 +1,16 @@
 """Contain logic for checking average files"""
-import re
 from typing import Union
 
+from .utils import cell_error
 from .errors import InvalidValue
 
 def invalid_value(line_number: int, column_number: int, val: str) -> Union[
         InvalidValue, None]:
     """Return an `InvalidValue` object if `val` is not a valid "averages"
     value."""
-    if re.search(r"^[0-9]+\.[0-9]{3}$", val):
-        return None
-    if re.search(r"^0\.0+$", val) or re.search("^0+$", val):
-        return None
-    return InvalidValue(
-        line_number, column_number, val, (
+    return cell_error(
+        r"^[0-9]+\.[0-9]{3}$", val, line=line_number, column=column_number,
+        value=val, message=(
             f"Invalid value '{val}'. "
-            "Expected string representing a number with exactly three decimal "
-            "places."))
+            "Expected string representing a number with exactly three "
+            "decimal places."))
diff --git a/quality_control/headers.py b/quality_control/headers.py
index 79d7e43..f4f4dad 100644
--- a/quality_control/headers.py
+++ b/quality_control/headers.py
@@ -27,14 +27,15 @@ def invalid_headings(
         enumerate(headings, start=2) if header not in strains)
 
 def duplicate_headings(
-        line_number: int, headers: Sequence[str]) -> Union[InvalidValue, None]:
+        line_number: int,
+        headers: Sequence[str]) -> Tuple[DuplicateHeading, ...]:
     """Return a tuple of `DuplicateHeading` objects for each column heading that
     is a duplicate of another column heading."""
     def __update_columns__(acc, item):
         if item[1] in acc.keys():
             return {**acc, item[1]: acc[item[1]] + (item[0],)}
         return {**acc, item[1]: (item[0],)}
-    repeated = {
+    repeated = {# type: ignore[var-annotated]
         heading: columns for heading, columns in
         reduce(__update_columns__, enumerate(headers, start=1), {}).items()
         if len(columns) > 1
diff --git a/quality_control/parsing.py b/quality_control/parsing.py
index f1f4f79..ba22e0c 100644
--- a/quality_control/parsing.py
+++ b/quality_control/parsing.py
@@ -1,15 +1,13 @@
 """Module handling the high-level parsing of the files"""
-
-import os
 import collections
 from enum import Enum
 from functools import partial
 from zipfile import ZipFile, is_zipfile
-from typing import Iterable, Generator, Callable, Optional
+from typing import Tuple, Union, Iterable, Generator, Callable, Optional
 
 import quality_control.average as avg
 import quality_control.standard_error as se
-from quality_control.errors import InvalidValue
+from quality_control.errors import InvalidValue, DuplicateHeading
 from quality_control.headers import (
     invalid_header, invalid_headings, duplicate_headings)
 
@@ -67,16 +65,16 @@ def se_errors(line_number, fields):
 def collect_errors(
         filepath: str, filetype: FileType, strains: list,
         update_progress: Optional[Callable] = None,
-        user_aborted: Optional[Callable] = lambda: False) -> Generator:
+        user_aborted: Callable = lambda: False) -> Generator:
     """Run checks against file and collect all the errors"""
-    errors = tuple()
+    errors:Tuple[Union[InvalidValue, DuplicateHeading], ...] = tuple()
     def __process_errors__(line_number, line, error_checker_fn, errors = tuple()):
         errs = error_checker_fn(
             line_number,
             tuple(field.strip() for field in line.split("\t")))
         if errs is None:
             return errors
-        if isinstance(errs, collections.Sequence):
+        if isinstance(errs, collections.abc.Sequence):
             return errors + tuple(error for error in errs if error is not None)
         return errors + (errs,)
 
diff --git a/quality_control/standard_error.py b/quality_control/standard_error.py
index aa7df3c..7e059ad 100644
--- a/quality_control/standard_error.py
+++ b/quality_control/standard_error.py
@@ -1,7 +1,7 @@
 """Contain logic for checking standard error files"""
-import re
 from typing import Union
 
+from .utils import cell_error
 from .errors import InvalidValue
 
 def invalid_value(
@@ -12,12 +12,9 @@ def invalid_value(
     `val` is not a valid input for standard error files, otherwise, it returns
     `None`.
     """
-    if re.search(r"^[0-9]+\.[0-9]{6,}$", val):
-        return None
-    if re.search(r"^0\.0+$", val) or re.search("^0+$", val):
-        return None
-    return InvalidValue(
-        line_number, column_number, val, (
+    return cell_error(
+        r"^[0-9]+\.[0-9]{6,}$", val, line=line_number, column=column_number,
+        value=val, message=(
             f"Invalid value '{val}'. "
-            "Expected string representing a number with at least six decimal "
-            "places."))
+            "Expected string representing a number with at least six "
+            "decimal places."))
diff --git a/quality_control/utils.py b/quality_control/utils.py
index 0072608..67301d6 100644
--- a/quality_control/utils.py
+++ b/quality_control/utils.py
@@ -1,7 +1,9 @@
 """Utilities that might be useful elsewhere."""
-
+import re
 from collections import namedtuple
 
+from .errors import InvalidValue
+
 ProgressIndicator = namedtuple(
     "ProgressIndicator", ("filesize", "processedsize", "currentline", "percent"))
 
@@ -19,3 +21,11 @@ def make_progress_calculator(filesize: int):
             ((processedsize/filesize) * 100))
 
     return __calculator__
+
+def cell_error(pattern, val, **error_kwargs):
+    "Return the error in the cell"
+    if re.search(pattern, val):
+        return None
+    if re.search(r"^0\.0+$", val) or re.search("^0+$", val):
+        return None
+    return InvalidValue(**error_kwargs)
diff --git a/scripts/worker.py b/scripts/worker.py
index ecdfaa2..c6e989f 100644
--- a/scripts/worker.py
+++ b/scripts/worker.py
@@ -1,20 +1,23 @@
+"""External worker script"""
 import os
 import sys
+import traceback
 from typing import Callable
-from zipfile import Path, ZipFile, is_zipfile
+from zipfile import ZipFile, is_zipfile
 
 import jsonpickle
 from redis import Redis
-from redis.exceptions import ConnectionError
+from redis.exceptions import ConnectionError # pylint: disable=[redefined-builtin]
 
-from .qc import cli_argument_parser
 from quality_control.utils import make_progress_calculator
-from quality_control.parsing import (
-    take, FileType, strain_names, collect_errors)
+from quality_control.parsing import FileType, strain_names, collect_errors
+from .qc import cli_argument_parser
 
 
 def make_progress_indicator(
-        redis_connection: Redis, job_id: str, progress_calc_fn: Callable) -> Callable:
+        redis_connection: Redis, job_id: str,
+        progress_calc_fn: Callable) -> Callable:
+    """Make function that will compute the progress and update redis"""
     def __indicator__(linenumber, linetext):
         progress = progress_calc_fn(linenumber, linetext)
         redis_connection.hset(name=job_id, mapping=progress._asdict())
@@ -24,6 +27,7 @@ def make_progress_indicator(
     return __indicator__
 
 def cli_args_valid(args):
+    "Check that the command-line arguments are provided and correct"
     if not os.path.exists(args.filepath):
         print(f"The file '{args.filepath}' does not exist.", file=sys.stderr)
         return None
@@ -33,14 +37,15 @@ def cli_args_valid(args):
         return None
 
     try:
-        conn = Redis.from_url(args.redisurl)
-    except ConnectionError as ce:
+        conn = Redis.from_url(args.redisurl) # pylint: disable=[unused-variable]
+    except ConnectionError as conn_err: # pylint: disable=[unused-variable]
         print(traceback.format_exc(), file=sys.stderr)
         return None
 
     return args
 
 def process_cli_arguments():
+    """Setup command-line parser"""
     parser = cli_argument_parser()
     parser.prog = "worker"
     parser.add_argument(
@@ -50,12 +55,14 @@ def process_cli_arguments():
     return cli_args_valid(parser.parse_args())
 
 def stream_error(redis_conn, job_id, error):
+    """Update redis with the most current error(s) found"""
     errors = jsonpickle.decode(
         redis_conn.hget(job_id, key="errors") or jsonpickle.encode(tuple()))
     redis_conn.hset(
         job_id, key="errors", value=jsonpickle.encode(errors + (error,)))
 
 def make_user_aborted(redis_conn, job_id):
+    """Mkae function that checks whether the user aborted the process"""
     def __aborted__():
         user_aborted = bool(int(
             redis_conn.hget(name=job_id, key="user_aborted") or "0"))
@@ -66,10 +73,12 @@ def make_user_aborted(redis_conn, job_id):
     return __aborted__
 
 def get_zipfile_size(filepath):
+    "Compute size of given zipfile"
     with ZipFile(filepath, "r") as zfile:
         return zfile.infolist()[0].file_size
 
 def main():
+    "entry point to the script"
     args = process_cli_arguments()
     if args is None:
         print("Quiting due to errors!", file=sys.stderr)
diff --git a/setup.py b/setup.py
index 6068493..24c0a25 100644
--- a/setup.py
+++ b/setup.py
@@ -1,3 +1,4 @@
+"""The setup module"""
 from setuptools import setup
 
 setup()