Do SonarCloud suggested corrections

Author: rohitgarud

asreviewcontrib/preprocess/deduplication/base.py

@@ -174,7 +174,7 @@ def _handle_missing_feature_values(self, pairs_df):
 
         return pairs_df
 
-    def _get_pair_rids(pairs_df):
+    def _get_pair_rids(self, pairs_df):
         """Get record_ids of pairs from the pairs dataframe"""
         pairs_rids = [
             tuple(sorted(pair))
@@ -183,7 +183,7 @@ def _get_pair_rids(pairs_df):
 
         return pairs_rids
 
-    def _get_groups_from_pairs(pair_rids):
+    def _get_groups_from_pairs(self, pair_rids):
         """Get groups of duplicate records from pairs"""
         groups = []
 
@@ -206,7 +206,7 @@ def _get_groups_from_pairs(pair_rids):
         groups = [tuple(sorted(group)) for group in groups]
         return groups
 
-    def _get_pairs_from_groups(groups):
+    def _get_pairs_from_groups(self, groups):
         """Get all pairs of duplicate records from groups"""
         pairs = []
 

asreviewcontrib/preprocess/deduplication/dd_utils.py

@@ -77,7 +77,7 @@ def clean_pages(pages):
 
     if pages:
         pages = re.sub(r"[^0-9-]", "", pages)
-        start, end = re.findall(r"(?P<start>[0-9]*)-?(?P<end>[0-9]*)", pages)[0]
+        start, end = re.findall(r"(?P<start>\d*)-?(?P<end>\d*)", pages)[0]
         if end:
             len_diff = len(start) - len(end)
             if len_diff > 0:
@@ -128,8 +128,7 @@ def clean_number(number):
 
 def clean_isbn(isbn):
     """Unify ISBNs/ISSNs to a common format."""
-    isbn = re.sub(r"\s\((Print|Electronic)\).*", "", isbn)
-    isbn = re.sub(r"\r", "; ", isbn)
+    isbn = re.sub(r"\s\((Print|Electronic)\).*", "", isbn).replace(r"\r", "; ")
     return isbn
 
 

asreviewcontrib/preprocess/entry_points/entrypoint.py

@@ -210,7 +210,7 @@ def execute(self, argv):
                 "subcommand",
                 nargs="?",
                 default=None,
-                help=f"Available commands:\n\n" f"{AVAILABLE_COMMANDS}",
+                help=f"Available commands:\n\n {AVAILABLE_COMMANDS}",
             )
 
             parser.add_argument(

asreviewcontrib/preprocess/io/xml_reader.py

@@ -87,10 +87,7 @@ def read_data(cls, fp):
                 abstract = record.find("abstract")[0].text
             except (AttributeError, TypeError):
                 abstract = None
-            # try:
-            #     label = record.find("label")[0].text
-            # except (AttributeError, TypeError):
-            #     label = None
+
             dataset_list.append(
                 {
                     "recordID": record_id,

asreviewcontrib/preprocess/update_data/openalex_updater.py

@@ -50,7 +50,7 @@ def retrieve_metadata(self, db, doi_list):
 
         return retrieved_metadata
 
-    def parse_metadata(retrieved_metadata):
+    def parse_metadata(self, retrieved_metadata):
         """Parse metadata and create pandas dataframe with required columns
 
         Parameters

asreviewcontrib/preprocess/webapp/gui.py

@@ -1,18 +1,17 @@
 import logging
 import os
-from gevent.pywsgi import WSGIServer
 
-from flask import Flask, render_template, request, redirect, url_for, flash
-from flask_cors import CORS
+from asreview.webapp.start_flask import _check_port_in_use, _open_browser
+from flask import Flask, flash, redirect, render_template, request, url_for
 from flask.json import jsonify
+from flask_cors import CORS
+from gevent.pywsgi import WSGIServer
 from werkzeug.exceptions import InternalServerError
 from werkzeug.utils import secure_filename
 
-from asreview.webapp.start_flask import _check_port_in_use, _open_browser
-
 try:
-    from flask_sqlalchemy import SQLAlchemy
     from flask_bootstrap import Bootstrap
+    from flask_sqlalchemy import SQLAlchemy
 except ImportError:
     print(
         "The GUI requires additional packages to be installed. Install optional ASReview-preprocess dependencies specific for GUI with 'pip install asreview-preprocess[gui]' or all dependencies with 'pip install asreview-preprocess[all]'"
@@ -78,14 +77,14 @@ def upload_file():
             if "file" not in request.files:
                 flash("No file part")
                 return redirect(request.url)
-            file = request.files["file"]
+            upload_file = request.files["file"]
 
-            if file.filename == "":
+            if upload_file.filename == "":
                 flash("No selected file")
                 return redirect(request.url)
-            if file and allowed_file(file.filename):
-                filename = secure_filename(file.filename)
-                file.save(os.path.join(app.config["UPLOAD_FOLDER"], filename))
+            if upload_file and allowed_file(upload_file.filename):
+                filename = secure_filename(upload_file.filename)
+                upload_file.save(os.path.join(app.config["UPLOAD_FOLDER"], filename))
                 return redirect(request.url)
         return """
         <!doctype html>
@@ -108,7 +107,6 @@ def launch_gui(args):
     # app.config["SQLALCHEMY_DATABASE_URI"] = "sqlite:///preprocess.db"
     # app.config["SQLALCHEMY_TRACK_MODIFICATIONS"] = False
     # db = SQLAlchemy(app)
-
     # ssl certificate, key and protocol
     certfile = args.certfile
     keyfile = args.keyfile
@@ -124,7 +122,7 @@ def launch_gui(args):
     port = args.port
     port_retries = args.port_retries
     # if port is already taken find another one
-    if not os.environ.get("FLASK_ENV", "") == "development":
+    if os.environ.get("FLASK_ENV", "") != "development":
         original_port = port
         while _check_port_in_use(host, port) is True:
             old_port = port