Refactor combine_journal_lists scripts to improve quality

scripts/combine_journal_lists_dotless.py

@@ -3,7 +3,7 @@
 """
 Python script for combining several journal abbreviation lists
 and producing an alphabetically sorted list. If the same journal
-names are repeated, only the version found last is retained.
+names are repeated, only the version found first is retained.
 
 This version of the script specifically combines the lists following the ISO4
 standard WITHOUT dots after abbreviated words.
@@ -13,37 +13,92 @@
 Output: writes file 'journalList_dotless.csv'
 """
 
+import csv
+import json
+from pathlib import Path
+import re
 import sys
-import pandas as pd
 
 # Define the list of CSV files
 import_order = [
-    'journals/journal_abbreviations_entrez.csv',
-    'journals/journal_abbreviations_medicus.csv',
-    'journals/journal_abbreviations_webofscience-dotless.csv'
+    "journals/journal_abbreviations_entrez.csv",
+    "journals/journal_abbreviations_medicus.csv",
+    "journals/journal_abbreviations_webofscience-dotless.csv",
 ]
 
 
-def main(output_filename):
-    # Read and merge CSV files
-    # dfs = [pd.read_csv(file, header=None) for file in import_order]
-    dfs = []
-    for file in import_order:
-        df = pd.read_csv(file, header=None)
-        dfs.append(df)
-        print(f"{file}: {len(df)}")
-    merged_df = pd.concat(dfs, ignore_index=True)
+def load_data(file_paths):
+    """Load and combine data from CSV files."""
+    journal_dict = {}
+    normalized_keys = set()
+    for path in file_paths:
+        with open(path, mode="r", encoding="utf-8") as file:
+            reader = csv.reader(file)
+            for row in reader:
+                name = row[0].strip()
+                abbr = row[1].strip()
 
-    # Drop duplicates based on the first column value and keep the last one obtained
-    merged_df.drop_duplicates(subset=[0], keep='last', inplace=True)
+                # Discard entries where name or abbr is missing
+                if not (name and abbr):
+                    continue
+                # Discard entries that are too long or too short
+                if len(name) >= 80 or len(name) <= 3:
+                    continue
+                # Discard names that start with non-alphanumeric characters
+                if not name[0].isalnum():
+                    continue
+                # Discard names that consist only of numbers
+                if name.replace(" ", "").isnumeric():
+                    continue
+                # Discard names containing \
+                if name.count("\\"):
+                    continue
+                # Discard entries where the first letters of name and abbr do not match
+                if abbr[0] != name.replace("The", "").replace("A ", "")[0]:
+                    continue
+                # Only keep the first occurrence
+                if name in journal_dict:
+                    continue
+                # Generate normalizedKey, keeping only the first match
+                normalized_key = normalize_name(name)
+                if normalized_key in normalized_keys:
+                    continue
 
-    # Sort alphabetically
-    sorted_df = merged_df.sort_values(by=[0])
+                journal_dict[name] = abbr
+                normalized_keys.add(normalized_key)  # Add to the set of used keys
+    return journal_dict
 
-    # Save the result to the specified CSV file and ensure values are quoted
-    sorted_df.to_csv(output_filename, index=False, header=False, quoting=1)
 
-    print(f"Write {output_filename}, Combined key count: {len(merged_df)}")
+def normalize_name(name):
+    """
+    Normalize the journal name by removing specified characters using regex.
+    See src/utils/str.ts -> normalizeKey()
+    """
+    return re.sub(r"\b(the|and)\b|[&\-:, ()]", "", name, flags=re.IGNORECASE).lower()
+
+
+def save_to_json(data, output_file):
+    """Save the data to a JSON file."""
+    with open(output_file, mode="w", encoding="utf-8") as json_file:
+        json.dump(data, json_file, indent=2, ensure_ascii=False)
+
+
+def save_to_csv(data, output_file):
+    """Save the data to a CSV file."""
+    with open(output_file, mode="w", newline="", encoding="utf-8") as csv_file:
+        writer = csv.writer(csv_file, quoting=1)
+        for name, abbr in data.items():
+            writer.writerow([name, abbr])
+
+
+def main(filename):
+    base_path = Path().cwd()
+    output_filename = base_path / filename
+    import_paths = [base_path / file for file in import_order]
+
+    journal_data = load_data(import_paths)
+    sorted_journal_data = dict(sorted(journal_data.items()))  # Sort alphabetically
+    save_to_csv(sorted_journal_data, output_filename)
 
 
 if __name__ == "__main__":

scripts/combine_journal_lists_dots.py

@@ -3,7 +3,7 @@
 """
 Python script for combining several journal abbreviation lists
 and producing an alphabetically sorted list. If the same journal
-names are repeated, only the version found last is retained.
+names are repeated, only the version found first is retained.
 
 This version of the script specifically combines the lists following the ISO4
 standard WITH dots after abbreviated words.
@@ -13,45 +13,102 @@
 Output: writes file 'journalList_dots.csv' (or specified output file)
 """
 
+import csv
+import json
+from pathlib import Path
+import re
 import sys
-import pandas as pd
 
-# Define the list of CSV files
 import_order = [
-    'journals/journal_abbreviations_acs.csv',
-    'journals/journal_abbreviations_ams.csv',
-    'journals/journal_abbreviations_general.csv',
-    'journals/journal_abbreviations_geology_physics.csv',
-    'journals/journal_abbreviations_ieee.csv',
-    'journals/journal_abbreviations_lifescience.csv',
-    'journals/journal_abbreviations_mathematics.csv',
-    'journals/journal_abbreviations_mechanical.csv',
-    'journals/journal_abbreviations_meteorology.csv',
-    'journals/journal_abbreviations_sociology.csv',
-    'journals/journal_abbreviations_webofscience-dots.csv'
+    # Keep IEEE before ubc, because IEEE has its own style.
+    "journals/journal_abbreviations_ieee.csv",
+    "journals/journal_abbreviations_acs.csv",
+    # Keep ubc before other jabref's, because ubc's data is more accurate.
+    "journals/journal_abbreviations_ubc.csv",
+    "journals/journal_abbreviations_ams.csv",
+    "journals/journal_abbreviations_general.csv",
+    "journals/journal_abbreviations_geology_physics.csv",
+    "journals/journal_abbreviations_lifescience.csv",
+    "journals/journal_abbreviations_mathematics.csv",
+    "journals/journal_abbreviations_mechanical.csv",
+    "journals/journal_abbreviations_meteorology.csv",
+    "journals/journal_abbreviations_sociology.csv",
+    "journals/journal_abbreviations_webofscience-dots.csv",
 ]
 
 
-def main(output_filename):
-    # Read and merge CSV files
-    # dfs = [pd.read_csv(file, header=None) for file in import_order]
-    dfs = []
-    for file in import_order:
-        df = pd.read_csv(file, header=None)
-        dfs.append(df)
-        print(f"{file}: {len(df)}")
-    merged_df = pd.concat(dfs, ignore_index=True)
+def load_data(file_paths):
+    """Load and combine data from CSV files."""
+    journal_dict = {}
+    normalized_keys = set()
+    for path in file_paths:
+        with open(path, mode="r", encoding="utf-8") as file:
+            reader = csv.reader(file)
+            for row in reader:
+                name = row[0].strip()
+                abbr = row[1].strip()
 
-    # Drop duplicates based on the first column value and keep the last one obtained
-    merged_df.drop_duplicates(subset=[0], keep='last', inplace=True)
+                # Discard entries where name or abbr is missing
+                if not (name and abbr):
+                    continue
+                # Discard entries that are too long or too short
+                if len(name) >= 80 or len(name) <= 3:
+                    continue
+                # Discard names that start with non-alphanumeric characters
+                if not name[0].isalnum():
+                    continue
+                # Discard names that consist only of numbers
+                if name.replace(" ", "").isnumeric():
+                    continue
+                # Discard names containing \
+                if name.count("\\"):
+                    continue
+                # Discard entries where the first letters of name and abbr do not match
+                if abbr[0] != name.replace("The", "").replace("A ", "")[0]:
+                    continue
+                # Only keep the first occurrence
+                if name in journal_dict:
+                    continue
+                # Generate normalizedKey, keeping only the first match
+                normalized_key = normalize_name(name)
+                if normalized_key in normalized_keys:
+                    continue
 
-    # Sort alphabetically
-    sorted_df = merged_df.sort_values(by=[0])
+                journal_dict[name] = abbr
+                normalized_keys.add(normalized_key)  # Add to the set of used keys
+    return journal_dict
 
-    # Save the result to the specified CSV file and ensure values are quoted
-    sorted_df.to_csv(output_filename, index=False, header=False, quoting=1)
 
-    print(f"Write {output_filename}, Combined key count: {len(merged_df)}")
+def normalize_name(name):
+    """
+    Normalize the journal name by removing specified characters using regex.
+    See src/utils/str.ts -> normalizeKey()
+    """
+    return re.sub(r"\b(the|and)\b|[&\-:, ()]", "", name, flags=re.IGNORECASE).lower()
+
+
+def save_to_json(data, output_file):
+    """Save the data to a JSON file."""
+    with open(output_file, mode="w", encoding="utf-8") as json_file:
+        json.dump(data, json_file, indent=2, ensure_ascii=False)
+
+
+def save_to_csv(data, output_file):
+    """Save the data to a CSV file."""
+    with open(output_file, mode="w", newline="", encoding="utf-8") as csv_file:
+        writer = csv.writer(csv_file, quoting=1)
+        for name, abbr in data.items():
+            writer.writerow([name, abbr])
+
+
+def main(filename):
+    base_path = Path().cwd()
+    output_filename = base_path / filename
+    import_paths = [base_path / file for file in import_order]
+
+    journal_data = load_data(import_paths)
+    sorted_journal_data = dict(sorted(journal_data.items()))  # Sort alphabetically
+    save_to_csv(sorted_journal_data, output_filename)
 
 
 if __name__ == "__main__":