Format with black

csv_metadata_quality/__main__.py

@@ -6,5 +6,5 @@ def main():
     app.run(argv)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

csv_metadata_quality/app.py

@@ -9,13 +9,37 @@ import sys
 
 
 def parse_args(argv):
-    parser = argparse.ArgumentParser(description='Metadata quality checker and fixer.')
+    parser = argparse.ArgumentParser(description="Metadata quality checker and fixer.")
-    parser.add_argument('--agrovoc-fields', '-a', help='Comma-separated list of fields to validate against AGROVOC, for example: dc.subject,cg.coverage.country')
+    parser.add_argument(
-    parser.add_argument('--input-file', '-i', help='Path to input file. Can be UTF-8 CSV or Excel XLSX.', required=True, type=argparse.FileType('r', encoding='UTF-8'))
+        "--agrovoc-fields",
-    parser.add_argument('--output-file', '-o', help='Path to output file (always CSV).', required=True, type=argparse.FileType('w', encoding='UTF-8'))
+        "-a",
-    parser.add_argument('--unsafe-fixes', '-u', help='Perform unsafe fixes.', action='store_true')
+        help="Comma-separated list of fields to validate against AGROVOC, for example: dc.subject,cg.coverage.country",
-    parser.add_argument('--version', '-V', action='version', version=f'CSV Metadata Quality v{VERSION}')
+    )
-    parser.add_argument('--exclude-fields', '-x', help='Comma-separated list of fields to skip, for example: dc.contributor.author,dc.identifier.citation')
+    parser.add_argument(
+        "--input-file",
+        "-i",
+        help="Path to input file. Can be UTF-8 CSV or Excel XLSX.",
+        required=True,
+        type=argparse.FileType("r", encoding="UTF-8"),
+    )
+    parser.add_argument(
+        "--output-file",
+        "-o",
+        help="Path to output file (always CSV).",
+        required=True,
+        type=argparse.FileType("w", encoding="UTF-8"),
+    )
+    parser.add_argument(
+        "--unsafe-fixes", "-u", help="Perform unsafe fixes.", action="store_true"
+    )
+    parser.add_argument(
+        "--version", "-V", action="version", version=f"CSV Metadata Quality v{VERSION}"
+    )
+    parser.add_argument(
+        "--exclude-fields",
+        "-x",
+        help="Comma-separated list of fields to skip, for example: dc.contributor.author,dc.identifier.citation",
+    )
     args = parser.parse_args()
 
     return args
@@ -40,11 +64,11 @@ def run(argv):
             skip = False
             # Split the list of excludes on ',' so we can test exact matches
             # rather than fuzzy matches with regexes or "if word in string"
-            for exclude in args.exclude_fields.split(','):
+            for exclude in args.exclude_fields.split(","):
                 if column == exclude and skip is False:
                     skip = True
             if skip:
-                print(f'Skipping {column}')
+                print(f"Skipping {column}")
 
                 continue
 
@@ -58,7 +82,7 @@ def run(argv):
         # Fix: missing space after comma. Only run on author and citation
         # fields for now, as this problem is mostly an issue in names.
         if args.unsafe_fixes:
-            match = re.match(r'^.*?(author|citation).*$', column)
+            match = re.match(r"^.*?(author|citation).*$", column)
             if match is not None:
                 df[column] = df[column].apply(fix.comma_space, field_name=column)
 
@@ -83,32 +107,32 @@ def run(argv):
         # Check: invalid AGROVOC subject
         if args.agrovoc_fields:
             # Identify fields the user wants to validate against AGROVOC
-            for field in args.agrovoc_fields.split(','):
+            for field in args.agrovoc_fields.split(","):
                 if column == field:
                     df[column] = df[column].apply(check.agrovoc, field_name=column)
 
         # Check: invalid language
-        match = re.match(r'^.*?language.*$', column)
+        match = re.match(r"^.*?language.*$", column)
         if match is not None:
             df[column] = df[column].apply(check.language)
 
         # Check: invalid ISSN
-        match = re.match(r'^.*?issn.*$', column)
+        match = re.match(r"^.*?issn.*$", column)
         if match is not None:
             df[column] = df[column].apply(check.issn)
 
         # Check: invalid ISBN
-        match = re.match(r'^.*?isbn.*$', column)
+        match = re.match(r"^.*?isbn.*$", column)
         if match is not None:
             df[column] = df[column].apply(check.isbn)
 
         # Check: invalid date
-        match = re.match(r'^.*?date.*$', column)
+        match = re.match(r"^.*?date.*$", column)
         if match is not None:
             df[column] = df[column].apply(check.date, field_name=column)
 
         # Check: filename extension
-        if column == 'filename':
+        if column == "filename":
             df[column] = df[column].apply(check.filename_extension)
 
     # Write

csv_metadata_quality/check.py

@@ -18,10 +18,10 @@ def issn(field):
         return
 
     # Try to split multi-value field on "||" separator
-    for value in field.split('||'):
+    for value in field.split("||"):
 
         if not issn.is_valid(value):
-            print(f'Invalid ISSN: {value}')
+            print(f"Invalid ISSN: {value}")
 
     return field
 
@@ -43,10 +43,10 @@ def isbn(field):
         return
 
     # Try to split multi-value field on "||" separator
-    for value in field.split('||'):
+    for value in field.split("||"):
 
         if not isbn.is_valid(value):
-            print(f'Invalid ISBN: {value}')
+            print(f"Invalid ISBN: {value}")
 
     return field
 
@@ -64,13 +64,13 @@ def separators(field):
         return
 
     # Try to split multi-value field on "||" separator
-    for value in field.split('||'):
+    for value in field.split("||"):
 
         # After splitting, see if there are any remaining "|" characters
-        match = re.findall(r'^.*?\|.*$', value)
+        match = re.findall(r"^.*?\|.*$", value)
 
         if match:
-            print(f'Invalid multi-value separator: {field}')
+            print(f"Invalid multi-value separator: {field}")
 
     return field
 
@@ -88,22 +88,22 @@ def date(field, field_name):
     from datetime import datetime
 
     if pd.isna(field):
-        print(f'Missing date ({field_name}).')
+        print(f"Missing date ({field_name}).")
 
         return
 
     # Try to split multi-value field on "||" separator
-    multiple_dates = field.split('||')
+    multiple_dates = field.split("||")
 
     # We don't allow multi-value date fields
     if len(multiple_dates) > 1:
-        print(f'Multiple dates not allowed ({field_name}): {field}')
+        print(f"Multiple dates not allowed ({field_name}): {field}")
 
         return field
 
     try:
         # Check if date is valid YYYY format
-        datetime.strptime(field, '%Y')
+        datetime.strptime(field, "%Y")
 
         return field
     except ValueError:
@@ -111,7 +111,7 @@ def date(field, field_name):
 
     try:
         # Check if date is valid YYYY-MM format
-        datetime.strptime(field, '%Y-%m')
+        datetime.strptime(field, "%Y-%m")
 
         return field
     except ValueError:
@@ -119,11 +119,11 @@ def date(field, field_name):
 
     try:
         # Check if date is valid YYYY-MM-DD format
-        datetime.strptime(field, '%Y-%m-%d')
+        datetime.strptime(field, "%Y-%m-%d")
 
         return field
     except ValueError:
-        print(f'Invalid date ({field_name}): {field}')
+        print(f"Invalid date ({field_name}): {field}")
 
         return field
 
@@ -140,7 +140,7 @@ def suspicious_characters(field, field_name):
         return
 
     # List of suspicious characters, for example:  ́ˆ~`
-    suspicious_characters = ['\u00B4', '\u02C6', '\u007E', '\u0060']
+    suspicious_characters = ["\u00B4", "\u02C6", "\u007E", "\u0060"]
 
     for character in suspicious_characters:
         # Find the position of the suspicious character in the string
@@ -156,8 +156,10 @@ def suspicious_characters(field, field_name):
             # character and spanning enough of the rest to give a preview,
             # but not too much to cause the line to break in terminals with
             # a default of 80 characters width.
-            suspicious_character_msg = f'Suspicious character ({field_name}): {field_subset}'
+            suspicious_character_msg = (
-            print(f'{suspicious_character_msg:1.80}')
+                f"Suspicious character ({field_name}): {field_subset}"
+            )
+            print(f"{suspicious_character_msg:1.80}")
 
     return field
 
@@ -177,22 +179,22 @@ def language(field):
     # need to handle "Other" values here...
 
     # Try to split multi-value field on "||" separator
-    for value in field.split('||'):
+    for value in field.split("||"):
 
         # After splitting, check if language value is 2 or 3 characters so we
         # can check it against ISO 639-2 or ISO 639-3 accordingly.
         if len(value) == 2:
             if not languages.get(alpha_2=value):
-                print(f'Invalid ISO 639-2 language: {value}')
+                print(f"Invalid ISO 639-2 language: {value}")
 
                 pass
         elif len(value) == 3:
             if not languages.get(alpha_3=value):
-                print(f'Invalid ISO 639-3 language: {value}')
+                print(f"Invalid ISO 639-3 language: {value}")
 
                 pass
         else:
-            print(f'Invalid language: {value}')
+            print(f"Invalid language: {value}")
 
     return field
 
@@ -220,12 +222,16 @@ def agrovoc(field, field_name):
         return
 
     # Try to split multi-value field on "||" separator
-    for value in field.split('||'):
+    for value in field.split("||"):
-        request_url = f'http://agrovoc.uniroma2.it/agrovoc/rest/v1/agrovoc/search?query={value}'
+        request_url = (
+            f"http://agrovoc.uniroma2.it/agrovoc/rest/v1/agrovoc/search?query={value}"
+        )
 
         # enable transparent request cache with thirty days expiry
         expire_after = timedelta(days=30)
-        requests_cache.install_cache('agrovoc-response-cache', expire_after=expire_after)
+        requests_cache.install_cache(
+            "agrovoc-response-cache", expire_after=expire_after
+        )
 
         request = requests.get(request_url)
 
@@ -236,8 +242,8 @@ def agrovoc(field, field_name):
             data = request.json()
 
             # check if there are any results
-            if len(data['results']) == 0:
+            if len(data["results"]) == 0:
-                print(f'Invalid AGROVOC ({field_name}): {value}')
+                print(f"Invalid AGROVOC ({field_name}): {value}")
 
     return field
 
@@ -260,10 +266,18 @@ def filename_extension(field):
         return
 
     # Try to split multi-value field on "||" separator
-    values = field.split('||')
+    values = field.split("||")
 
     # List of common filename extentions
-    common_filename_extensions = ['.pdf', '.doc', '.docx', '.ppt', '.pptx', '.xls', '.xlsx']
+    common_filename_extensions = [
+        ".pdf",
+        ".doc",
+        ".docx",
+        ".ppt",
+        ".pptx",
+        ".xls",
+        ".xlsx",
+    ]
 
     # Iterate over all values
     for value in values:
@@ -272,7 +286,7 @@ def filename_extension(field):
 
         for filename_extension in common_filename_extensions:
             # Check for extension at the end of the filename
-            pattern = re.escape(filename_extension) + r'$'
+            pattern = re.escape(filename_extension) + r"$"
             match = re.search(pattern, value, re.IGNORECASE)
 
             if match is not None:
@@ -282,6 +296,6 @@ def filename_extension(field):
                 break
 
         if filename_extension_match is False:
-            print(f'Filename with uncommon extension: {value}')
+            print(f"Filename with uncommon extension: {value}")
 
     return field

csv_metadata_quality/fix.py

@@ -16,23 +16,23 @@ def whitespace(field):
     values = list()
 
     # Try to split multi-value field on "||" separator
-    for value in field.split('||'):
+    for value in field.split("||"):
         # Strip leading and trailing whitespace
         value = value.strip()
 
         # Replace excessive whitespace (>2) with one space
-        pattern = re.compile(r'\s{2,}')
+        pattern = re.compile(r"\s{2,}")
         match = re.findall(pattern, value)
 
         if match:
-            print(f'Excessive whitespace: {value}')
+            print(f"Excessive whitespace: {value}")
-            value = re.sub(pattern, ' ', value)
+            value = re.sub(pattern, " ", value)
 
         # Save cleaned value
         values.append(value)
 
     # Create a new field consisting of all values joined with "||"
-    new_field = '||'.join(values)
+    new_field = "||".join(values)
 
     return new_field
 
@@ -48,21 +48,21 @@ def separators(field):
     values = list()
 
     # Try to split multi-value field on "||" separator
-    for value in field.split('||'):
+    for value in field.split("||"):
         # After splitting, see if there are any remaining "|" characters
-        pattern = re.compile(r'\|')
+        pattern = re.compile(r"\|")
         match = re.findall(pattern, value)
 
         if match:
-            print(f'Fixing invalid multi-value separator: {value}')
+            print(f"Fixing invalid multi-value separator: {value}")
 
-            value = re.sub(pattern, '||', value)
+            value = re.sub(pattern, "||", value)
 
         # Save cleaned value
         values.append(value)
 
     # Create a new field consisting of all values joined with "||"
-    new_field = '||'.join(values)
+    new_field = "||".join(values)
 
     return new_field
 
@@ -86,36 +86,36 @@ def unnecessary_unicode(field):
         return
 
     # Check for zero-width space characters (U+200B)
-    pattern = re.compile(r'\u200B')
+    pattern = re.compile(r"\u200B")
     match = re.findall(pattern, field)
 
     if match:
-        print(f'Removing unnecessary Unicode (U+200B): {field}')
+        print(f"Removing unnecessary Unicode (U+200B): {field}")
-        field = re.sub(pattern, '', field)
+        field = re.sub(pattern, "", field)
 
     # Check for replacement characters (U+FFFD)
-    pattern = re.compile(r'\uFFFD')
+    pattern = re.compile(r"\uFFFD")
     match = re.findall(pattern, field)
 
     if match:
-        print(f'Removing unnecessary Unicode (U+FFFD): {field}')
+        print(f"Removing unnecessary Unicode (U+FFFD): {field}")
-        field = re.sub(pattern, '', field)
+        field = re.sub(pattern, "", field)
 
     # Check for no-break spaces (U+00A0)
-    pattern = re.compile(r'\u00A0')
+    pattern = re.compile(r"\u00A0")
     match = re.findall(pattern, field)
 
     if match:
-        print(f'Removing unnecessary Unicode (U+00A0): {field}')
+        print(f"Removing unnecessary Unicode (U+00A0): {field}")
-        field = re.sub(pattern, '', field)
+        field = re.sub(pattern, "", field)
 
     # Check for soft hyphens (U+00AD), sometimes preceeded with a normal hyphen
-    pattern = re.compile(r'\u002D*?\u00AD')
+    pattern = re.compile(r"\u002D*?\u00AD")
     match = re.findall(pattern, field)
 
     if match:
-        print(f'Replacing unnecessary Unicode (U+00AD): {field}')
+        print(f"Replacing unnecessary Unicode (U+00AD): {field}")
-        field = re.sub(pattern, '-', field)
+        field = re.sub(pattern, "-", field)
 
     return field
 
@@ -128,7 +128,7 @@ def duplicates(field):
         return
 
     # Try to split multi-value field on "||" separator
-    values = field.split('||')
+    values = field.split("||")
 
     # Initialize an empty list to hold the de-duplicated values
     new_values = list()
@@ -139,10 +139,10 @@ def duplicates(field):
         if value not in new_values:
             new_values.append(value)
         else:
-            print(f'Dropping duplicate value: {value}')
+            print(f"Dropping duplicate value: {value}")
 
     # Create a new field consisting of all values joined with "||"
-    new_field = '||'.join(new_values)
+    new_field = "||".join(new_values)
 
     return new_field
 
@@ -169,11 +169,11 @@ def newlines(field):
         return
 
     # Check for Unix line feed (LF)
-    match = re.findall(r'\n', field)
+    match = re.findall(r"\n", field)
 
     if match:
-        print(f'Removing newline: {field}')
+        print(f"Removing newline: {field}")
-        field = field.replace('\n', '')
+        field = field.replace("\n", "")
 
     return field
 
@@ -193,10 +193,10 @@ def comma_space(field, field_name):
         return
 
     # Check for comma followed by a word character
-    match = re.findall(r',\w', field)
+    match = re.findall(r",\w", field)
 
     if match:
-        print(f'Adding space after comma ({field_name}): {field}')
+        print(f"Adding space after comma ({field_name}): {field}")
-        field = re.sub(r',(\w)', r', \1', field)
+        field = re.sub(r",(\w)", r", \1", field)
 
     return field

csv_metadata_quality/version.py

@@ -1 +1 @@
-VERSION = '0.2.2'
+VERSION = "0.2.2"