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@ -6,5 +6,5 @@ def main():
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app.run(argv)
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if __name__ == '__main__':
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if __name__ == "__main__":
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main()
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@ -9,13 +9,37 @@ import sys
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def parse_args(argv):
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parser = argparse.ArgumentParser(description='Metadata quality checker and fixer.')
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parser.add_argument('--agrovoc-fields', '-a', help='Comma-separated list of fields to validate against AGROVOC, for example: dc.subject,cg.coverage.country')
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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'))
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parser.add_argument('--output-file', '-o', help='Path to output file (always CSV).', required=True, type=argparse.FileType('w', encoding='UTF-8'))
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parser.add_argument('--unsafe-fixes', '-u', help='Perform unsafe fixes.', action='store_true')
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parser.add_argument('--version', '-V', action='version', version=f'CSV Metadata Quality v{VERSION}')
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parser.add_argument('--exclude-fields', '-x', help='Comma-separated list of fields to skip, for example: dc.contributor.author,dc.identifier.citation')
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parser = argparse.ArgumentParser(description="Metadata quality checker and fixer.")
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parser.add_argument(
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"--agrovoc-fields",
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"-a",
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help="Comma-separated list of fields to validate against AGROVOC, for example: dc.subject,cg.coverage.country",
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)
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parser.add_argument(
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"--input-file",
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"-i",
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help="Path to input file. Can be UTF-8 CSV or Excel XLSX.",
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required=True,
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type=argparse.FileType("r", encoding="UTF-8"),
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)
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parser.add_argument(
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"--output-file",
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"-o",
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help="Path to output file (always CSV).",
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required=True,
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type=argparse.FileType("w", encoding="UTF-8"),
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)
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parser.add_argument(
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"--unsafe-fixes", "-u", help="Perform unsafe fixes.", action="store_true"
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)
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parser.add_argument(
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"--version", "-V", action="version", version=f"CSV Metadata Quality v{VERSION}"
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)
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parser.add_argument(
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"--exclude-fields",
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"-x",
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help="Comma-separated list of fields to skip, for example: dc.contributor.author,dc.identifier.citation",
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)
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args = parser.parse_args()
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return args
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@ -40,11 +64,11 @@ def run(argv):
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skip = False
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# Split the list of excludes on ',' so we can test exact matches
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# rather than fuzzy matches with regexes or "if word in string"
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for exclude in args.exclude_fields.split(','):
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for exclude in args.exclude_fields.split(","):
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if column == exclude and skip is False:
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skip = True
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if skip:
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print(f'Skipping {column}')
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print(f"Skipping {column}")
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continue
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@ -58,7 +82,7 @@ def run(argv):
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# Fix: missing space after comma. Only run on author and citation
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# fields for now, as this problem is mostly an issue in names.
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if args.unsafe_fixes:
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match = re.match(r'^.*?(author|citation).*$', column)
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match = re.match(r"^.*?(author|citation).*$", column)
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if match is not None:
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df[column] = df[column].apply(fix.comma_space, field_name=column)
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@ -83,32 +107,32 @@ def run(argv):
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# Check: invalid AGROVOC subject
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if args.agrovoc_fields:
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# Identify fields the user wants to validate against AGROVOC
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for field in args.agrovoc_fields.split(','):
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for field in args.agrovoc_fields.split(","):
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if column == field:
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df[column] = df[column].apply(check.agrovoc, field_name=column)
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# Check: invalid language
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match = re.match(r'^.*?language.*$', column)
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match = re.match(r"^.*?language.*$", column)
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if match is not None:
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df[column] = df[column].apply(check.language)
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# Check: invalid ISSN
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match = re.match(r'^.*?issn.*$', column)
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match = re.match(r"^.*?issn.*$", column)
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if match is not None:
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df[column] = df[column].apply(check.issn)
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# Check: invalid ISBN
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match = re.match(r'^.*?isbn.*$', column)
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match = re.match(r"^.*?isbn.*$", column)
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if match is not None:
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df[column] = df[column].apply(check.isbn)
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# Check: invalid date
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match = re.match(r'^.*?date.*$', column)
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match = re.match(r"^.*?date.*$", column)
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if match is not None:
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df[column] = df[column].apply(check.date, field_name=column)
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# Check: filename extension
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if column == 'filename':
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if column == "filename":
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df[column] = df[column].apply(check.filename_extension)
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# Write
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@ -18,10 +18,10 @@ def issn(field):
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return
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# Try to split multi-value field on "||" separator
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for value in field.split('||'):
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for value in field.split("||"):
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if not issn.is_valid(value):
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print(f'Invalid ISSN: {value}')
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print(f"Invalid ISSN: {value}")
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return field
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@ -43,10 +43,10 @@ def isbn(field):
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return
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# Try to split multi-value field on "||" separator
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for value in field.split('||'):
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for value in field.split("||"):
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if not isbn.is_valid(value):
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print(f'Invalid ISBN: {value}')
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print(f"Invalid ISBN: {value}")
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return field
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@ -64,13 +64,13 @@ def separators(field):
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return
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# Try to split multi-value field on "||" separator
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for value in field.split('||'):
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for value in field.split("||"):
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# After splitting, see if there are any remaining "|" characters
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match = re.findall(r'^.*?\|.*$', value)
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match = re.findall(r"^.*?\|.*$", value)
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if match:
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print(f'Invalid multi-value separator: {field}')
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print(f"Invalid multi-value separator: {field}")
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return field
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@ -88,22 +88,22 @@ def date(field, field_name):
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from datetime import datetime
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if pd.isna(field):
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print(f'Missing date ({field_name}).')
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print(f"Missing date ({field_name}).")
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return
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# Try to split multi-value field on "||" separator
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multiple_dates = field.split('||')
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multiple_dates = field.split("||")
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# We don't allow multi-value date fields
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if len(multiple_dates) > 1:
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print(f'Multiple dates not allowed ({field_name}): {field}')
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print(f"Multiple dates not allowed ({field_name}): {field}")
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return field
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try:
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# Check if date is valid YYYY format
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datetime.strptime(field, '%Y')
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datetime.strptime(field, "%Y")
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return field
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except ValueError:
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@ -111,7 +111,7 @@ def date(field, field_name):
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try:
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# Check if date is valid YYYY-MM format
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datetime.strptime(field, '%Y-%m')
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datetime.strptime(field, "%Y-%m")
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return field
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except ValueError:
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@ -119,11 +119,11 @@ def date(field, field_name):
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try:
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# Check if date is valid YYYY-MM-DD format
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datetime.strptime(field, '%Y-%m-%d')
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datetime.strptime(field, "%Y-%m-%d")
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return field
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except ValueError:
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print(f'Invalid date ({field_name}): {field}')
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print(f"Invalid date ({field_name}): {field}")
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return field
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@ -140,7 +140,7 @@ def suspicious_characters(field, field_name):
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return
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# List of suspicious characters, for example: ́ˆ~`
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suspicious_characters = ['\u00B4', '\u02C6', '\u007E', '\u0060']
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suspicious_characters = ["\u00B4", "\u02C6", "\u007E", "\u0060"]
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for character in suspicious_characters:
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# Find the position of the suspicious character in the string
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@ -156,8 +156,10 @@ def suspicious_characters(field, field_name):
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# character and spanning enough of the rest to give a preview,
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# but not too much to cause the line to break in terminals with
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# a default of 80 characters width.
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suspicious_character_msg = f'Suspicious character ({field_name}): {field_subset}'
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print(f'{suspicious_character_msg:1.80}')
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suspicious_character_msg = (
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f"Suspicious character ({field_name}): {field_subset}"
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)
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print(f"{suspicious_character_msg:1.80}")
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return field
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@ -177,22 +179,22 @@ def language(field):
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# need to handle "Other" values here...
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# Try to split multi-value field on "||" separator
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for value in field.split('||'):
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for value in field.split("||"):
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# After splitting, check if language value is 2 or 3 characters so we
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# can check it against ISO 639-2 or ISO 639-3 accordingly.
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if len(value) == 2:
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if not languages.get(alpha_2=value):
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print(f'Invalid ISO 639-2 language: {value}')
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print(f"Invalid ISO 639-2 language: {value}")
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pass
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elif len(value) == 3:
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if not languages.get(alpha_3=value):
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print(f'Invalid ISO 639-3 language: {value}')
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print(f"Invalid ISO 639-3 language: {value}")
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pass
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else:
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print(f'Invalid language: {value}')
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print(f"Invalid language: {value}")
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return field
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@ -220,12 +222,16 @@ def agrovoc(field, field_name):
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return
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# Try to split multi-value field on "||" separator
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for value in field.split('||'):
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request_url = f'http://agrovoc.uniroma2.it/agrovoc/rest/v1/agrovoc/search?query={value}'
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for value in field.split("||"):
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request_url = (
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f"http://agrovoc.uniroma2.it/agrovoc/rest/v1/agrovoc/search?query={value}"
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)
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# enable transparent request cache with thirty days expiry
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expire_after = timedelta(days=30)
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requests_cache.install_cache('agrovoc-response-cache', expire_after=expire_after)
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requests_cache.install_cache(
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"agrovoc-response-cache", expire_after=expire_after
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)
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request = requests.get(request_url)
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@ -236,8 +242,8 @@ def agrovoc(field, field_name):
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data = request.json()
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# check if there are any results
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if len(data['results']) == 0:
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print(f'Invalid AGROVOC ({field_name}): {value}')
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if len(data["results"]) == 0:
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print(f"Invalid AGROVOC ({field_name}): {value}")
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return field
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@ -260,10 +266,18 @@ def filename_extension(field):
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return
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# Try to split multi-value field on "||" separator
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values = field.split('||')
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values = field.split("||")
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# List of common filename extentions
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common_filename_extensions = ['.pdf', '.doc', '.docx', '.ppt', '.pptx', '.xls', '.xlsx']
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common_filename_extensions = [
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".pdf",
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".doc",
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".docx",
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".ppt",
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".pptx",
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".xls",
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".xlsx",
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]
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# Iterate over all values
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for value in values:
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@ -272,7 +286,7 @@ def filename_extension(field):
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for filename_extension in common_filename_extensions:
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# Check for extension at the end of the filename
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pattern = re.escape(filename_extension) + r'$'
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pattern = re.escape(filename_extension) + r"$"
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match = re.search(pattern, value, re.IGNORECASE)
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if match is not None:
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@ -282,6 +296,6 @@ def filename_extension(field):
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break
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if filename_extension_match is False:
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print(f'Filename with uncommon extension: {value}')
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print(f"Filename with uncommon extension: {value}")
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return field
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@ -16,23 +16,23 @@ def whitespace(field):
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values = list()
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# Try to split multi-value field on "||" separator
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for value in field.split('||'):
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for value in field.split("||"):
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# Strip leading and trailing whitespace
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value = value.strip()
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# Replace excessive whitespace (>2) with one space
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pattern = re.compile(r'\s{2,}')
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pattern = re.compile(r"\s{2,}")
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match = re.findall(pattern, value)
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if match:
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print(f'Excessive whitespace: {value}')
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value = re.sub(pattern, ' ', value)
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print(f"Excessive whitespace: {value}")
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value = re.sub(pattern, " ", value)
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# Save cleaned value
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values.append(value)
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# Create a new field consisting of all values joined with "||"
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new_field = '||'.join(values)
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new_field = "||".join(values)
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return new_field
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@ -48,21 +48,21 @@ def separators(field):
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values = list()
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# Try to split multi-value field on "||" separator
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for value in field.split('||'):
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for value in field.split("||"):
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# After splitting, see if there are any remaining "|" characters
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pattern = re.compile(r'\|')
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pattern = re.compile(r"\|")
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match = re.findall(pattern, value)
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if match:
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print(f'Fixing invalid multi-value separator: {value}')
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print(f"Fixing invalid multi-value separator: {value}")
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value = re.sub(pattern, '||', value)
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value = re.sub(pattern, "||", value)
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# Save cleaned value
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values.append(value)
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# Create a new field consisting of all values joined with "||"
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new_field = '||'.join(values)
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new_field = "||".join(values)
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return new_field
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@ -86,36 +86,36 @@ def unnecessary_unicode(field):
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return
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# Check for zero-width space characters (U+200B)
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pattern = re.compile(r'\u200B')
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pattern = re.compile(r"\u200B")
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match = re.findall(pattern, field)
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if match:
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print(f'Removing unnecessary Unicode (U+200B): {field}')
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field = re.sub(pattern, '', field)
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print(f"Removing unnecessary Unicode (U+200B): {field}")
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field = re.sub(pattern, "", field)
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# Check for replacement characters (U+FFFD)
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pattern = re.compile(r'\uFFFD')
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pattern = re.compile(r"\uFFFD")
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match = re.findall(pattern, field)
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if match:
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print(f'Removing unnecessary Unicode (U+FFFD): {field}')
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field = re.sub(pattern, '', field)
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print(f"Removing unnecessary Unicode (U+FFFD): {field}")
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field = re.sub(pattern, "", field)
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# Check for no-break spaces (U+00A0)
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pattern = re.compile(r'\u00A0')
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pattern = re.compile(r"\u00A0")
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match = re.findall(pattern, field)
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if match:
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print(f'Removing unnecessary Unicode (U+00A0): {field}')
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field = re.sub(pattern, '', field)
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print(f"Removing unnecessary Unicode (U+00A0): {field}")
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field = re.sub(pattern, "", field)
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# Check for soft hyphens (U+00AD), sometimes preceeded with a normal hyphen
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pattern = re.compile(r'\u002D*?\u00AD')
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pattern = re.compile(r"\u002D*?\u00AD")
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match = re.findall(pattern, field)
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|
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if match:
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print(f'Replacing unnecessary Unicode (U+00AD): {field}')
|
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field = re.sub(pattern, '-', field)
|
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print(f"Replacing unnecessary Unicode (U+00AD): {field}")
|
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field = re.sub(pattern, "-", field)
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|
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return field
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@ -128,7 +128,7 @@ def duplicates(field):
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return
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|
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# Try to split multi-value field on "||" separator
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values = field.split('||')
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values = field.split("||")
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# Initialize an empty list to hold the de-duplicated values
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new_values = list()
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@ -139,10 +139,10 @@ def duplicates(field):
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if value not in new_values:
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new_values.append(value)
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else:
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print(f'Dropping duplicate value: {value}')
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print(f"Dropping duplicate value: {value}")
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|
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# Create a new field consisting of all values joined with "||"
|
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new_field = '||'.join(new_values)
|
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new_field = "||".join(new_values)
|
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|
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return new_field
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@ -169,11 +169,11 @@ def newlines(field):
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return
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|
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# Check for Unix line feed (LF)
|
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match = re.findall(r'\n', field)
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match = re.findall(r"\n", field)
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|
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if match:
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print(f'Removing newline: {field}')
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field = field.replace('\n', '')
|
||||
print(f"Removing newline: {field}")
|
||||
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}')
|
||||
field = re.sub(r',(\w)', r', \1', field)
|
||||
print(f"Adding space after comma ({field_name}): {field}")
|
||||
field = re.sub(r",(\w)", r", \1", field)
|
||||
|
||||
return field
|
||||
|
||||
@ -1 +1 @@
|
||||
VERSION = '0.2.2'
|
||||
VERSION = "0.2.2"
|
||||
|
||||
Loading…
Reference in New Issue
Block a user