mirror of
https://github.com/qurator-spk/modstool.git
synced 2025-06-26 20:19:56 +02:00
🎨 Rename qurator.modstool to qurator.mods4pandas
This commit is contained in:
parent
1d2c5e2d10
commit
3c2e59f0ed
36 changed files with 6 additions and 6 deletions
336
qurator/mods4pandas/mods4pandas.py
Executable file
336
qurator/mods4pandas/mods4pandas.py
Executable file
|
|
@ -0,0 +1,336 @@
|
|||
#!/usr/bin/env python3
|
||||
import csv
|
||||
import logging
|
||||
import os
|
||||
import re
|
||||
import warnings
|
||||
from lxml import etree as ET
|
||||
from itertools import groupby
|
||||
from operator import attrgetter
|
||||
from typing import List
|
||||
from collections.abc import MutableMapping, Sequence
|
||||
|
||||
import click
|
||||
import pandas as pd
|
||||
from tqdm import tqdm
|
||||
|
||||
from .lib import sorted_groupby, TagGroup, ns, flatten
|
||||
|
||||
|
||||
|
||||
logger = logging.getLogger('modstool')
|
||||
|
||||
def mods_to_dict(mods, raise_errors=True):
|
||||
"""Convert MODS metadata to a nested dictionary"""
|
||||
|
||||
# The approach taken here is to handle each element explicitly. This also means that ignored elements are ignored
|
||||
# explicitly.
|
||||
|
||||
value = {}
|
||||
|
||||
# Iterate through each group of tags
|
||||
for tag, group in sorted_groupby(mods, key=attrgetter('tag')):
|
||||
group = list(group)
|
||||
if tag == '{http://www.loc.gov/mods/v3}location':
|
||||
def only_current_location(location):
|
||||
return location.get('type') != 'former'
|
||||
value['location'] = TagGroup(tag, group) \
|
||||
.filter(only_current_location) \
|
||||
.has_attributes([{}, {'type': 'current'}]) \
|
||||
.is_singleton().descend(raise_errors)
|
||||
elif tag == '{http://www.loc.gov/mods/v3}physicalLocation':
|
||||
def no_display_label(physical_location):
|
||||
return physical_location.get('displayLabel') is None
|
||||
value['physicalLocation'] = TagGroup(tag, group).filter(no_display_label).text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}shelfLocator':
|
||||
# This element should not be repeated according to MODS-AP 2.3.1, however a few of the files contain
|
||||
# a second element with empty text and a "displayLabel" attribute set.
|
||||
def no_display_label(shelf_locator):
|
||||
return shelf_locator.get('displayLabel') is None
|
||||
value['shelfLocator'] = TagGroup(tag, group) \
|
||||
.filter(no_display_label) \
|
||||
.force_singleton() \
|
||||
.has_no_attributes() \
|
||||
.text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}originInfo':
|
||||
def has_event_type(origin_info):
|
||||
# According to MODS-AP 2.3.1, every originInfo should have its eventType set. However, some
|
||||
# are empty and not fixable.
|
||||
return origin_info.attrib.get('eventType') is not None
|
||||
tag_group = TagGroup(tag, group).fix_event_type().filter(has_event_type, warn="has no eventType")
|
||||
for event_type, grouped_group in sorted_groupby(tag_group.group, key=lambda g: g.attrib['eventType']):
|
||||
for n, e in enumerate(grouped_group):
|
||||
value['originInfo-{}{}'.format(event_type, n)] = mods_to_dict(e, raise_errors)
|
||||
elif tag == '{http://www.loc.gov/mods/v3}place':
|
||||
value['place'] = TagGroup(tag, group).force_singleton(warn=False).has_no_attributes().descend(raise_errors)
|
||||
elif tag == '{http://www.loc.gov/mods/v3}placeTerm':
|
||||
value['placeTerm'] = TagGroup(tag, group).is_singleton().has_attributes({'type': 'text'}).text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}dateIssued':
|
||||
value['dateIssued'] = TagGroup(tag, group) \
|
||||
.fix_date() \
|
||||
.sort(key=lambda d: d.attrib.get('keyDate') == 'yes', reverse=True) \
|
||||
.ignore_attributes() \
|
||||
.force_singleton() \
|
||||
.text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}dateCreated':
|
||||
value['dateCreated'] = TagGroup(tag, group) \
|
||||
.fix_date() \
|
||||
.sort(key=lambda d: d.attrib.get('keyDate') == 'yes', reverse=True) \
|
||||
.ignore_attributes() \
|
||||
.force_singleton() \
|
||||
.text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}dateCaptured':
|
||||
value['dateCaptured'] = TagGroup(tag, group).fix_date().ignore_attributes().is_singleton().text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}dateOther':
|
||||
value['dateOther'] = TagGroup(tag, group).fix_date().ignore_attributes().is_singleton().text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}publisher':
|
||||
value['publisher'] = TagGroup(tag, group).force_singleton(warn=False).has_no_attributes().text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}edition':
|
||||
value['edition'] = TagGroup(tag, group).force_singleton().has_no_attributes().text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}classification':
|
||||
authorities = {e.attrib['authority'] for e in group}
|
||||
for authority in authorities:
|
||||
sub_group = [e for e in group if e.attrib.get('authority') == authority]
|
||||
value['classification-{}'.format(authority)] = TagGroup(tag, sub_group).text_set()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}recordInfo':
|
||||
value['recordInfo'] = TagGroup(tag, group).is_singleton().has_no_attributes().descend(raise_errors)
|
||||
elif tag == '{http://www.loc.gov/mods/v3}recordIdentifier':
|
||||
value['recordIdentifier'] = TagGroup(tag, group).is_singleton().has_attributes({'source': 'gbv-ppn'}).text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}identifier':
|
||||
for e in group:
|
||||
if len(e.attrib) != 1:
|
||||
raise ValueError('Unknown attributes for identifier {}'.format(e.attrib))
|
||||
value['identifier-{}'.format(e.attrib['type'])] = e.text
|
||||
elif tag == '{http://www.loc.gov/mods/v3}titleInfo':
|
||||
def only_standard_title(title_info):
|
||||
return title_info.attrib.get('type') is None
|
||||
value['titleInfo'] = TagGroup(tag, group) \
|
||||
.filter(only_standard_title) \
|
||||
.is_singleton().has_no_attributes().descend(raise_errors)
|
||||
elif tag == '{http://www.loc.gov/mods/v3}title':
|
||||
value['title'] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}partName':
|
||||
value['partName'] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}subTitle':
|
||||
value['subTitle'] = TagGroup(tag, group).force_singleton().has_no_attributes().text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}note':
|
||||
# This could be useful if distinguished by type attribute.
|
||||
pass
|
||||
elif tag == '{http://www.loc.gov/mods/v3}part':
|
||||
pass
|
||||
elif tag == '{http://www.loc.gov/mods/v3}abstract':
|
||||
value['abstract'] = TagGroup(tag, group).has_no_attributes().text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}subject':
|
||||
authorities = {e.attrib.get('authority') for e in group}
|
||||
for authority in authorities:
|
||||
k = 'subject-{}'.format(authority) if authority is not None else 'subject'
|
||||
sub_group = [e for e in group if e.attrib.get('authority') == authority]
|
||||
value[k] = TagGroup(tag, sub_group).force_singleton().descend(raise_errors)
|
||||
elif tag == '{http://www.loc.gov/mods/v3}topic':
|
||||
TagGroup(tag, group).text_set()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}cartographics':
|
||||
pass
|
||||
elif tag == '{http://www.loc.gov/mods/v3}geographic':
|
||||
TagGroup(tag, group).text_set()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}temporal':
|
||||
TagGroup(tag, group).text_set()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}genre':
|
||||
authorities = {e.attrib.get('authority') for e in group}
|
||||
for authority in authorities:
|
||||
k = 'genre-{}'.format(authority) if authority is not None else 'genre'
|
||||
value[k] = {e.text for e in group if e.attrib.get('authority') == authority}
|
||||
elif tag == '{http://www.loc.gov/mods/v3}language':
|
||||
value["language"] = TagGroup(tag, group) \
|
||||
.merge_sub_tags_to_set()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}languageTerm':
|
||||
value['languageTerm'] = TagGroup(tag, group) \
|
||||
.has_attributes({'authority': 'iso639-2b', 'type': 'code'}) \
|
||||
.text_set()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}scriptTerm':
|
||||
value['scriptTerm'] = TagGroup(tag, group) \
|
||||
.fix_script_term() \
|
||||
.has_attributes({'authority': 'iso15924', 'type': 'code'}) \
|
||||
.text_set()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}relatedItem':
|
||||
pass
|
||||
elif tag == '{http://www.loc.gov/mods/v3}name':
|
||||
for n, e in enumerate(group):
|
||||
value['name{}'.format(n)] = mods_to_dict(e, raise_errors)
|
||||
elif tag == '{http://www.loc.gov/mods/v3}role':
|
||||
value["role"] = TagGroup(tag, group) \
|
||||
.has_no_attributes() \
|
||||
.merge_sub_tags_to_set()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}roleTerm':
|
||||
value['roleTerm'] = TagGroup(tag, group) \
|
||||
.has_attributes({'authority': 'marcrelator', 'type': 'code'}) \
|
||||
.text_set()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}namePart':
|
||||
for e in group:
|
||||
if not e.attrib.get('type'):
|
||||
value['namePart'] = e.text
|
||||
else:
|
||||
value['namePart-{}'.format(e.attrib['type'])] = e.text
|
||||
elif tag == '{http://www.loc.gov/mods/v3}nameIdentifier':
|
||||
# TODO Use this (e.g. <mods:nameIdentifier type="ppn">106168096</mods:nameIdentifier>) or the
|
||||
# mods:name@valueURI to disambiguate
|
||||
pass
|
||||
elif tag == '{http://www.loc.gov/mods/v3}displayForm':
|
||||
value['displayForm'] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}physicalDescription':
|
||||
pass
|
||||
elif tag == '{http://www.loc.gov/mods/v3}extension':
|
||||
pass
|
||||
elif tag == '{http://www.loc.gov/mods/v3}accessCondition':
|
||||
for e in group:
|
||||
if not e.attrib.get('type'):
|
||||
raise ValueError('Unknown attributes for accessCondition {}'.format(e.attrib))
|
||||
value['accessCondition-{}'.format(e.attrib['type'])] = e.text
|
||||
elif tag == '{http://www.loc.gov/mods/v3}typeOfResource':
|
||||
value['typeOfResource'] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
|
||||
elif tag == '{http://www.loc.gov/mods/v3}mods':
|
||||
# XXX Ignore nested mods:mods for now (used in mods:subject)
|
||||
pass
|
||||
else:
|
||||
if raise_errors:
|
||||
raise ValueError('Unknown tag "{}"'.format(tag))
|
||||
else:
|
||||
pass
|
||||
|
||||
return value
|
||||
|
||||
|
||||
def mets_to_dict(mets, raise_errors=True):
|
||||
"""Convert METS metadata to a nested dictionary"""
|
||||
|
||||
# The approach taken here is to handle each element explicitly. This also means that ignored elements are ignored
|
||||
# explicitly.
|
||||
|
||||
value = {}
|
||||
|
||||
# Iterate through each group of tags
|
||||
for tag, group in sorted_groupby(mets, key=attrgetter('tag')):
|
||||
group = list(group)
|
||||
|
||||
# XXX Namespaces seem to use a trailing / sometimes, sometimes not.
|
||||
# (e.g. {http://www.loc.gov/METS/} vs {http://www.loc.gov/METS})
|
||||
if tag == '{http://www.loc.gov/METS/}amdSec':
|
||||
pass # TODO
|
||||
elif tag == '{http://www.loc.gov/METS/}dmdSec':
|
||||
pass # TODO
|
||||
elif tag == '{http://www.loc.gov/METS/}metsHdr':
|
||||
pass # TODO
|
||||
elif tag == '{http://www.loc.gov/METS/}structLink':
|
||||
pass # TODO
|
||||
elif tag == '{http://www.loc.gov/METS/}structMap':
|
||||
pass # TODO
|
||||
elif tag == '{http://www.loc.gov/METS/}fileSec':
|
||||
value['fileSec'] = TagGroup(tag, group) \
|
||||
.is_singleton().descend(raise_errors)
|
||||
elif tag == '{http://www.loc.gov/METS/}fileGrp':
|
||||
for e in group:
|
||||
use = e.attrib.get('USE')
|
||||
if not use:
|
||||
raise ValueError('No USE attribute for fileGrp {}'.format(e))
|
||||
value[f'fileGrp-{use}-count'] = len(e)
|
||||
else:
|
||||
if raise_errors:
|
||||
print(value)
|
||||
raise ValueError('Unknown tag "{}"'.format(tag))
|
||||
else:
|
||||
pass
|
||||
|
||||
return value
|
||||
|
||||
|
||||
@click.command()
|
||||
@click.argument('mets_files', type=click.Path(exists=True), required=True, nargs=-1)
|
||||
@click.option('--output', '-o', 'output_file', type=click.Path(), help='Output pickle file',
|
||||
default='mods_info_df.pkl', show_default=True)
|
||||
@click.option('--output-csv', type=click.Path(), help='Output CSV file')
|
||||
@click.option('--output-xlsx', type=click.Path(), help='Output Excel .xlsx file')
|
||||
def process(mets_files: List[str], output_file: str, output_csv: str, output_xlsx: str):
|
||||
"""
|
||||
A tool to convert the MODS metadata in INPUT to a pandas DataFrame.
|
||||
|
||||
INPUT is assumed to be a METS document with MODS metadata. INPUT may optionally be a directory. The tool then reads
|
||||
all files in the directory.
|
||||
|
||||
modstool writes two output files: A pickled pandas DataFrame and a CSV file with all conversion warnings.
|
||||
"""
|
||||
|
||||
# Extend file list if directories are given
|
||||
mets_files_real = []
|
||||
for m in mets_files:
|
||||
if os.path.isdir(m):
|
||||
logger.info('Scanning directory {}'.format(m))
|
||||
mets_files_real.extend(f.path for f in tqdm(os.scandir(m), leave=False)
|
||||
if f.is_file() and not f.name.startswith('.'))
|
||||
else:
|
||||
mets_files_real.append(m)
|
||||
|
||||
# Process METS files
|
||||
with open(output_file + '.warnings.csv', 'w') as csvfile:
|
||||
csvwriter = csv.writer(csvfile)
|
||||
mods_info = []
|
||||
logger.info('Processing METS files')
|
||||
for mets_file in tqdm(mets_files_real, leave=False):
|
||||
try:
|
||||
root = ET.parse(mets_file).getroot()
|
||||
mets = root # XXX .find('mets:mets', ns) does not work here
|
||||
mods = root.find('mets:dmdSec//mods:mods', ns)
|
||||
|
||||
with warnings.catch_warnings(record=True) as caught_warnings:
|
||||
warnings.simplefilter('always') # do NOT filter double occurrences
|
||||
|
||||
# MODS
|
||||
d = flatten(mods_to_dict(mods, raise_errors=True))
|
||||
# METS
|
||||
d_mets = flatten(mets_to_dict(mets, raise_errors=True))
|
||||
for k, v in d_mets.items():
|
||||
d[f"mets_{k}"] = v
|
||||
# "meta"
|
||||
d['mets_file'] = mets_file
|
||||
|
||||
mods_info.append(d)
|
||||
|
||||
if caught_warnings:
|
||||
# PyCharm thinks caught_warnings is not Iterable:
|
||||
# noinspection PyTypeChecker
|
||||
for caught_warning in caught_warnings:
|
||||
csvwriter.writerow([mets_file, caught_warning.message])
|
||||
except Exception as e:
|
||||
logger.error('Exception in {}: {}'.format(mets_file, e))
|
||||
#import traceback; traceback.print_exc()
|
||||
|
||||
# Convert the mods_info List[Dict] to a pandas DataFrame
|
||||
columns = []
|
||||
for m in mods_info:
|
||||
for c in m.keys():
|
||||
if c not in columns:
|
||||
columns.append(c)
|
||||
data = [[m.get(c) for c in columns] for m in mods_info]
|
||||
index = [m['recordInfo_recordIdentifier'] for m in mods_info] # PPN
|
||||
mods_info_df = pd.DataFrame(data=data, index=index, columns=columns)
|
||||
|
||||
# Pickle the DataFrame
|
||||
logger.info('Writing DataFrame to {}'.format(output_file))
|
||||
mods_info_df.to_pickle(output_file)
|
||||
if output_csv:
|
||||
logger.info('Writing CSV to {}'.format(output_csv))
|
||||
mods_info_df.to_csv(output_csv)
|
||||
if output_xlsx:
|
||||
logger.info('Writing Excel .xlsx to {}'.format(output_xlsx))
|
||||
mods_info_df.to_excel(output_xlsx)
|
||||
|
||||
|
||||
def main():
|
||||
logging.basicConfig(level=logging.INFO)
|
||||
|
||||
for prefix, uri in ns.items():
|
||||
ET.register_namespace(prefix, uri)
|
||||
|
||||
process()
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
main()
|
||||
Loading…
Add table
Add a link
Reference in a new issue