Merge branch 'feat/alto'
commit
a2fb3ee387
@ -1 +0,0 @@
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from .modstool import *
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@ -0,0 +1,202 @@
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#!/usr/bin/env python3
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import csv
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import logging
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import os
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import re
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import warnings
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import sys
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from xml.dom.expatbuilder import Namespaces
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from lxml import etree as ET
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from itertools import groupby
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from operator import attrgetter
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from typing import List
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from collections.abc import MutableMapping, Sequence
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import click
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import pandas as pd
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import numpy as np
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from tqdm import tqdm
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from .lib import TagGroup, sorted_groupby, flatten, ns
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logger = logging.getLogger('alto4pandas')
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def alto_to_dict(alto, raise_errors=True):
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"""Convert ALTO metadata to a nested dictionary"""
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value = {}
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# Iterate through each group of tags
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for tag, group in sorted_groupby(alto, key=attrgetter('tag')):
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group = list(group)
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localname = ET.QName(tag).localname
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if localname == 'Description':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().descend(raise_errors)
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elif localname == 'MeasurementUnit':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
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elif localname == 'OCRProcessing':
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value[localname] = TagGroup(tag, group).is_singleton().descend(raise_errors)
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elif localname == 'Processing':
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# TODO This enumerated descent is used more than once, DRY!
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for n, e in enumerate(group):
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value[f'{localname}{n}'] = alto_to_dict(e, raise_errors)
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elif localname == 'ocrProcessingStep':
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for n, e in enumerate(group):
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value[f'{localname}{n}'] = alto_to_dict(e, raise_errors)
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elif localname == 'preProcessingStep':
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for n, e in enumerate(group):
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value[f'{localname}{n}'] = alto_to_dict(e, raise_errors)
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elif localname == 'processingDateTime':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
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elif localname == 'processingSoftware':
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value[localname] = TagGroup(tag, group).is_singleton().descend(raise_errors)
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elif localname == 'processingAgency':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
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elif localname == 'processingStepDescription':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
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elif localname == 'processingStepSettings':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
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elif localname == 'softwareCreator':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
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elif localname == 'softwareName':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
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elif localname == 'softwareVersion':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
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elif localname == 'sourceImageInformation':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().descend(raise_errors)
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elif localname == 'fileName':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text()
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elif localname == 'Layout':
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value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().descend(raise_errors)
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elif localname == 'Page':
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alto_namespace = ET.QName(group[0]).namespace
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namespaces={"alto": alto_namespace}
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value[localname] = {}
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value[localname].update(TagGroup(tag, group).is_singleton().attributes())
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value[localname].update(TagGroup(tag, group).subelement_counts())
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value[localname].update(TagGroup(tag, group).xpath_statistics("//alto:String/@WC", namespaces))
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elif localname == 'Styles':
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pass
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elif localname == 'Tags':
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pass
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else:
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if raise_errors:
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print(value)
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raise ValueError('Unknown tag "{}"'.format(tag))
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else:
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pass
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return value
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def walk(m):
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# XXX do this in modstool, too
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if os.path.isdir(m):
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tqdm.write(f'Scanning directory {m}')
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for f in tqdm(os.scandir(m), leave=False):
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if f.is_file() and not f.name.startswith('.'):
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yield f.path
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elif f.is_dir():
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try:
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yield from walk(f.path)
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except PermissionError:
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warnings.warn(f"Error walking {f.path}")
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else:
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yield m.path
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@click.command()
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@click.argument('alto_files', type=click.Path(exists=True), required=True, nargs=-1)
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@click.option('--output', '-o', 'output_file', type=click.Path(), help='Output pickle file',
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default='alto_info_df.pkl', show_default=True)
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@click.option('--output-csv', type=click.Path(), help='Output CSV file')
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@click.option('--output-xlsx', type=click.Path(), help='Output Excel .xlsx file')
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def process(alto_files: List[str], output_file: str, output_csv: str, output_xlsx: str):
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"""
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A tool to convert the ALTO metadata in INPUT to a pandas DataFrame.
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INPUT is assumed to be a ALTO document. INPUT may optionally be a directory. The tool then reads
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all files in the directory.
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alto4pandas writes two output files: A pickled pandas DataFrame and a CSV file with all conversion warnings.
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"""
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# Extend file list if directories are given
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alto_files_real = []
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for m in alto_files:
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for x in walk(m):
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alto_files_real.append(x)
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# Process ALTO files
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with open(output_file + '.warnings.csv', 'w') as csvfile:
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csvwriter = csv.writer(csvfile)
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alto_info = []
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logger.info('Processing ALTO files')
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for alto_file in tqdm(alto_files_real, leave=False):
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try:
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root = ET.parse(alto_file).getroot()
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alto = root # XXX .find('alto:alto', ns) does not work here
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with warnings.catch_warnings(record=True) as caught_warnings:
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warnings.simplefilter('always') # do NOT filter double occurrences
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# ALTO
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d = flatten(alto_to_dict(alto, raise_errors=True))
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# "meta"
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d['alto_file'] = alto_file
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d['alto_xmlns'] = ET.QName(alto).namespace
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alto_info.append(d)
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if caught_warnings:
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# PyCharm thinks caught_warnings is not Iterable:
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# noinspection PyTypeChecker
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for caught_warning in caught_warnings:
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csvwriter.writerow([alto_file, caught_warning.message])
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except Exception as e:
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logger.error('Exception in {}: {}'.format(alto_file, e))
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import traceback; traceback.print_exc()
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# Convert the alto_info List[Dict] to a pandas DataFrame
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columns = []
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for m in alto_info:
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for c in m.keys():
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if c not in columns:
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columns.append(c)
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data = [[m.get(c) for c in columns] for m in alto_info]
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index = [m['alto_file'] for m in alto_info] # TODO use ppn + page?
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alto_info_df = pd.DataFrame(data=data, index=index, columns=columns)
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# Pickle the DataFrame
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logger.info('Writing DataFrame to {}'.format(output_file))
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alto_info_df.to_pickle(output_file)
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if output_csv:
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logger.info('Writing CSV to {}'.format(output_csv))
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alto_info_df.to_csv(output_csv)
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if output_xlsx:
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logger.info('Writing Excel .xlsx to {}'.format(output_xlsx))
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alto_info_df.to_excel(output_xlsx)
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def main():
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logging.basicConfig(level=logging.INFO)
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for prefix, uri in ns.items():
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ET.register_namespace(prefix, uri)
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process()
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if __name__ == '__main__':
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main()
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@ -0,0 +1,285 @@
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from itertools import groupby
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import re
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import warnings
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from typing import List, Sequence, MutableMapping
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import numpy as np
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from lxml import etree as ET
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__all__ = ["ns"]
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ns = {
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'mets': 'http://www.loc.gov/METS/',
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'mods': 'http://www.loc.gov/mods/v3',
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"alto": "http://www.loc.gov/standards/alto/ns-v2"
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}
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class TagGroup:
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"""Helper class to simplify the parsing and checking of MODS metadata"""
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def __init__(self, tag, group: List[ET.Element]):
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self.tag = tag
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self.group = group
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def __str__(self):
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return '\n'.join(str(ET.tostring(e), 'utf-8').strip() for e in self.group)
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def is_singleton(self):
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if len(self.group) != 1:
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raise ValueError('More than one instance: {}'.format(self))
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return self
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def has_no_attributes(self):
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return self.has_attributes({})
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def has_attributes(self, attrib):
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if not isinstance(attrib, Sequence):
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attrib = [attrib]
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if not all(e.attrib in attrib for e in self.group):
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raise ValueError('One or more element has unexpected attributes: {}'.format(self))
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return self
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def ignore_attributes(self):
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# This serves as documentation for now.
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return self
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def sort(self, key=None, reverse=False):
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self.group = sorted(self.group, key=key, reverse=reverse)
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return self
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def text(self, separator='\n'):
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t = ''
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for e in self.group:
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if t != '':
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t += separator
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if e.text:
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t += e.text
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return t
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def text_set(self):
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return {e.text for e in self.group}
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def descend(self, raise_errors):
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return _to_dict(self.is_singleton().group[0], raise_errors)
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def filter(self, cond, warn=None):
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new_group = []
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for e in self.group:
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if cond(e):
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new_group.append(e)
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else:
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if warn:
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warnings.warn('Filtered {} element ({})'.format(self.tag, warn))
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return TagGroup(self.tag, new_group)
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def force_singleton(self, warn=True):
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if len(self.group) == 1:
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return self
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else:
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if warn:
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warnings.warn('Forced single instance of {}'.format(self.tag))
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return TagGroup(self.tag, self.group[:1])
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RE_ISO8601_DATE = r'^\d{2}(\d{2}|XX)(-\d{2}-\d{2})?$' # Note: Includes non-specific century dates like '18XX'
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RE_GERMAN_DATE = r'^(?P<dd>\d{2})\.(?P<mm>\d{2})\.(?P<yyyy>\d{4})$'
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def fix_date(self):
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for e in self.group:
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if e.attrib.get('encoding') == 'w3cdtf':
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# This should be 'iso8601' according to MODS-AP 2.3.1
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warnings.warn('Changed w3cdtf encoding to iso8601')
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e.attrib['encoding'] = 'iso8601'
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new_group = []
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for e in self.group:
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if e.attrib.get('encoding') == 'iso8601' and re.match(self.RE_ISO8601_DATE, e.text):
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new_group.append(e)
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elif re.match(self.RE_ISO8601_DATE, e.text):
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warnings.warn('Added iso8601 encoding to date {}'.format(e.text))
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e.attrib['encoding'] = 'iso8601'
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new_group.append(e)
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elif re.match(self.RE_GERMAN_DATE, e.text):
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warnings.warn('Converted date {} to iso8601 encoding'.format(e.text))
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m = re.match(self.RE_GERMAN_DATE, e.text)
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e.text = '{}-{}-{}'.format(m.group('yyyy'), m.group('mm'), m.group('dd'))
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e.attrib['encoding'] = 'iso8601'
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new_group.append(e)
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else:
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warnings.warn('Not a iso8601 date: "{}"'.format(e.text))
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new_group.append(e)
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self.group = new_group
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# Notes:
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# - There are dates with the misspelled qualifier 'aproximate'
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# - Rough periods are sometimes given either by:
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# - years like '19xx'
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# - or 'approximate' date ranges with point="start"/"end" attributes set
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# (this could be correct according to MODS-AP 2.3.1)
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# - Some very specific dates like '06.08.1820' are sometimes given the 'approximate' qualifier
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# - Sometimes, approximate date ranges are given in the text "1785-1800 (ca.)"
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return self
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def fix_event_type(self):
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# According to MODS-AP 2.3.1, every originInfo should have its eventType set.
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# Fix this for special cases.
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for e in self.group:
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if e.attrib.get('eventType') is None:
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try:
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if e.find('mods:publisher', ns).text.startswith('Staatsbibliothek zu Berlin') and \
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e.find('mods:edition', ns).text == '[Electronic ed.]':
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e.attrib['eventType'] = 'digitization'
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warnings.warn('Fixed eventType for electronic ed.')
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continue
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except AttributeError:
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pass
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try:
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if e.find('mods:dateIssued', ns) is not None:
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e.attrib['eventType'] = 'publication'
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warnings.warn('Fixed eventType for an issued origin')
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continue
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except AttributeError:
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pass
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try:
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if e.find('mods:dateCreated', ns) is not None:
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e.attrib['eventType'] = 'production'
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warnings.warn('Fixed eventType for a created origin')
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continue
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except AttributeError:
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pass
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return self
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def fix_script_term(self):
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for e in self.group:
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# MODS-AP 2.3.1 is not clear about this, but it looks like that this should be lower case.
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if e.attrib['authority'] == 'ISO15924':
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e.attrib['authority'] = 'iso15924'
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warnings.warn('Changed scriptTerm authority to lower case')
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return self
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def merge_sub_tags_to_set(self):
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from .modstool import mods_to_dict
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value = {}
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sub_dicts = [mods_to_dict(e) for e in self.group]
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sub_tags = {k for d in sub_dicts for k in d.keys()}
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for sub_tag in sub_tags:
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s = set()
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for d in sub_dicts:
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v = d.get(sub_tag)
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if v:
|
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# There could be multiple scriptTerms in one language element, e.g. Antiqua and Fraktur in a
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||||
# German language document.
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||||
if isinstance(v, set):
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||||
s.update(v)
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||||
else:
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||||
s.add(v)
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||||
value[sub_tag] = s
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||||
return value
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||||
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||||
def attributes(self):
|
||||
"""
|
||||
Return a merged dict of all attributes of the tag group.
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||||
|
||||
Probably most useful if used on a singleton, for example:
|
||||
|
||||
value['Page'] = TagGroup(tag, group).is_singleton().attributes()
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||||
"""
|
||||
attrib = {}
|
||||
for e in self.group:
|
||||
for a, v in e.attrib.items():
|
||||
a_localname = ET.QName(a).localname
|
||||
attrib[a_localname] = v
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||||
return attrib
|
||||
|
||||
def subelement_counts(self):
|
||||
counts = {}
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||||
for e in self.group:
|
||||
for x in e.iter():
|
||||
tag = ET.QName(x.tag).localname
|
||||
key = f"{tag}-count"
|
||||
counts[key] = counts.get(key, 0) + 1
|
||||
return counts
|
||||
|
||||
def xpath_statistics(self, xpath_expr, namespaces):
|
||||
"""
|
||||
Extract values and calculate statistics
|
||||
|
||||
Extract values using the given XPath expression, convert them to float and return descriptive
|
||||
statistics on the values.
|
||||
"""
|
||||
values = []
|
||||
for e in self.group:
|
||||
r = e.xpath(xpath_expr, namespaces=namespaces)
|
||||
values += r
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||||
values = np.array([float(v) for v in values])
|
||||
|
||||
statistics = {}
|
||||
if values.size > 0:
|
||||
statistics[f'{xpath_expr}-mean'] = np.mean(values)
|
||||
statistics[f'{xpath_expr}-median'] = np.median(values)
|
||||
statistics[f'{xpath_expr}-std'] = np.std(values)
|
||||
statistics[f'{xpath_expr}-min'] = np.min(values)
|
||||
statistics[f'{xpath_expr}-max'] = np.max(values)
|
||||
return statistics
|
||||
|
||||
|
||||
|
||||
|
||||
def sorted_groupby(iterable, key=None):
|
||||
"""
|
||||
Sort iterable by key and then group by the same key.
|
||||
|
||||
itertools.groupby() assumes that the iterable is already sorted. This function
|
||||
conveniently sorts the iterable first, and then groups its elements.
|
||||
"""
|
||||
return groupby(sorted(iterable, key=key), key=key)
|
||||
|
||||
|
||||
def _to_dict(root, raise_errors):
|
||||
from .modstool import mods_to_dict, mets_to_dict
|
||||
from .alto4pandas import alto_to_dict
|
||||
|
||||
root_name = ET.QName(root.tag)
|
||||
if root_name.namespace == "http://www.loc.gov/mods/v3":
|
||||
return mods_to_dict(root, raise_errors)
|
||||
elif root_name.namespace == "http://www.loc.gov/METS/":
|
||||
return mets_to_dict(root, raise_errors)
|
||||
elif root_name.namespace in [
|
||||
"http://schema.ccs-gmbh.com/ALTO",
|
||||
"http://www.loc.gov/standards/alto/",
|
||||
"http://www.loc.gov/standards/alto/ns-v2#",
|
||||
"http://www.loc.gov/standards/alto/ns-v4#",
|
||||
]:
|
||||
return alto_to_dict(root, raise_errors)
|
||||
else:
|
||||
raise ValueError(f"Unknown namespace {root_name.namespace}")
|
||||
|
||||
|
||||
def flatten(d: MutableMapping, parent='', separator='_'):
|
||||
"""
|
||||
Flatten the given nested dict.
|
||||
|
||||
It is assumed that d maps strings to either another dictionary (similarly structured) or some other value.
|
||||
"""
|
||||
items = []
|
||||
|
||||
for k, v in d.items():
|
||||
if parent:
|
||||
new_key = parent + separator + k
|
||||
else:
|
||||
new_key = k
|
||||
|
||||
if isinstance(v, MutableMapping):
|
||||
items.extend(flatten(v, new_key, separator=separator).items())
|
||||
else:
|
||||
items.append((new_key, v))
|
||||
|
||||
return dict(items)
|
||||
|
||||
@ -0,0 +1,39 @@
|
||||
import xml.etree.ElementTree as ET
|
||||
|
||||
|
||||
from qurator.modstool.alto4pandas import alto_to_dict
|
||||
from qurator.modstool.lib import flatten
|
||||
|
||||
|
||||
def dict_fromstring(x):
|
||||
return flatten(alto_to_dict(ET.fromstring(x)))
|
||||
|
||||
def test_Page_counts():
|
||||
"""
|
||||
Elements below Layout/Page should be counted
|
||||
"""
|
||||
d = dict_fromstring("""
|
||||
<alto xmlns="http://www.loc.gov/standards/alto/ns-v2#">
|
||||
<Layout>
|
||||
<Page ID="Page1" PHYSICAL_IMG_NR="1">
|
||||
<TextBlock ID="Page1_Block1">
|
||||
<TextLine>
|
||||
<String STYLE="bold" WC="0.8937500119" CONTENT="Staatsbibliothek" />
|
||||
</TextLine>
|
||||
<TextLine>
|
||||
<String STYLE="bold" WC="0.8899999857" CONTENT="zu" />
|
||||
<String STYLE="bold" WC="0.9866666794" CONTENT="Berlin" />
|
||||
</TextLine>
|
||||
<TextLine>
|
||||
<String STYLE="bold" WC="1." CONTENT="WM" />
|
||||
<String STYLE="bold" WC="0.8927272558" CONTENT="Preußischer" />
|
||||
<String STYLE="bold" WC="0.9058333039" CONTENT="Kulturbesitz" />
|
||||
</TextLine>
|
||||
</TextBlock>
|
||||
</Page>
|
||||
</Layout>
|
||||
</alto>
|
||||
""")
|
||||
assert d['Layout_Page_TextBlock-count'] == 1
|
||||
assert d['Layout_Page_TextLine-count'] == 3
|
||||
assert d['Layout_Page_String-count'] == 6
|
||||
@ -0,0 +1 @@
|
||||
pytest
|
||||
Loading…
Reference in New Issue