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mc2skos.py
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mc2skos.py
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#!/usr/bin/env python
# encoding=utf8
#
# Script to convert MARC 21 Classification records
# (serialized as MARCXML) to SKOS concepts. See
# README.md for more information.
import sys
import re
import time
import warnings
from datetime import datetime
from iso639 import languages
import argparse
from rdflib.namespace import OWL, RDF, SKOS, DCTERMS, XSD, Namespace
from rdflib import URIRef, Literal, Graph, BNode
from otsrdflib import OrderedTurtleSerializer
import json
import rdflib_jsonld.serializer as json_ld
import pkg_resources
import skosify
import logging
import logging.handlers
from . import __version__
from .constants import Constants
from .element import Element
from .record import InvalidRecordError, ClassificationRecord, AuthorityRecord
from .reader import MarcFileReader
from .vocabularies import Vocabularies
logging.captureWarnings(True)
warnings.simplefilter('always', DeprecationWarning)
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
formatter = logging.Formatter('[%(asctime)s %(levelname)s] %(message)s')
console_handler = logging.StreamHandler()
console_handler.setLevel(logging.DEBUG)
console_handler.setFormatter(formatter)
logger.addHandler(console_handler)
WD = Namespace('http://data.ub.uio.no/webdewey-terms#')
MADS = Namespace('http://www.loc.gov/mads/rdf/v1#')
def add_record_to_graph(graph, record, options):
# Add record to graph
# logger.debug('Adding: %s', record.uri)
# Strictly, we do not need to explicitly state here that <A> and <B> are instances
# of skos:Concept, because such statements are entailed by the definition
# of skos:semanticRelation.
record_uri = URIRef(record.uri)
graph.add((record_uri, RDF.type, SKOS.Concept))
# Add skos:topConceptOf or skos:inScheme
for scheme_uri in record.scheme_uris:
if record.is_top_concept:
graph.add((record_uri, SKOS.topConceptOf, URIRef(scheme_uri)))
else:
graph.add((record_uri, SKOS.inScheme, URIRef(scheme_uri)))
if record.created is not None:
graph.add((record_uri, DCTERMS.created, Literal(record.created.strftime('%F'), datatype=XSD.date)))
if record.modified is not None:
graph.add((record_uri, DCTERMS.modified, Literal(record.modified.strftime('%F'), datatype=XSD.date)))
# Add classification number as skos:notation
if record.notation:
if record.record_type == Constants.TABLE_RECORD: # OBS! Sjekk add tables
graph.add((record_uri, SKOS.notation, Literal('T' + record.notation)))
else:
graph.add((record_uri, SKOS.notation, Literal(record.notation)))
# Add local control number as dcterms:identifier
if record.control_number:
graph.add((record_uri, DCTERMS.identifier, Literal(record.control_number)))
# Add caption as skos:prefLabel
if record.prefLabel:
graph.add((record_uri, SKOS.prefLabel, Literal(record.prefLabel, lang=record.lang)))
elif options.get('include_webdewey') and len(record.altLabel) != 0:
# If the --webdewey flag is set, we will use the first index term as prefLabel
caption = record.altLabel.pop(0)['term']
if len(record.altLabel) != 0:
caption = caption + ', …'
graph.add((record_uri, SKOS.prefLabel, Literal(caption, lang=record.lang)))
# Add index terms as skos:altLabel
if options.get('include_altlabels'):
for label in record.altLabel:
graph.add((record_uri, SKOS.altLabel, Literal(label['term'], lang=record.lang)))
# Add relations (SKOS:broader, SKOS:narrower, SKOS:xxxMatch, etc.)
for relation in record.relations:
if relation.get('uri') is not None:
graph.add((record_uri, relation.get('relation'), URIRef(relation['uri'])))
# Add notes
if not options.get('exclude_notes'):
for note in record.definition:
graph.add((record_uri, SKOS.definition, Literal(note, lang=record.lang)))
for note in record.note:
graph.add((record_uri, SKOS.note, Literal(note, lang=record.lang)))
for note in record.editorialNote:
graph.add((record_uri, SKOS.editorialNote, Literal(note, lang=record.lang)))
for note in record.scopeNote:
graph.add((record_uri, SKOS.scopeNote, Literal(note, lang=record.lang)))
for note in record.historyNote:
graph.add((record_uri, SKOS.historyNote, Literal(note, lang=record.lang)))
for note in record.changeNote:
graph.add((record_uri, SKOS.changeNote, Literal(note, lang=record.lang)))
for note in record.example:
graph.add((record_uri, SKOS.example, Literal(note, lang=record.lang)))
# Deprecated?
if record.deprecated:
graph.add((record_uri, OWL.deprecated, Literal(True)))
# Add synthesized number components
if options.get('include_components') and len(record.components) != 0:
component = record.components.pop(0)
component_uri = URIRef(record.scheme.uri('concept', collection='class', object=component))
b1 = BNode()
graph.add((record_uri, MADS.componentList, b1))
graph.add((b1, RDF.first, component_uri))
for component in record.components:
component_uri = URIRef(record.scheme.uri('concept', collection='class', object=component))
b2 = BNode()
graph.add((b1, RDF.rest, b2))
graph.add((b2, RDF.first, component_uri))
b1 = b2
graph.add((b1, RDF.rest, RDF.nil))
# Add webDewey extras
if options.get('include_webdewey'):
for key, values in record.webDeweyExtras.items():
for value in values:
graph.add((record_uri, WD[key], Literal(value, lang=record.lang)))
def process_record(graph, rec, **kwargs):
"""Convert a single MARC21 classification or authority record to RDF."""
el = Element(rec)
leader = el.text('mx:leader')
if leader is None:
raise InvalidRecordError('Record does not have a leader',
control_number=el.text('mx:controlfield[@tag="001"]'))
if leader[6] == 'w':
if kwargs.get('skip_classification'):
return
rec = ClassificationRecord(el, kwargs)
elif leader[6] == 'z':
if kwargs.get('skip_authority'):
return
rec = AuthorityRecord(el, kwargs)
else:
raise InvalidRecordError('Record is not a Marc21 Classification or Authority record',
control_number=el.text('mx:controlfield[@tag="001"]'))
if rec.is_public():
add_record_to_graph(graph, rec, kwargs)
def process_records(records, graph=None, **options):
n = 0
if graph is None:
graph = Graph()
for record in records:
n += 1
try:
process_record(graph, record, **options)
except InvalidRecordError as e:
record_id = e.control_number or '#%d' % n
logger.warning('Ignoring record %s: %s', record_id, e)
if options.get('expand'):
logger.info('Expanding RDF via basic SKOS inference')
skosify.infer.skos_related(graph)
skosify.infer.skos_topConcept(graph)
skosify.infer.skos_hierarchical(graph, narrower=True)
if options.get('skosify'):
logger.info('Running Skosify with config file %s', options['skosify'])
config = skosify.config(options['skosify'])
graph = skosify.skosify(graph, **config)
return graph
def main():
parser = argparse.ArgumentParser(description='Convert MARC21 Classification to SKOS/RDF')
parser.add_argument('infile', nargs='?', help='Input XML file')
parser.add_argument('outfile', nargs='?', help='Output RDF file')
parser.add_argument('--version', action='version', version='%(prog)s ' + __version__)
parser.add_argument('-v', '--verbose', dest='verbose', action='store_true', help='More verbose output')
parser.add_argument('-o', '--outformat', dest='outformat', metavar='FORMAT', nargs='?',
help='Output format: turtle (default), jskos, or ndjson')
parser.add_argument('--include', action='append', dest='include', default=[],
help='RDF file(s) to include in the output (e.g. to define a concept scheme). '
'Must be the same format as {outformat}.')
parser.add_argument('--uri', dest='base_uri', help='Concept URI template. See vocabularies.yml for examples.')
parser.add_argument('--scheme', dest='scheme',
help='Concept scheme, either an URI or a key from vocabularies.yml (For a list: mc2skos --list).')
parser.add_argument('--whitespace', dest='whitespace', metavar='STRING',
help='Replace whitespaces in URI templates with this.')
parser.add_argument('--altlabels', '--indexterms', dest='altlabels', action='store_true',
help='Include altlabels (from 7XX or 4XX).')
parser.add_argument('--notes', dest='notes', action='store_true',
help='Include note fields (DEPRECATED as including notes is now the default).')
parser.add_argument('--exclude_notes', dest='exclude_notes', action='store_true',
help='Exclude note fields.')
parser.add_argument('--components', dest='components', action='store_true',
help='Include component information from 765.')
parser.add_argument('--webdewey', dest='webdewey', action='store_true',
help='Include non-standard WebDewey notes from 680.')
parser.add_argument('--skip-classification', dest='skip_classification', action='store_true',
help='Skip classification records')
parser.add_argument('--skip-authority', dest='skip_authority', action='store_true',
help='Skip authority records')
parser.add_argument('--expand', dest='expand', action='store_true',
help='Use Skosify to infer skos:hasTopConcept, skos:narrower and skos:related')
parser.add_argument('--skosify', dest='skosify',
help='Run Skosify with given configuration file')
parser.add_argument('-l', '--list-schemes', dest='list_schemes', action='store_true',
help='List default concept schemes.')
args = parser.parse_args()
if args.notes:
warnings.warn('--notes is deprecated as including notes is now the default. '
'The inverse option --exclude_notes has been added to exclude notes.',
DeprecationWarning)
with pkg_resources.resource_stream(__name__, 'vocabularies.yml') as fp:
vocabularies = Vocabularies()
vocabularies.load_yaml(fp)
vocabularies.set_default_scheme(
generic=args.base_uri,
scheme=args.scheme,
whitespace=args.whitespace
)
if args.list_schemes:
print('Schemes:')
for voc in vocabularies:
print('- %s' % voc)
return
supported_formats = ['turtle', 'jskos', 'ndjson']
if not args.outformat and args.outfile:
ext = args.outfile.rpartition('.')[-1]
if ext in supported_formats:
args.outformat = ext
if not args.outformat:
args.outformat = 'turtle'
elif args.outformat not in supported_formats:
raise ValueError("Format not supported, must be one of '%s'." % "', '".join(supported_formats))
graph = Graph()
for filename in args.include:
if args.outformat == 'turtle':
graph.load(filename, format='turtle')
else:
graph.load(filename, format='json-ld')
nm = graph.namespace_manager
nm.bind('dcterms', DCTERMS)
nm.bind('skos', SKOS)
nm.bind('wd', WD)
nm.bind('mads', MADS)
nm.bind('owl', OWL)
if args.verbose:
console_handler.setLevel(logging.DEBUG)
else:
console_handler.setLevel(logging.INFO)
if args.infile is None:
raise ValueError('Filename not specified')
options = {
'include_altlabels': args.altlabels,
'exclude_notes': args.exclude_notes,
'include_components': args.components,
'include_webdewey': args.webdewey,
'skip_classification': args.skip_classification,
'skip_authority': args.skip_authority,
'expand': args.expand,
'skosify': args.skosify,
'vocabularies': vocabularies
}
marc = MarcFileReader(args.infile)
graph = process_records(marc.records(), graph, **options)
if not graph:
logger.warning('RDF result is empty!')
return
if args.outfile and args.outfile != '-':
out_file = open(args.outfile, 'wb')
else:
if (sys.version_info > (3, 0)):
out_file = sys.stdout.buffer
else:
out_file = sys.stdout
if args.outformat == 'turtle':
# @TODO: Perhaps use OrderedTurtleSerializer if available, but fallback to default Turtle serializer if not?
serializer = OrderedTurtleSerializer(graph)
serializer.class_order = [
SKOS.ConceptScheme,
SKOS.Concept,
]
serializer.sorters = [
(r'/([0-9A-Z\-]+)--([0-9.\-;:]+)/e', lambda x: 'C{}--{}'.format(x[0], x[1])), # table numbers
(r'/([0-9.\-;:]+)/e', lambda x: 'B' + x[0]), # standard schedule numbers
(r'^(.+)$', lambda x: 'A' + x[0]), # fallback
]
serializer.serialize(out_file)
elif args.outformat in ['jskos', 'ndjson']:
s = pkg_resources.resource_string(__name__, 'jskos-context.json').decode('utf-8')
context = json.loads(s)
jskos = json_ld.from_rdf(graph, context)
if args.outformat == 'jskos':
jskos['@context'] = u'https://gbv.github.io/jskos/context.json'
out_file.write(json.dumps(jskos, sort_keys=True, indent=2).encode('utf-8'))
else:
for record in jskos['@graph'] if '@graph' in jskos else [jskos]:
record['@context'] = u'https://gbv.github.io/jskos/context.json'
out_file.write(json.dumps(record, sort_keys=True).encode('utf-8') + b'\n')
if args.outfile and args.outfile != '-':
logger.info('Wrote %s: %s' % (args.outformat, args.outfile))