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#!/usr/bin/env python3
"""
NB: adapted to work as a library for PDF extraction. Will probably be
re-written eventually to be correct, complete, and robust; this is just a
first iteration.
This script tries to extract everything from a GROBID TEI XML fulltext dump:
- header metadata
- affiliations
- references (with context)
- abstract
- fulltext
- tables, figures, equations
A flag can be specified to disable copyright encumbered bits (--no-emcumbered):
- abstract
- fulltext
- tables, figures, equations
Prints JSON to stdout, errors to stderr
"""
import io
import json
import argparse
import xml.etree.ElementTree as ET
ns = "http://www.tei-c.org/ns/1.0"
def all_authors(elem):
names = []
for author in elem.findall('.//{%s}author' % ns):
pn = author.find('./{%s}persName' % ns)
if not pn:
continue
given_name = pn.findtext('./{%s}forename' % ns) or None
surname = pn.findtext('./{%s}surname' % ns) or None
full_name = ' '.join(pn.itertext())
obj = dict(name=full_name, given_name=given_name, surname=surname)
ae = author.find('./{%s}affiliation' % ns)
if ae:
affiliation = dict()
for on in ae.findall('./{%s}orgName' % ns):
affiliation[on.get('type')] = on.text
addr_e = ae.find('./{%s}address' % ns)
if addr_e:
address = dict()
for t in addr_e.getchildren():
address[t.tag.split('}')[-1]] = t.text
if address:
affiliation['address'] = address
#affiliation['address'] = {
# 'post_code': addr.findtext('./{%s}postCode' % ns) or None,
# 'settlement': addr.findtext('./{%s}settlement' % ns) or None,
# 'country': addr.findtext('./{%s}country' % ns) or None,
#}
obj['affiliation'] = affiliation
names.append(obj)
return names
def journal_info(elem):
journal = dict()
journal['name'] = elem.findtext('.//{%s}monogr/{%s}title' % (ns, ns))
journal['publisher'] = elem.findtext('.//{%s}publicationStmt/{%s}publisher' % (ns, ns))
if journal['publisher'] == '':
journal['publisher'] = None
journal['issn'] = elem.findtext('.//{%s}idno[@type="ISSN"]' % ns)
journal['eissn'] = elem.findtext('.//{%s}idno[@type="eISSN"]' % ns)
journal['volume'] = elem.findtext('.//{%s}biblScope[@unit="volume"]' % ns)
journal['issue'] = elem.findtext('.//{%s}biblScope[@unit="issue"]' % ns)
return journal
def biblio_info(elem):
ref = dict()
ref['id'] = elem.attrib.get('{http://www.w3.org/XML/1998/namespace}id')
# Title stuff is messy in references...
ref['title'] = elem.findtext('.//{%s}analytic/{%s}title' % (ns, ns))
other_title = elem.findtext('.//{%s}monogr/{%s}title' % (ns, ns))
if other_title:
if ref['title']:
ref['journal'] = other_title
else:
ref['journal'] = None
ref['title'] = other_title
ref['authors'] = all_authors(elem)
ref['publisher'] = elem.findtext('.//{%s}publicationStmt/{%s}publisher' % (ns, ns))
if ref['publisher'] == '':
ref['publisher'] = None
date = elem.find('.//{%s}date[@type="published"]' % ns)
ref['date'] = (date != None) and date.attrib.get('when')
ref['volume'] = elem.findtext('.//{%s}biblScope[@unit="volume"]' % ns)
ref['issue'] = elem.findtext('.//{%s}biblScope[@unit="issue"]' % ns)
el = elem.find('.//{%s}ptr[@target]' % ns)
if el is not None:
ref['url'] = el.attrib['target']
# Hand correction
if ref['url'].endswith(".Lastaccessed"):
ref['url'] = ref['url'].replace(".Lastaccessed", "")
else:
ref['url'] = None
return ref
def teixml2json(content, encumbered=True):
if type(content) == str:
content = io.StringIO(content)
elif type(content) == bytes:
content = io.BytesIO(content)
info = dict()
#print(content)
#print(content.getvalue())
tree = ET.parse(content)
tei = tree.getroot()
header = tei.find('.//{%s}teiHeader' % ns)
if header is None:
raise ValueError("XML does not look like TEI format")
application_tag = header.findall('.//{%s}appInfo/{%s}application' % (ns, ns))[0]
info['grobid_version'] = application_tag.attrib['version']
info['grobid_timestamp'] = application_tag.attrib['when']
info['title'] = header.findtext('.//{%s}analytic/{%s}title' % (ns, ns))
info['authors'] = all_authors(header.find('.//{%s}sourceDesc/{%s}biblStruct' % (ns, ns)))
info['journal'] = journal_info(header)
date = header.find('.//{%s}date[@type="published"]' % ns)
info['date'] = (date != None) and date.attrib.get('when')
info['fatcat_release'] = header.findtext('.//{%s}idno[@type="fatcat"]' % ns)
info['doi'] = header.findtext('.//{%s}idno[@type="DOI"]' % ns)
if info['doi']:
info['doi'] = info['doi'].lower()
refs = []
for (i, bs) in enumerate(tei.findall('.//{%s}listBibl/{%s}biblStruct' % (ns, ns))):
ref = biblio_info(bs)
ref['index'] = i
refs.append(ref)
info['citations'] = refs
if encumbered:
el = tei.find('.//{%s}profileDesc/{%s}abstract' % (ns, ns))
info['abstract'] = (el or None) and " ".join(el.itertext()).strip()
el = tei.find('.//{%s}text/{%s}body' % (ns, ns))
info['body'] = (el or None) and " ".join(el.itertext()).strip()
el = tei.find('.//{%s}back/{%s}div[@type="acknowledgement"]' % (ns, ns))
info['acknowledgement'] = (el or None) and " ".join(el.itertext()).strip()
el = tei.find('.//{%s}back/{%s}div[@type="annex"]' % (ns, ns))
info['annex'] = (el or None) and " ".join(el.itertext()).strip()
return info
def main(): # pragma no cover
parser = argparse.ArgumentParser(
description="GROBID TEI XML to JSON",
usage="%(prog)s [options] <teifile>...")
parser.add_argument("--no-encumbered",
action="store_true",
help="don't include ambiguously copyright encumbered fields (eg, abstract, body)")
parser.add_argument("teifiles", nargs='+')
args = parser.parse_args()
for filename in args.teifiles:
content = open(filename, 'r')
print(json.dumps(
teixml2json(content,
encumbered=(not args.no_encumbered))))
if __name__=='__main__': # pragma no cover
main()
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