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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 argparse
import io
import json
import xml.etree.ElementTree as ET
from typing import Any, AnyStr, Dict, List, Optional
xml_ns = "http://www.w3.org/XML/1998/namespace"
ns = "http://www.tei-c.org/ns/1.0"
def all_authors(elem: Optional[ET.Element]) -> List[Dict[str, Any]]:
if not elem:
return []
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[str, Any] = dict(name=full_name)
if given_name:
obj["given_name"] = given_name
if surname:
obj["surname"] = surname
ae = author.find("./{%s}affiliation" % ns)
if ae:
affiliation: Dict[str, Any] = dict()
for on in ae.findall("./{%s}orgName" % ns):
on_type = on.get("type")
if on_type:
affiliation[on_type] = on.text
addr_e = ae.find("./{%s}address" % ns)
if addr_e:
address = dict()
for t in addr_e:
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: ET.Element) -> Dict[str, Any]:
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)
keys = list(journal.keys())
# remove empty/null keys
for k in keys:
if not journal[k]:
journal.pop(k)
return journal
def biblio_info(elem: ET.Element) -> Dict[str, Any]:
ref: Dict[str, Any] = 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 is not 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: AnyStr, encumbered: bool = True) -> Dict[str, Any]:
if isinstance(content, str):
tree = ET.parse(io.StringIO(content))
elif isinstance(content, bytes):
tree = ET.parse(io.BytesIO(content))
info: Dict[str, Any] = dict()
# print(content)
# print(content.getvalue())
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"].strip()
info["grobid_timestamp"] = application_tag.attrib["when"].strip()
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 is not 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
text = tei.find(".//{%s}text" % (ns))
# print(text.attrib)
if text and text.attrib.get("{%s}lang" % xml_ns):
info["language_code"] = text.attrib["{%s}lang" % xml_ns] # xml:lang
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()
# remove empty/null keys
keys = list(info.keys())
for k in keys:
if not info[k]:
info.pop(k)
return info
def main() -> None: # pragma no cover
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
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").read()
print(
json.dumps(
teixml2json(content, encumbered=(not args.no_encumbered)),
sort_keys=True,
))
if __name__ == "__main__": # pragma no cover
main()
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