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import io
import json
import xml.etree.ElementTree as ET
from typing import Any, AnyStr, Dict, List, Optional
from .types import *
xml_ns = "http://www.w3.org/XML/1998/namespace"
ns = "http://www.tei-c.org/ns/1.0"
def _string_to_tree(content: AnyStr) -> ET:
if isinstance(content, str):
return ET.parse(io.StringIO(content))
elif isinstance(content, bytes):
return ET.parse(io.BytesIO(content))
if isinstance(content, io.StringIO) or isinstance(content, io.BytesIO):
return ET.parse(content)
elif isinstance(content, ET):
return content
else:
raise TypeError(
f"expected XML as string or bytes, got: {type(content)}")
def _parse_authors(elem: Optional[ET.Element],
ns: str = ns) -> List[GrobidAffiliation]:
if not elem:
return []
names = []
for author in elem.findall(f".//{{{ns}}}author"):
pn = author.find(f"./{{{ns}}}persName")
if not pn:
continue
given_name = pn.findtext(f"./{{{ns}}}forename") or None
surname = pn.findtext(f"./{{{ns}}}surname") or None
full_name = " ".join([t.strip() for t in pn.itertext()
if t.strip()]).strip()
obj: Dict[str, Any] = dict(name=full_name)
if given_name:
obj["given_name"] = given_name
if surname:
obj["surname"] = surname
ae = author.find(f"./{{{ns}}}affiliation")
if ae:
affiliation: Dict[str, Any] = dict()
for on in ae.findall(f"./{{{ns}}}orgName"):
on_type = on.get("type")
if on_type:
affiliation[on_type] = on.text
addr_e = ae.find(f"./{{{ns}}}address")
if addr_e:
address = dict()
for t in addr_e.getchildren():
address[t.tag.split("}")[-1]] = t.text
if address:
address['post_code'] = address.pop('postCode', None)
affiliation["address"] = GrobidAddress(**address)
# previously:
# 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"] = GrobidAffiliation(**affiliation)
names.append(GrobidAuthor(**obj))
return names
def _parse_citation(elem: ET.Element, ns: str = ns) -> GrobidCitation:
ref: Dict[str, Any] = dict()
ref["id"] = elem.attrib.get("{http://www.w3.org/XML/1998/namespace}id")
ref["unstructured"] = elem.findtext('.//{%s}note[@type="raw_reference"]' %
ns)
# Title stuff is messy in references...
ref["title"] = elem.findtext(f".//{{{ns}}}analytic/{{{ns}}}title")
other_title = elem.findtext(f".//{{{ns}}}monogr/{{{ns}}}title")
if other_title:
if ref["title"]:
ref["journal"] = other_title
else:
ref["journal"] = None
ref["title"] = other_title
ref["authors"] = _parse_authors(elem, ns=ns)
ref["publisher"] = elem.findtext(
f".//{{{ns}}}publicationStmt/{{{ns}}}publisher")
if not ref["publisher"]:
ref["publisher"] = elem.findtext(
f".//{{{ns}}}imprint/{{{ns}}}publisher")
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)
ref["doi"] = elem.findtext('.//{%s}idno[@type="DOI"]' % ns)
ref["arxiv_id"] = elem.findtext('.//{%s}idno[@type="arXiv"]' % ns)
if ref["arxiv_id"] and ref["arxiv_id"].startswith("arXiv:"):
ref["arxiv_id"] = ref["arxiv_id"][6:]
ref["pmcid"] = elem.findtext('.//{%s}idno[@type="PMCID"]' % ns)
ref["pmid"] = elem.findtext('.//{%s}idno[@type="PMID"]' % ns)
el = elem.find('.//{%s}biblScope[@unit="page"]' % ns)
if el is not None:
if el.attrib.get("from") and el.attrib.get("to"):
ref["pages"] = "{}-{}".format(el.attrib["from"], el.attrib["to"])
else:
ref["pages"] = el.text
el = elem.find(".//{%s}ptr[@target]" % ns)
if el is not None:
ref["url"] = el.attrib["target"]
# Hand correction
# TODO: move this elsewhere
if ref["url"].endswith(".Lastaccessed"):
ref["url"] = ref["url"].replace(".Lastaccessed", "")
if ref["url"].startswith("<"):
ref["url"] = ref["url"][1:]
if ">" in ref["url"]:
ref["url"] = ref["url"].split(">")[0]
else:
ref["url"] = None
return GrobidCitation(**ref)
def _parse_journal(elem: ET.Element, ns: str = ns) -> GrobidJournal:
journal = dict()
journal["name"] = elem.findtext(f".//{{{ns}}}monogr/{{{ns}}}title")
journal["publisher"] = elem.findtext(
f".//{{{ns}}}publicationStmt/{{{ns}}}publisher")
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)
journal["abbrev"] = None
return GrobidJournal(**journal)
def _parse_header(elem: ET.Element, ns: str = ns) -> GrobidHeader:
header = elem
info = dict()
info["title"] = header.findtext(f".//{{{ns}}}analytic/{{{ns}}}title")
info["authors"] = _parse_authors(
header.find(f".//{{{ns}}}sourceDesc/{{{ns}}}biblStruct"))
info["journal"] = _parse_journal(header)
date = header.find(f'.//{{{ns}}}date[@type="published"]')
info["date"] = (date is not None) and date.attrib.get("when")
info["doi"] = header.findtext(f'.//{{{ns}}}idno[@type="DOI"]')
if info["doi"]:
info["doi"] = info["doi"].lower()
return GrobidHeader(**info)
def parse_document_xml(xml_text: AnyStr) -> GrobidDocument:
"""
Use this function to parse TEI-XML of a full document or header processed
by GROBID.
Eg, the output of '/api/processFulltextDocument' or '/api/processHeader'
"""
tree = _string_to_tree(xml_text)
tei = tree.getroot()
info = dict()
header = tei.find(f".//{{{ns}}}teiHeader")
if header is None:
raise ValueError("XML does not look like TEI format")
application_tag = header.findall(
f".//{{{ns}}}appInfo/{{{ns}}}application")[0]
doc = GrobidDocument(
grobid_version=application_tag.attrib["version"].strip(),
grobid_timestamp=application_tag.attrib["when"].strip(),
header=_parse_header(header),
# TODO: pdf_md5=header.findtext(f'.//{{{ns}}}idno[@type="MD5"]') or None,
)
refs = []
for (i, bs) in enumerate(
tei.findall(f".//{{{ns}}}listBibl/{{{ns}}}biblStruct")):
ref = _parse_citation(bs)
ref.index = i
refs.append(ref)
doc.citations = refs
text = tei.find(f".//{{{ns}}}text")
# print(text.attrib)
if text and text.attrib.get(f"{{{xml_ns}}}lang"):
doc.language_code = text.attrib[f"{{{xml_ns}}}lang"] # xml:lang
el = tei.find(f".//{{{ns}}}profileDesc/{{{ns}}}abstract")
doc.abstract = (el or None) and " ".join(el.itertext()).strip()
el = tei.find(f".//{{{ns}}}text/{{{ns}}}body")
doc.body = (el or None) and " ".join(el.itertext()).strip()
el = tei.find(f'.//{{{ns}}}back/{{{ns}}}div[@type="acknowledgement"]')
doc.acknowledgement = (el or None) and " ".join(el.itertext()).strip()
el = tei.find(f'.//{{{ns}}}back/{{{ns}}}div[@type="annex"]')
doc.annex = (el or None) and " ".join(el.itertext()).strip()
return doc
def parse_citations_xml(xml_text: AnyStr) -> List[GrobidCitation]:
"""
Use this function to parse TEI-XML of one or more references.
Eg, the output of '/api/processReferences' or '/api/processCitation'.
"""
# XXX: this replacement shouldn't be needed?
xml_text = xml_text.replace('xmlns="http://www.tei-c.org/ns/1.0"', "")
tree = _string_to_tree(xml_text)
root = tree.getroot()
if root.tag == 'biblStruct':
ref = _parse_citation(root, ns='')
ref.index = 0
return [ref]
refs = []
for (i, bs) in enumerate(tree.findall(f".//biblStruct")):
ref = _parse_citation(bs, ns='')
ref.index = i
refs.append(ref)
return refs
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