diff options
| -rwxr-xr-x | fatcat_scholar/grobid2json.py | 236 | ||||
| -rw-r--r-- | fatcat_scholar/query_citation.py | 13 | ||||
| -rw-r--r-- | fatcat_scholar/transform.py | 8 | ||||
| -rw-r--r-- | tests/test_grobid2json.py | 11 | ||||
| -rw-r--r-- | tests/test_refs_transform.py | 5 |
5 files changed, 21 insertions, 252 deletions
diff --git a/fatcat_scholar/grobid2json.py b/fatcat_scholar/grobid2json.py deleted file mode 100755 index c99b9ed..0000000 --- a/fatcat_scholar/grobid2json.py +++ /dev/null @@ -1,236 +0,0 @@ -#!/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 - -This file copied from the sandcrawler repository. -""" - -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], ns: str = ns) -> 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.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: ET.Element) -> Dict[str, Any]: - 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) - 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, ns: str = ns) -> Dict[str, Any]: - 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"] = all_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 - 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 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(f".//{{{ns}}}appInfo/{{{ns}}}application")[0] - info["grobid_version"] = application_tag.attrib["version"].strip() - info["grobid_timestamp"] = application_tag.attrib["when"].strip() - info["title"] = header.findtext(f".//{{{ns}}}analytic/{{{ns}}}title") - info["authors"] = all_authors( - header.find(f".//{{{ns}}}sourceDesc/{{{ns}}}biblStruct") - ) - 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(f".//{{{ns}}}listBibl/{{{ns}}}biblStruct")): - 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(f".//{{{ns}}}profileDesc/{{{ns}}}abstract") - info["abstract"] = (el or None) and " ".join(el.itertext()).strip() - el = tei.find(f".//{{{ns}}}text/{{{ns}}}body") - info["body"] = (el or None) and " ".join(el.itertext()).strip() - el = tei.find(f'.//{{{ns}}}back/{{{ns}}}div[@type="acknowledgement"]') - info["acknowledgement"] = (el or None) and " ".join(el.itertext()).strip() - el = tei.find(f'.//{{{ns}}}back/{{{ns}}}div[@type="annex"]') - 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() diff --git a/fatcat_scholar/query_citation.py b/fatcat_scholar/query_citation.py index 6cc9086..dea4f02 100644 --- a/fatcat_scholar/query_citation.py +++ b/fatcat_scholar/query_citation.py @@ -10,9 +10,7 @@ timeout and try/except! In the future, perhaps should be async so it can run in parallel with "regular" query? """ -import io import sys -import xml.etree.ElementTree as ET from typing import Any, Optional, Tuple import fuzzycat.common @@ -20,9 +18,9 @@ import fuzzycat.verify import requests from fatcat_openapi_client import ReleaseContrib, ReleaseEntity, ReleaseExtIds from fuzzycat.matching import match_release_fuzzy +from grobid_tei_xml import parse_citations_xml from fatcat_scholar.api_entities import entity_to_dict -from fatcat_scholar.grobid2json import biblio_info def grobid_process_citation( @@ -47,11 +45,10 @@ def grobid_process_citation( def transform_grobid(raw_xml: str) -> Optional[dict]: - # first, remove any xmlns stuff - raw_xml = raw_xml.replace('xmlns="http://www.tei-c.org/ns/1.0"', "") - tree = ET.parse(io.StringIO(raw_xml)) - root = tree.getroot() - ref = biblio_info(root, ns="") + ref_list = parse_citations_xml(raw_xml) + if not ref_list: + return None + ref = ref_list[0] if not any(ref.values()): return None return ref diff --git a/fatcat_scholar/transform.py b/fatcat_scholar/transform.py index f805e7b..caeff21 100644 --- a/fatcat_scholar/transform.py +++ b/fatcat_scholar/transform.py @@ -8,9 +8,9 @@ from typing import Any, Dict, List, Optional, Sequence import sentry_sdk from fatcat_openapi_client import FileEntity, ReleaseEntity, WebcaptureEntity +from grobid_tei_xml import parse_document_xml from fatcat_scholar.config import GIT_REVISION, settings -from fatcat_scholar.grobid2json import teixml2json from fatcat_scholar.identifiers import clean_doi, clean_pmcid from fatcat_scholar.schema import ( AccessType, @@ -521,7 +521,8 @@ def transform_heavy(heavy: IntermediateBundle) -> Optional[ScholarDoc]: if f.ident == heavy.grobid_fulltext["file_ident"] ][0] try: - tei_dict: Optional[dict] = teixml2json(heavy.grobid_fulltext["tei_xml"]) + tei_doc = parse_document_xml(heavy.grobid_fulltext["tei_xml"]) + tei_dict = tei_doc.to_legacy_dict() except xml.etree.ElementTree.ParseError: tei_dict = None if tei_dict: @@ -900,7 +901,8 @@ def refs_from_heavy(heavy: IntermediateBundle) -> Sequence[RefStructured]: for r in heavy.releases if r.ident == heavy.grobid_fulltext["release_ident"] ][0] - tei_dict = teixml2json(heavy.grobid_fulltext["tei_xml"]) + tei_doc = parse_document_xml(heavy.grobid_fulltext["tei_xml"]) + tei_dict = tei_doc.to_legacy_dict() fulltext_refs = refs_from_grobid(fulltext_release, tei_dict) crossref_refs: List[RefStructured] = [] diff --git a/tests/test_grobid2json.py b/tests/test_grobid2json.py index 345fd91..adf36a1 100644 --- a/tests/test_grobid2json.py +++ b/tests/test_grobid2json.py @@ -1,12 +1,17 @@ -from fatcat_scholar.grobid2json import teixml2json +from grobid_tei_xml import parse_document_xml -def test_grobid_teixml2json() -> None: +def test_grobid_parse() -> None: + """ + This function formerly tested the grobid2json file in this project. Now it + tests backwards-compatibility of the grobid_tei_xml library. + """ with open("tests/files/example_grobid.tei.xml", "r") as f: blob = f.read() - obj = teixml2json(blob, True) + doc = parse_document_xml(blob) + obj = doc.to_legacy_dict() assert ( obj["title"] diff --git a/tests/test_refs_transform.py b/tests/test_refs_transform.py index 5f15adf..2fc210f 100644 --- a/tests/test_refs_transform.py +++ b/tests/test_refs_transform.py @@ -1,8 +1,8 @@ import json from fatcat_openapi_client import ReleaseEntity +from grobid_tei_xml import parse_document_xml -from fatcat_scholar.grobid2json import teixml2json from fatcat_scholar.transform import refs_from_crossref, refs_from_grobid @@ -19,7 +19,8 @@ def test_transform_refs_grobid() -> None: ext_ids={}, ) - tei_dict = teixml2json(blob, True) + tei_doc = parse_document_xml(blob) + tei_dict = tei_doc.to_legacy_dict() refs = refs_from_grobid(dummy_release, tei_dict) ref = refs[12] |