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#!/usr/bin/env python3
import base64
import json
from typing import Any, Dict, List, Optional
import fatcat_openapi_client
from fatcat_openapi_client import ApiClient, FileEntity, ReleaseEntity
from fatcat_tools.normal import clean_doi, clean_str
from .common import MAX_ABSTRACT_LENGTH, EntityImporter, make_rel_url
class GrobidMetadataImporter(EntityImporter):
"""
This is a complex case: we need to parse and create both file and release entities.
The "primary" entity here is really File, not Release. If a matching File
exists, we bail in want(); if not we insert the Release during parsing, and
insert both.
TODO: should instead check if the File has any releases; if not, insert and update.
TODO: relaxing 'None' constraint on parse_record() might make this refactor-able.
"""
def __init__(self, api: ApiClient, **kwargs) -> None:
eg_desc = kwargs.get(
"editgroup_description",
"Import of release and file metadata, as extracted from PDFs by GROBID.",
)
eg_extra = kwargs.get("editgroup_extra", dict())
eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.GrobidMetadataImporter")
super().__init__(api, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs)
self.default_link_rel = kwargs.get("default_link_rel", "web")
self.longtail_oa = kwargs.get("longtail_oa", False)
def want(self, raw_record: Any) -> bool:
return True
def parse_record(self, row: str) -> Optional[FileEntity]:
fields = row.split("\t")
sha1_key = fields[0]
cdx = json.loads(fields[1])
mimetype = fields[2]
file_size = int(fields[3])
grobid_meta = json.loads(fields[4])
fe = self.parse_file_metadata(sha1_key, cdx, mimetype, file_size)
re = self.parse_grobid_json(grobid_meta)
if not (fe and re):
return None
# lookup existing file SHA1
existing = None
try:
existing = self.api.lookup_file(sha1=fe.sha1)
except fatcat_openapi_client.rest.ApiException as err:
if err.status != 404:
raise err
# if file is already in here, presumably not actually long-tail
# HACK: this is doing an exists check in parse_record(), which is weird
# TODO: this is where we should check if the file actually has
# release_ids and/or URLs associated with it
if existing and not self.bezerk_mode:
self.counts["exists"] += 1
self.counts["skip"] -= 1
return None
release_edit = self.create_release(re)
fe.release_ids.append(release_edit.ident)
return fe
def parse_grobid_json(self, obj: Dict[str, Any]) -> Optional[ReleaseEntity]:
if not obj.get("title"):
return None
extra_grobid: Dict[str, Any] = dict()
abstract = obj.get("abstract")
if abstract and len(abstract) < MAX_ABSTRACT_LENGTH and len(abstract) > 10:
abobj = fatcat_openapi_client.ReleaseAbstract(
mimetype="text/plain", content=clean_str(obj.get("abstract"))
)
abstracts = [abobj]
else:
abstracts = []
contribs = []
for i, a in enumerate(obj.get("authors", [])):
contribs.append(
fatcat_openapi_client.ReleaseContrib(
index=i,
raw_name=clean_str(a["name"]),
given_name=clean_str(a.get("given_name")),
surname=clean_str(a.get("surname")),
role="author",
extra=None,
)
)
refs = []
for raw in obj.get("citations", []):
cite_extra: Dict[str, Any] = dict()
year = None
if raw.get("date"):
try:
year = int(raw["date"].strip()[:4])
except (IndexError, ValueError):
pass
for key in ("volume", "url", "issue", "publisher"):
if raw.get(key):
cite_extra[key] = clean_str(raw[key])
if raw.get("authors"):
cite_extra["authors"] = [clean_str(a["name"]) for a in raw["authors"]]
refs.append(
fatcat_openapi_client.ReleaseRef(
key=clean_str(raw.get("id")),
year=year,
title=clean_str(raw["title"]),
extra=cite_extra or None,
)
)
release_date = None
release_year = None
if obj.get("date"):
# only returns year, ever?
release_year = int(obj["date"][:4])
extra: Dict[str, Any] = dict()
doi = clean_doi(obj.get("doi"))
if doi:
extra["doi"] = doi
if obj["journal"] and obj["journal"].get("name"):
extra["container_name"] = clean_str(obj["journal"]["name"])
# TODO: ISSN/eISSN handling? or just journal name lookup?
if extra_grobid:
extra["grobid"] = extra_grobid
if self.longtail_oa:
extra["longtail_oa"] = True
clean_title = clean_str(obj["title"], force_xml=True)
if not clean_title or len(clean_title) < 2:
return None
title = clean_title
re = fatcat_openapi_client.ReleaseEntity(
title=title,
release_type="article-journal",
release_date=release_date,
release_year=release_year,
contribs=contribs,
refs=refs,
publisher=clean_str(obj["journal"].get("publisher")),
volume=clean_str(obj["journal"].get("volume")),
issue=clean_str(obj["journal"].get("issue")),
abstracts=abstracts or None,
ext_ids=fatcat_openapi_client.ReleaseExtIds(),
extra=extra or None,
)
return re
def parse_file_metadata(
self, sha1_key: str, cdx: Dict[str, Any], mimetype: str, file_size: int
) -> FileEntity:
sha1 = (
base64.b16encode(base64.b32decode(sha1_key.replace("sha1:", "")))
.decode("ascii")
.lower()
)
fe = fatcat_openapi_client.FileEntity(
sha1=sha1,
size=int(file_size),
mimetype=mimetype,
release_ids=[],
urls=[],
)
# parse URLs and CDX
original = cdx["url"]
assert len(cdx["dt"]) >= 8
wayback = "https://web.archive.org/web/{}/{}".format(cdx["dt"], original)
fe.urls.append(fatcat_openapi_client.FileUrl(url=wayback, rel="webarchive"))
original_url = make_rel_url(original, default_link_rel=self.default_link_rel)
if original_url is not None:
fe.urls.append(
fatcat_openapi_client.FileUrl(rel=original_url[0], url=original_url[1])
)
return fe
def try_update(self, re: FileEntity) -> bool:
# did the exists check in 'parse_record()', because we needed to create a release
return True
def insert_batch(self, batch: List[FileEntity]) -> None:
self.api.create_file_auto_batch(
fatcat_openapi_client.FileAutoBatch(
editgroup=fatcat_openapi_client.Editgroup(
description=self.editgroup_description, extra=self.editgroup_extra
),
entity_list=batch,
)
)
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