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#!/usr/bin/env python3
import sys
import json
import base64
import datetime
import fatcat_client
from .common import EntityImporter, clean, make_rel_url
MAX_ABSTRACT_BYTES=4096
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, **kwargs):
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):
return True
def parse_record(self, row):
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_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):
if not obj.get('title'):
return None
extra_grobid = dict()
abstract = obj.get('abstract')
if abstract and len(abstract) < MAX_ABSTRACT_BYTES and len(abstract) > 10:
abobj = fatcat_client.ReleaseAbstract(
mimetype="text/plain",
content=clean(obj.get('abstract')))
abstracts = [abobj]
else:
abstracts = None
contribs = []
for i, a in enumerate(obj.get('authors', [])):
contribs.append(fatcat_client.ReleaseContrib(
index=i,
raw_name=clean(a['name']),
given_name=clean(a.get('given_name')),
surname=clean(a.get('surname')),
role="author",
extra=None))
refs = []
for raw in obj.get('citations', []):
cite_extra = dict()
year = None
if raw.get('date'):
try:
year = int(raw['date'].strip()[:4])
except:
pass
for key in ('volume', 'url', 'issue', 'publisher'):
if raw.get(key):
cite_extra[key] = clean(raw[key])
if raw.get('authors'):
cite_extra['authors'] = [clean(a['name']) for a in raw['authors']]
if not cite_extra:
cite_extra = None
refs.append(fatcat_client.ReleaseRef(
key=clean(raw.get('id')),
year=year,
title=clean(raw['title']),
extra=cite_extra))
release_date = None
release_year = None
if obj.get('date'):
# only returns year, ever?
release_year = int(obj['date'][:4])
extra = dict()
if obj.get('doi'):
extra['doi'] = obj['doi']
if obj['journal'] and obj['journal'].get('name'):
extra['container_name'] = clean(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
if not extra:
extra = None
title = clean(obj['title'], force_xml=True)
if not title or len(title) < 2:
return None
re = fatcat_client.ReleaseEntity(
title=title,
release_type="article-journal",
release_date=release_date,
release_year=release_year,
contribs=contribs,
refs=refs,
publisher=clean(obj['journal'].get('publisher')),
volume=clean(obj['journal'].get('volume')),
issue=clean(obj['journal'].get('issue')),
abstracts=abstracts,
ext_ids=fatcat_client.ReleaseExtIds(),
extra=extra)
return re
def parse_file_metadata(self, sha1_key, cdx, mimetype, file_size):
sha1 = base64.b16encode(base64.b32decode(sha1_key.replace('sha1:', ''))).decode('ascii').lower()
fe = fatcat_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_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_client.FileUrl(rel=original_url[0], url=original_url[1]))
return fe
def try_update(self, entity):
# did the exists check in 'parse_record()', because we needed to create a release
return True
def insert_batch(self, batch):
self.api.create_file_auto_batch(fatcat_client.FileAutoBatch(
editgroup=fatcat_client.Editgroup(
description=self.editgroup_description,
extra=self.editgroup_extra),
entity_list=batch))
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