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import sys
import json
import argparse
import datetime
from bs4 import BeautifulSoup
from fatcat_covid19.common import *
UNWANTED_ABSTRACT_PREFIXES = [
# roughly sort this long to short
'Abstract No Abstract ',
'Publisher Summary ',
'Abstract ',
'ABSTRACT ',
'Summary ',
'Background: ',
'Background ',
]
def fulltext_to_elasticsearch(row, force_bool=True):
"""
Converts from fulltext content and release model/schema to elasticsearch
oriented schema.
Returns: dict
Raises exception on error (never returns None)
"""
if not 'fatcat_release' in row:
# skip papers that don't match to a fatcat release
return None
release = row['fatcat_release']
abstracts = []
abstract_langs = []
# first, easy fatcat metadata
t = {
'fatcat_ident': release['ident'],
'fatcat_revision': release['revision'],
'fulltext': dict(),
}
BIBLIO_KEYS = [
'work_id',
'title',
'subtitle',
'original_title',
'release_type',
'release_stage',
'release_year',
'release_date',
'withdrawn_status',
'language',
'volume',
'issue',
'pages',
'number',
'license',
]
EXT_IDS = [
'doi',
'pmid',
'pmcid',
'isbn13',
'wikidata_qid',
'arxiv_id',
'jstor_id',
'mag_id',
]
for key in BIBLIO_KEYS:
t[key] = release.get(key) or None
for key in EXT_IDS:
t[key] = release['ext_ids'].get(key) or None
t['contrib_count'] = len(release['contribs'] or [])
if release.get('abstracts'):
for a in release['abstracts']:
# hack to (partially) clean up common JATS abstract display case
if a.get('mimetype') == 'application/xml+jats' or "</" in a['content']:
a['content'] = BeautifulSoup(a['content'], "lxml").get_text()
# hack to remove abstract prefixes
for prefix in UNWANTED_ABSTRACT_PREFIXES:
if a['content'].startswith(prefix):
a['content'] = a['content'][len(prefix):]
break
a['content'] = a['content'].strip()
if a['content']:
abstracts.append(a['content'].strip())
if a.get('lang'):
abstract_langs.append(a['lang'])
contrib_names = []
contrib_affiliations = []
creator_ids = []
for c in (release['contribs'] or []):
if c.get('raw_name'):
contrib_names.append(c['raw_name'])
elif c.get('surname'):
contrib_names.append(c['surname'])
if c.get('creator_id'):
creator_ids.append(c['creator_id'])
if c.get('raw_affiliation'):
contrib_affiliations.append(c['raw_affiliation'])
t['contrib_names'] = contrib_names
t['creator_ids'] = creator_ids
t['affiliations'] = contrib_affiliations
container = release.get('container')
if container:
t['publisher'] = container.get('publisher')
t['container_name'] = container.get('name')
t['container_original_name'] = container.get('original_name')
# this is container.ident, not release.container_id, because there may
# be a redirect involved
t['container_id'] = container['ident']
t['container_issnl'] = container.get('issnl')
t['container_type'] = container.get('container_type')
if container.get('extra'):
c_extra = container['extra']
if c_extra.get('country'):
t['country_code'] = c_extra['country']
t['country_code_upper'] = c_extra['country'].upper()
# fall back to release-level container metadata if container not linked or
# missing context
if not t.get('publisher'):
t['publisher'] = release.get('publisher')
if not t.get('container_name') and release.get('extra'):
t['container_name'] = release['extra'].get('container_name')
extra = release['extra'] or dict()
if extra:
if not t.get('container_name'):
t['container_name'] = extra.get('container_name')
# backwards compatible subtitle fetching
if not t['subtitle'] and extra.get('subtitle'):
if type(extra['subtitle']) == list:
t['subtitle'] = extra['subtitle'][0]
else:
t['subtitle'] = extra['subtitle']
t['first_page'] = None
if release.get('pages'):
first = release['pages'].split('-')[0]
first = first.replace('p', '')
if first.isdigit():
t['first_page'] = first
# TODO: non-numerical first pages
t['doi_registrar'] = None
if extra and t['doi']:
for k in ('crossref', 'datacite', 'jalc'):
if k in extra:
t['doi_registrar'] = k
if not 'doi_registrar' in t:
t['doi_registrar'] = 'crossref'
if t['doi']:
t['doi_prefix'] = t['doi'].split('/')[0]
# special-case medrxiv/biorxiv content
if not t.get('release_stage') and not t.get('container_name') and (t.get('doi') or '').startswith('10.1101/20'):
t['container_name'] = 'biorXiv/medrXiv'
t['release_stage'] = 'draft'
if t.get('release_type') in ['post', None]:
t['release_type'] = 'article-journal'
# special-case arxiv
if not t.get('container_name') and t.get('arxiv_id'):
t['container_name'] = 'arXiv'
# then the fulltext stuff
t['fulltext']['status'] = row.get('fulltext_status', 'none')
if 'fulltext_file' in row:
full = row['fulltext_file']
t['fulltext']['sha1'] = full['sha1']
t['fulltext']['pdf_url'] = "/" + full['pdf_path']
if full.get('pdftotext_path'):
t['fulltext']['pdftotext_url'] = "/" + full['pdftotext_path']
if full.get('thumbnail_path'):
t['fulltext']['thumbnail_url'] = "/" + full['thumbnail_path']
if full.get('grobid_xml_path'):
t['fulltext']['grobid_xml_url'] = "/" + full['grobid_xml_path']
for url in full.get('urls', []):
if url.get('rel') in ('webarchive', 'archive') and 'archive.org/' in url['url']:
t['fulltext']['ia_pdf_url'] = url['url']
break
if 'fulltext_grobid' in row:
grobid = row['fulltext_grobid']
if grobid.get('abstract'):
abstracts.append(grobid['abstract'])
abstract_langs.append(grobid['language_code'])
t['fulltext']['abstract'] = grobid.get('abstract', None)
t['fulltext']['body'] = grobid.get('body', None)
t['fulltext']['acknowledgement'] = grobid.get('acknowledgement', None)
t['fulltext']['annex'] = grobid.get('annex', None)
t['fulltext']['lang'] = grobid.get('language_code', None)
elif 'fulltext_pdftotext' in row:
pdftotext = row['fulltext_pdftotext']
t['fulltext']['body'] = pdftotext.get('body', None)
# then other metadata stuff
if row.get('source_tags'):
# will get set-uniq at the end
t['source_tags'] = row['source_tags']
else:
t['source_tags'] = []
if 'cord19_paper' in row:
t['source_tags'].append('cord19')
paper = row['cord19_paper']
t['cord19_uid'] = paper['cord_uid']
if paper.get('who_covidence_id'):
t['who_covidence_id'] = paper['who_covidence_id']
t['source_tags'].append('who')
if paper.get('abstract') and not abstracts:
abstracts.append(paper['abstract'])
if not t['license']:
t['license'] = paper.get('license') or None
if 'fatcat_hit' in row:
t['source_tags'].append('fatcat')
t['abstract'] = abstracts
t['abstract_lang'] = list(set(abstract_langs))
t['source_tags'] = list(set(t['source_tags']))
### filter out some documents
# figures, component of a larger work, drop it
if t['title'].lower().startswith('figure') and not t.get('release_type'):
return None
### clean up some documents
# protein databank
if t.get('doi_prefix') == '10.2210' and not t.get('release_type'):
t['release_type'] = 'dataset'
t['release_stage'] = 'published'
t['container_name'] = 'Protein Data Bank'
return t
def transform_es_file(json_input, json_output):
"""
Takes *enriched* JSON objects which include fatcat metadata and fulltext
content, and outputs JSON lines in fatcat_fulltext schema.
"""
for l in json_input:
l = json.loads(l)
result = fulltext_to_elasticsearch(l)
if result:
print(json.dumps(result, sort_keys=True), file=json_output)
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