diff options
Diffstat (limited to 'fatcat_covid19')
| -rw-r--r-- | fatcat_covid19/transform.py | 204 |
1 files changed, 204 insertions, 0 deletions
diff --git a/fatcat_covid19/transform.py b/fatcat_covid19/transform.py new file mode 100644 index 0000000..c31c9f4 --- /dev/null +++ b/fatcat_covid19/transform.py @@ -0,0 +1,204 @@ + +import sys +import json +import argparse +import datetime + +from fatcat_covid19.common import * + + +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']: + abstracts.append(a['content']) + 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] + + # 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'] + + 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 + + t['abstract'] = abstracts + t['abstract_lang'] = list(set(abstract_langs)) + + t['source_tags'] = list(set(t['source_tags'])) + + 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, args) + if result: + print(json.dumps(result, sort_keys=True), file=json_output) |