diff options
Diffstat (limited to 'python/fatcat_tools')
| -rw-r--r-- | python/fatcat_tools/harvest/doi_registrars.py | 14 | ||||
| -rw-r--r-- | python/fatcat_tools/harvest/harvest_common.py | 10 | ||||
| -rw-r--r-- | python/fatcat_tools/harvest/oaipmh.py | 15 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/__init__.py | 1 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/common.py | 9 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/datacite.py | 75 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/ingest.py | 25 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/shadow.py | 195 | ||||
| -rw-r--r-- | python/fatcat_tools/transforms/ingest.py | 8 | ||||
| -rw-r--r-- | python/fatcat_tools/workers/changelog.py | 52 |
10 files changed, 353 insertions, 51 deletions
diff --git a/python/fatcat_tools/harvest/doi_registrars.py b/python/fatcat_tools/harvest/doi_registrars.py index 33f44600..d2d71d3c 100644 --- a/python/fatcat_tools/harvest/doi_registrars.py +++ b/python/fatcat_tools/harvest/doi_registrars.py @@ -70,8 +70,8 @@ class HarvestCrossrefWorker: def fail_fast(err, msg): if err is not None: - print("Kafka producer delivery error: {}".format(err)) - print("Bailing out...") + print("Kafka producer delivery error: {}".format(err), file=sys.stderr) + print("Bailing out...", file=sys.stderr) # TODO: should it be sys.exit(-1)? raise KafkaException(err) @@ -117,7 +117,7 @@ class HarvestCrossrefWorker: if http_resp.status_code == 503: # crude backoff; now redundant with session exponential # backoff, but allows for longer backoff/downtime on remote end - print("got HTTP {}, pausing for 30 seconds".format(http_resp.status_code)) + print("got HTTP {}, pausing for 30 seconds".format(http_resp.status_code), file=sys.stderr) # keep kafka producer connection alive self.producer.poll(0) time.sleep(30.0) @@ -131,7 +131,7 @@ class HarvestCrossrefWorker: items = self.extract_items(resp) count += len(items) print("... got {} ({} of {}), HTTP fetch took {}".format(len(items), count, - self.extract_total(resp), http_resp.elapsed)) + self.extract_total(resp), http_resp.elapsed), file=sys.stderr) #print(json.dumps(resp)) for work in items: self.producer.produce( @@ -156,7 +156,7 @@ class HarvestCrossrefWorker: while True: current = self.state.next(continuous) if current: - print("Fetching DOIs updated on {} (UTC)".format(current)) + print("Fetching DOIs updated on {} (UTC)".format(current), file=sys.stderr) self.fetch_date(current) self.state.complete(current, kafka_topic=self.state_topic, @@ -164,11 +164,11 @@ class HarvestCrossrefWorker: continue if continuous: - print("Sleeping {} seconds...".format(self.loop_sleep)) + print("Sleeping {} seconds...".format(self.loop_sleep), file=sys.stderr) time.sleep(self.loop_sleep) else: break - print("{} DOI ingest caught up".format(self.name)) + print("{} DOI ingest caught up".format(self.name), file=sys.stderr) class HarvestDataciteWorker(HarvestCrossrefWorker): diff --git a/python/fatcat_tools/harvest/harvest_common.py b/python/fatcat_tools/harvest/harvest_common.py index 78830a1c..310366bd 100644 --- a/python/fatcat_tools/harvest/harvest_common.py +++ b/python/fatcat_tools/harvest/harvest_common.py @@ -57,6 +57,10 @@ class HarvestState: if catchup_days or start_date or end_date: self.enqueue_period(start_date, end_date, catchup_days) + def __str__(self): + return '<HarvestState to_process={}, completed={}>'.format( + len(self.to_process), len(self.completed)) + def enqueue_period(self, start_date=None, end_date=None, catchup_days=14): """ This function adds a time period to the "TODO" list, unless the dates @@ -129,7 +133,7 @@ class HarvestState: def fail_fast(err, msg): if err: raise KafkaException(err) - print("Commiting status to Kafka: {}".format(kafka_topic)) + print("Commiting status to Kafka: {}".format(kafka_topic), file=sys.stderr) producer_conf = kafka_config.copy() producer_conf.update({ 'delivery.report.only.error': True, @@ -154,7 +158,7 @@ class HarvestState: if not kafka_topic: return - print("Fetching state from kafka topic: {}".format(kafka_topic)) + print("Fetching state from kafka topic: {}".format(kafka_topic), file=sys.stderr) def fail_fast(err, msg): if err: raise KafkaException(err) @@ -191,4 +195,4 @@ class HarvestState: # verify that we got at least to HWM assert c >= hwm[1] - print("... got {} state update messages, done".format(c)) + print("... got {} state update messages, done".format(c), file=sys.stderr) diff --git a/python/fatcat_tools/harvest/oaipmh.py b/python/fatcat_tools/harvest/oaipmh.py index f908ba83..11b5fa0a 100644 --- a/python/fatcat_tools/harvest/oaipmh.py +++ b/python/fatcat_tools/harvest/oaipmh.py @@ -49,13 +49,14 @@ class HarvestOaiPmhWorker: self.name = "unnamed" self.state = HarvestState(start_date, end_date) self.state.initialize_from_kafka(self.state_topic, self.kafka_config) + print(self.state, file=sys.stderr) def fetch_date(self, date): def fail_fast(err, msg): if err is not None: - print("Kafka producer delivery error: {}".format(err)) - print("Bailing out...") + print("Kafka producer delivery error: {}".format(err), file=sys.stderr) + print("Bailing out...", file=sys.stderr) # TODO: should it be sys.exit(-1)? raise KafkaException(err) @@ -79,14 +80,14 @@ class HarvestOaiPmhWorker: 'until': date_str, }) except sickle.oaiexceptions.NoRecordsMatch: - print("WARN: no OAI-PMH records for this date: {} (UTC)".format(date_str)) + print("WARN: no OAI-PMH records for this date: {} (UTC)".format(date_str), file=sys.stderr) return count = 0 for item in records: count += 1 if count % 50 == 0: - print("... up to {}".format(count)) + print("... up to {}".format(count), file=sys.stderr) producer.produce( self.produce_topic, item.raw.encode('utf-8'), @@ -99,7 +100,7 @@ class HarvestOaiPmhWorker: while True: current = self.state.next(continuous) if current: - print("Fetching DOIs updated on {} (UTC)".format(current)) + print("Fetching DOIs updated on {} (UTC)".format(current), file=sys.stderr) self.fetch_date(current) self.state.complete(current, kafka_topic=self.state_topic, @@ -107,11 +108,11 @@ class HarvestOaiPmhWorker: continue if continuous: - print("Sleeping {} seconds...".format(self.loop_sleep)) + print("Sleeping {} seconds...".format(self.loop_sleep), file=sys.stderr) time.sleep(self.loop_sleep) else: break - print("{} OAI-PMH ingest caught up".format(self.name)) + print("{} OAI-PMH ingest caught up".format(self.name), file=sys.stderr) class HarvestArxivWorker(HarvestOaiPmhWorker): diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py index d936605f..10557ef8 100644 --- a/python/fatcat_tools/importers/__init__.py +++ b/python/fatcat_tools/importers/__init__.py @@ -28,3 +28,4 @@ from .arabesque import ArabesqueMatchImporter, ARABESQUE_MATCH_WHERE_CLAUSE from .wayback_static import auto_wayback_static from .cdl_dash_dat import auto_cdl_dash_dat from .ingest import IngestFileResultImporter, SavePaperNowFileImporter +from .shadow import ShadowLibraryImporter diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py index 1ffbd6e7..a84ce90f 100644 --- a/python/fatcat_tools/importers/common.py +++ b/python/fatcat_tools/importers/common.py @@ -194,6 +194,8 @@ DOMAIN_REL_MAP = { "www.scielo.cl": "repository", "www.scielo.org.mx": "repository", "zenodo.org": "repository", + "www.biorxiv.org": "repository", + "www.medrxiv.org": "repository", "citeseerx.ist.psu.edu": "aggregator", "publisher-connector.core.ac.uk": "aggregator", @@ -220,6 +222,13 @@ DOMAIN_REL_MAP = { "www.nature.com": "publisher", "www.pnas.org": "publisher", "www.tandfonline.com": "publisher", + "www.frontiersin.org": "publisher", + "www.degruyter.com": "publisher", + "www.mdpi.com": "publisher", + "www.ahajournals.org": "publisher", + "ehp.niehs.nih.gov": "publisher", + "journals.tsu.ru": "publisher", + "www.cogentoa.com": "publisher", "www.researchgate.net": "academicsocial", "academia.edu": "academicsocial", diff --git a/python/fatcat_tools/importers/datacite.py b/python/fatcat_tools/importers/datacite.py index 2f77481a..4e382348 100644 --- a/python/fatcat_tools/importers/datacite.py +++ b/python/fatcat_tools/importers/datacite.py @@ -1,11 +1,11 @@ """ Prototype importer for datacite.org data. -Example input document at: https://gist.github.com/miku/5610a2d64e3fee82d16f5d3f3a295fc8. +Example input document: https://api.datacite.org/dois/10.7916/d8-f93n-rk51 -Datacite being an aggregator, the data is varied and exposes a couple of -problems in content and structure. A few fields habe their own parsing -functions (parse_datacite_...), which can be tested more easily. +Datacite being an aggregator, the data is heterogenous and exposes a couple of +problems in content and structure. A few fields have their own parsing +functions (parse_datacite_...), which may help testing. """ import collections @@ -311,6 +311,16 @@ class DataciteImporter(EntityImporter): release_date, release_month, release_year = parse_datacite_dates( attributes.get('dates', [])) + # Some records do not use the "dates" field (e.g. micropub), but: + # "attributes.published" or "attributes.publicationYear" + if not any((release_date, release_month, release_year)): + release_date, release_month, release_year = parse_single_date(attributes.get('publicationYear')) + if not any((release_date, release_month, release_year)): + release_date, release_month, release_year = parse_single_date(attributes.get('published')) + + if not any((release_date, release_month, release_year)): + print('[{}] record w/o date: {}'.format(doi, obj), file=sys.stderr) + # Start with clear stages, e.g. published. TODO(martin): we could # probably infer a bit more from the relations, e.g. # "IsPreviousVersionOf" or "IsNewVersionOf". @@ -380,6 +390,11 @@ class DataciteImporter(EntityImporter): len(container_name))) container_name = container_name[0] + # Exception: https://www.micropublication.org/, see: !MR24. + if container_id is None and container_name is None: + if publisher and publisher.lower().startswith('micropublication'): + container_name = publisher + # Volume and issue. volume = container.get('volume') issue = container.get('issue') @@ -490,7 +505,7 @@ class DataciteImporter(EntityImporter): if len(text) > MAX_ABSTRACT_LENGTH: text = text[:MAX_ABSTRACT_LENGTH] + " [...]" - # Detect language. + # Detect language. This is fuzzy and may be removed, if too unreliable. lang = None try: lang = langdetect.detect(text) @@ -719,8 +734,10 @@ class DataciteImporter(EntityImporter): if name: name = clean(name) - if not name: + if not any((name, given_name, surname)): continue + if not name: + name = "{} {}".format(given_name or '', surname or '').strip() if name in name_blacklist: continue if name.lower() in UNKNOWN_MARKERS_LOWER: @@ -924,6 +941,32 @@ def parse_datacite_titles(titles): return title, original_language_title, subtitle +def parse_single_date(value): + """ + Given a single string containing a date in arbitrary format, try to return + tuple (date: datetime.date, month: int, year: int). + """ + if not value: + return None, None, None + if isinstance(value, int): + value = str(value) + parser = dateparser.DateDataParser() + try: + # Results in a dict with keys: date_obj, period, locale. + parse_result = parser.get_date_data(value) + # A datetime object, later we need a date, only. + result = parse_result['date_obj'] + if result is not None: + if parse_result['period'] == 'year': + return None, None, result.year + elif parse_result['period'] == 'month': + return None, result.month, result.year + else: + return result.date(), result.month, result.year + except TypeError as err: + print("{} date parsing failed with: {}".format(value, err), file=sys.stderr) + + return None, None, None def parse_datacite_dates(dates): """ @@ -966,7 +1009,7 @@ def parse_datacite_dates(dates): ) def parse_item(item): - result, value, year_only = None, item.get('date', ''), False + result, value, year_only = None, item.get('date', '') or '', False release_date, release_month, release_year = None, None, None for layout, granularity in common_patterns: @@ -981,23 +1024,7 @@ def parse_datacite_dates(dates): if result is None: print('fallback for {}'.format(value), file=sys.stderr) - parser = dateparser.DateDataParser() - try: - # Results in a dict with keys: date_obj, period, locale. - parse_result = parser.get_date_data(value) - - # A datetime object, later we need a date, only. - result = parse_result['date_obj'] - if result is not None: - if parse_result['period'] == 'year': - return None, None, result.year - elif parse_result['period'] == 'month': - return None, result.month, result.year - else: - return result.date(), result.month, result.year - except TypeError as err: - print("{} date parsing failed with: {}".format(value, err), - file=sys.stderr) + release_date, release_month, release_year = parse_single_date(value) if result is None: # Unparsable date. diff --git a/python/fatcat_tools/importers/ingest.py b/python/fatcat_tools/importers/ingest.py index bdfd2835..4772bfaa 100644 --- a/python/fatcat_tools/importers/ingest.py +++ b/python/fatcat_tools/importers/ingest.py @@ -31,6 +31,12 @@ class IngestFileResultImporter(EntityImporter): 'fatcat-ingest-container', 'fatcat-ingest', 'arabesque', + 'mag-corpus', + 'mag', + 'unpaywall-corpus', + 'unpaywall', + 's2-corpus', + 's2', ] if kwargs.get('skip_source_whitelist', False): self.ingest_request_source_whitelist = [] @@ -54,11 +60,14 @@ class IngestFileResultImporter(EntityImporter): self.counts['skip-hit'] += 1 return False source = row['request'].get('ingest_request_source') + if not source: + self.counts['skip-ingest_request_source'] += 1 + return False if self.ingest_request_source_whitelist and source not in self.ingest_request_source_whitelist: self.counts['skip-ingest_request_source'] += 1 return False if source.startswith('arabesque'): - if row['request'].get('link_source') not in ('arxiv', 'pmc', 'unpaywall', 'doi'): + if row['request'].get('link_source') not in ('arxiv', 'pmc', 'unpaywall', 'doi', 'mag', 's2'): self.counts['skip-arabesque-source'] += 1 return False if source.startswith('savepapernow'): @@ -131,7 +140,12 @@ class IngestFileResultImporter(EntityImporter): if not 'terminal_dt' in terminal: terminal['terminal_dt'] = terminal['dt'] assert len(terminal['terminal_dt']) == 14 - url = make_rel_url(terminal['terminal_url'], self.default_link_rel) + + default_rel = self.default_link_rel + if request.get('link_source') == 'doi': + default_rel = 'publisher' + default_rel = request.get('rel', default_rel) + url = make_rel_url(terminal['terminal_url'], default_rel) if not url: self.counts['skip-url'] += 1 @@ -152,8 +166,8 @@ class IngestFileResultImporter(EntityImporter): release_ids=[release_ident], urls=urls, ) - if fatcat and fatcat.get('edit_extra'): - fe.edit_extra = fatcat['edit_extra'] + if request.get('edit_extra'): + fe.edit_extra = request['edit_extra'] else: fe.edit_extra = dict() if request.get('ingest_request_source'): @@ -229,6 +243,9 @@ class SavePaperNowFileImporter(IngestFileResultImporter): def want(self, row): source = row['request'].get('ingest_request_source') + if not source: + self.counts['skip-ingest_request_source'] += 1 + return False if not source.startswith('savepapernow'): self.counts['skip-not-savepapernow'] += 1 return False diff --git a/python/fatcat_tools/importers/shadow.py b/python/fatcat_tools/importers/shadow.py new file mode 100644 index 00000000..4cd22775 --- /dev/null +++ b/python/fatcat_tools/importers/shadow.py @@ -0,0 +1,195 @@ + +import sys +import json +import sqlite3 +import itertools +import fatcat_openapi_client + +from fatcat_tools.normal import * +from .common import EntityImporter, make_rel_url, SANE_MAX_RELEASES, SANE_MAX_URLS + + +class ShadowLibraryImporter(EntityImporter): + """ + Importer for shadow library files (matched to releases) + + Input format is JSON with keys: + - shadow + - shadow_corpus (string slug) + - shadow_id (string) + - doi + - pmid + - isbn13 + - file_meta + - sha1hex + - sha256hex + - md5hex + - size_bytes + - mimetype + - cdx (may be null) + - url + - datetime + """ + + def __init__(self, api, **kwargs): + + eg_desc = kwargs.pop('editgroup_description', None) or "Import of 'Shadow Library' file/release matches" + eg_extra = kwargs.pop('editgroup_extra', dict()) + eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.ShadowLibraryImporter') + super().__init__(api, + editgroup_description=eg_desc, + editgroup_extra=eg_extra, + **kwargs) + self.default_link_rel = kwargs.get("default_link_rel", "web") + + def want(self, raw_record): + """ + Only want to import records with complete file-level metadata + """ + fm = raw_record['file_meta'] + if not (fm['mimetype'] and fm['md5hex'] and fm['sha256hex'] and fm['size_bytes']): + self.counts['skip-file-meta-incomplete'] += 1 + return False + if fm['mimetype'] != 'application/pdf': + self.counts['skip-not-pdf'] += 1 + return False + return True + + def parse_record(self, obj): + """ + We do the release lookup in this method. Try DOI, then PMID, last ISBN13. + """ + + shadow_corpus = obj['shadow']['shadow_corpus'] + assert shadow_corpus == shadow_corpus.strip().lower() + doi = clean_doi(obj['shadow'].get('doi')) + pmid = clean_pmid(obj['shadow'].get('pmid')) + isbn13 = clean_isbn13(obj['shadow'].get('isbn13')) + shadow_id = obj['shadow'].get('shadow_id').strip() + assert shadow_id + + extra = { '{}_id'.format(shadow_corpus): shadow_id } + for (ext_type, ext_id) in [('doi', doi), ('pmid', pmid), ('isbn13', isbn13)]: + if not ext_id: + continue + extra['{}_{}'.format(shadow_corpus, ext_type)] = ext_id + + # lookup release via several idents + re = None + for (ext_type, ext_id) in [('doi', doi), ('pmid', pmid), ('isbn13', isbn13)]: + if not ext_id: + continue + try: + re = self.api.lookup_release(**{ext_type: ext_id}) + except fatcat_openapi_client.rest.ApiException as err: + if err.status not in (404, 400): + raise err + re = None + if re: + break + + if not re: + self.counts['skip-release-not-found'] += 1 + return None + + release_ids = [re.ident,] + + # parse single CDX into URLs (if exists) + urls = [] + if obj.get('cdx'): + url = make_rel_url(obj['cdx']['url'], default_link_rel=self.default_link_rel) + if url != None: + urls.append(url) + wayback = "https://web.archive.org/web/{}/{}".format( + obj['cdx']['datetime'], + obj['cdx']['url']) + urls.append(("webarchive", wayback)) + urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls] + + fe = fatcat_openapi_client.FileEntity( + md5=obj['file_meta']['md5hex'], + sha1=obj['file_meta']['sha1hex'], + sha256=obj['file_meta']['sha256hex'], + size=int(obj['file_meta']['size_bytes']), + mimetype=obj['file_meta']['mimetype'] or None, + release_ids=release_ids, + urls=urls, + extra=dict(shadows=extra), + ) + return fe + + def try_update(self, fe): + # lookup sha1, or create new entity + 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 not existing: + return True + + if not existing.extra: + existing.extra = {} + + if existing.extra.get('shadows') and list(fe.extra['shadows'].keys())[0] in existing.extra['shadows']: + # already imported from this shadow library; skip + self.counts['exists'] += 1 + return False + + # check for edit conflicts + if existing.ident in [e.ident for e in self._edits_inflight]: + self.counts['skip-update-inflight'] += 1 + return False + if fe.sha1 in [e.sha1 for e in self._edits_inflight]: + raise Exception("Inflight insert; shouldn't happen") + + # minimum viable "existing" URL cleanup to fix dupes and broken links: + # remove 'None' wayback URLs, and set archive.org rel 'archive' + existing.urls = [u for u in existing.urls if not ('://web.archive.org/web/None/' in u.url)] + for i in range(len(existing.urls)): + u = existing.urls[i] + if u.rel == 'repository' and '://archive.org/download/' in u.url: + existing.urls[i].rel = 'archive' + if u.rel == 'social': + u.rel = 'academicsocial' + + # merge the existing into this one and update + merged_urls = {} + for u in fe.urls + existing.urls: + merged_urls[u.url] = u + existing.urls = list(merged_urls.values()) + if not existing.extra.get('shadows'): + existing.extra['shadows'] = fe.extra['shadows'] + else: + existing.extra['shadows'].update(fe.extra['shadows']) + + # do these "plus ones" because we really want to do these updates when possible + if len(existing.urls) > SANE_MAX_URLS + 1: + self.counts['skip-update-too-many-url'] += 1 + return None + existing.release_ids = list(set(fe.release_ids + existing.release_ids)) + if len(existing.release_ids) > SANE_MAX_RELEASES + 1: + self.counts['skip-update-too-many-releases'] += 1 + return None + existing.mimetype = existing.mimetype or fe.mimetype + existing.size = existing.size or fe.size + existing.md5 = existing.md5 or fe.md5 + existing.sha1 = existing.sha1 or fe.sha1 + existing.sha256 = existing.sha256 or fe.sha256 + edit = self.api.update_file(self.get_editgroup_id(), existing.ident, existing) + # add sha1 to non-entity edit row, so we can do more aggressive + # group-level de-dupe + edit.sha1 = existing.sha1 + self._edits_inflight.append(edit) + self.counts['update'] += 1 + return False + + def insert_batch(self, batch): + 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)) + diff --git a/python/fatcat_tools/transforms/ingest.py b/python/fatcat_tools/transforms/ingest.py index 27a4fb93..22b5154e 100644 --- a/python/fatcat_tools/transforms/ingest.py +++ b/python/fatcat_tools/transforms/ingest.py @@ -23,16 +23,16 @@ def release_ingest_request(release, ingest_request_source='fatcat', ingest_type= url = "https://arxiv.org/pdf/{}.pdf".format(release.ext_ids.arxiv) link_source = "arxiv" link_source_id = release.ext_ids.arxiv - elif release.ext_ids.doi: - url = "https://doi.org/{}".format(release.ext_ids.doi) - link_source = "doi" - link_source_id = release.ext_ids.doi elif release.ext_ids.pmcid: # TODO: how to tell if an author manuscript in PMC vs. published? #url = "https://www.ncbi.nlm.nih.gov/pmc/articles/{}/pdf/".format(release.ext_ids.pmcid) url = "http://europepmc.org/backend/ptpmcrender.fcgi?accid={}&blobtype=pdf".format(release.ext_ids.pmcid) link_source = "pmc" link_source_id = release.ext_ids.pmcid + elif release.ext_ids.doi: + url = "https://doi.org/{}".format(release.ext_ids.doi) + link_source = "doi" + link_source_id = release.ext_ids.doi if not url: return None diff --git a/python/fatcat_tools/workers/changelog.py b/python/fatcat_tools/workers/changelog.py index c8584ccf..b84d5e70 100644 --- a/python/fatcat_tools/workers/changelog.py +++ b/python/fatcat_tools/workers/changelog.py @@ -102,6 +102,12 @@ class EntityUpdatesWorker(FatcatWorker): # ccdc.cam.ac.uk: crystal structures "10.5517/", ] + self.live_pdf_ingest_doi_prefix_acceptlist = [ + # biorxiv and medrxiv + "10.1101/", + # researchgate + "10.13140/", + ] def want_live_ingest(self, release, ingest_request): """ @@ -115,13 +121,55 @@ class EntityUpdatesWorker(FatcatWorker): link_source = ingest_request.get('ingest_request') ingest_type = ingest_request.get('ingest_type') + doi = ingest_request.get('ext_ids', {}).get('doi') + + is_document = release.release_type in ( + 'article-journal', + 'paper-conference', + 'article', + 'report', + 'chapter', + 'manuscript', + 'review', + 'thesis', + 'letter', + 'editorial', + 'abstract', + 'entry', + 'patent', + 'post', + 'review-book', + ) + is_not_pdf = release.release_type in ( + 'dataset', + 'stub', + 'software', + 'figure', + 'graphic', + ) + + # accept list sets a default "crawl it" despite OA metadata for + # known-OA DOI prefixes + in_acceptlist = False + if doi: + for prefix in self.live_pdf_ingest_doi_prefix_acceptlist: + if doi.startswith(prefix): + in_acceptlist = True if self.ingest_oa_only and link_source not in ('arxiv', 'pmc'): es = release_to_elasticsearch(release) - if not es['is_oa']: + # most datacite documents are in IRs and should be crawled + is_datacite_doc = False + if release.extra and ('datacite' in release.extra) and is_document: + is_datacite_doc = True + if not (es['is_oa'] or in_acceptlist or is_datacite_doc): return False - doi = ingest_request.get('ext_ids', {}).get('doi') + # if ingest_type is pdf but release_type is almost certainly not a PDF, + # skip it. This is mostly a datacite thing. + if ingest_type == "pdf" and is_not_pdf: + return False + if ingest_type == "pdf" and doi: for prefix in self.ingest_pdf_doi_prefix_blocklist: if doi.startswith(prefix): |