import fatcat_openapi_client from .common import EntityImporter, make_rel_url class IngestFileResultImporter(EntityImporter): def __init__(self, api, require_grobid=True, **kwargs): eg_desc = kwargs.pop('editgroup_description', None) or "Files crawled from web using sandcrawler ingest tool" eg_extra = kwargs.pop('editgroup_extra', dict()) eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestFileResultImporter') kwargs['do_updates'] = kwargs.get("do_updates", False) super().__init__(api, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs) self.use_glutton_match = False self.default_link_rel = kwargs.get("default_link_rel", "web") assert self.default_link_rel self.require_grobid = require_grobid if self.require_grobid: print("Requiring GROBID status == 200 (for PDFs)") else: print("NOT checking GROBID success") self.ingest_request_source_allowlist = [ 'fatcat-changelog', 'fatcat-ingest-container', 'fatcat-ingest', 'arabesque', 'mag-corpus', 'mag', 'unpaywall-corpus', 'unpaywall', 's2-corpus', 's2', ] if kwargs.get('skip_source_allowlist', False): self.ingest_request_source_allowlist = [] def want(self, row): """ Logic here probably needs work (TODO): - Direct ingests via DOI from fatcat-changelog should probably go through regardless of GROBID status - We should filter/block things like single-page PDFs here - public/anonymous submissions could require successful biblio-glutton match, or some other sanity check on the fatcat side (eg, fuzzy title match) - handle the case of release_stage not being 'published'; if pre-print, potentially create a new release. The current logic is intentionally conservative as a first step. """ if row.get('hit') != True: 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', 'mag', 's2'): self.counts['skip-arabesque-source'] += 1 return False if source.startswith('savepapernow'): # never process async savepapernow requests self.counts['skip-savepapernow'] += 1 return False if not row.get('file_meta'): self.counts['skip-file-meta'] += 1 return False # type-specific filters if row['request'].get('ingest_type') == 'pdf': if self.require_grobid and row.get('grobid', {}).get('status_code') != 200: self.counts['skip-grobid'] += 1 return False if row['file_meta'].get('mimetype') not in ("application/pdf",): self.counts['skip-mimetype'] += 1 return False elif row['request'].get('ingest_type') == 'xml': if row['file_meta'].get('mimetype') not in ("application/xml", "application/jats+xml", "application/tei+xml", "text/xml"): self.counts['skip-mimetype'] += 1 return False else: self.counts['skip-ingest-type'] += 1 return False return True def parse_record(self, row): request = row['request'] fatcat = request.get('fatcat') file_meta = row['file_meta'] # double check that want() filtered request correctly (eg, old requests) if request.get('ingest_type') not in ('pdf', 'xml'): self.counts['skip-ingest-type'] += 1 return None assert (request['ingest_type'], file_meta['mimetype']) in [ ("pdf", "application/pdf"), ("xml", "application/xml"), ("xml", "application/jats+xml"), ("xml", "application/tei+xml"), ("xml", "text/xml"), ] # identify release by fatcat ident, or extid lookup, or biblio-glutton match release_ident = None if fatcat and fatcat.get('release_ident'): release_ident = fatcat.get('release_ident') elif request.get('ext_ids'): # if no fatcat ident, try extids for extid_type in ('doi', 'pmid', 'pmcid', 'arxiv'): extid = request['ext_ids'].get(extid_type) if not extid: continue try: release = self.api.lookup_release(**{extid_type: extid}) except fatcat_openapi_client.rest.ApiException as err: if err.status == 404: continue elif err.status == 400: self.counts['warn-extid-invalid'] += 1 continue raise err # verify release_stage if request.get('release_stage') and release.release_stage: if request['release_stage'] != release.release_stage: self.counts['skip-release-stage'] += 1 return None release_ident = release.ident break if self.use_glutton_match and not release_ident and row.get('grobid'): # try biblio-glutton extracted hit if row['grobid'].get('fatcat_release'): release_ident = row['grobid']['fatcat_release'].split('_')[-1] self.counts['glutton-match'] += 1 if not release_ident: self.counts['skip-release-not-found'] += 1 return None terminal = row.get('terminal') if not terminal: # support old cdx-only ingest results cdx = row.get('cdx') if not cdx: # TODO: support archive.org hits? self.counts['skip-no-terminal'] += 1 return None else: terminal = { 'terminal_url': cdx['url'], 'terminal_dt': cdx['datetime'], 'terminal_status_code': cdx.get('status_code') or cdx.get('http_status'), } # work around old schema if not 'terminal_url' in terminal: terminal['terminal_url'] = terminal['url'] if not 'terminal_dt' in terminal: terminal['terminal_dt'] = terminal['dt'] assert len(terminal['terminal_dt']) == 14 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 return None wayback = "https://web.archive.org/web/{}/{}".format( terminal['terminal_dt'], terminal['terminal_url']) urls = [url, ("webarchive", wayback)] urls = [fatcat_openapi_client.FileUrl(rel=rel, url=url) for (rel, url) in urls] fe = fatcat_openapi_client.FileEntity( md5=file_meta['md5hex'], sha1=file_meta['sha1hex'], sha256=file_meta['sha256hex'], size=file_meta['size_bytes'], mimetype=file_meta['mimetype'], release_ids=[release_ident], urls=urls, ) if request.get('edit_extra'): fe.edit_extra = request['edit_extra'] else: fe.edit_extra = dict() if request.get('ingest_request_source'): fe.edit_extra['ingest_request_source'] = request['ingest_request_source'] if request.get('link_source') and request.get('link_source_id'): fe.edit_extra['link_source'] = request['link_source'] fe.edit_extra['link_source_id'] = request['link_source_id'] if not fe.edit_extra: fe.edit_extra = None 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 # check for existing edits-in-progress with same file hash for other in self._entity_queue: if other.sha1 == fe.sha1: self.counts['skip-in-queue'] += 1 return False if not existing: return True # NOTE: the following checks all assume there is an existing item if (fe.release_ids[0] in existing.release_ids) and existing.urls: # TODO: could still, in theory update with the new URL? self.counts['exists'] += 1 return False if not self.do_updates: self.counts['skip-update-disabled'] += 1 return False # TODO: for now, never update self.counts['skip-update-disabled'] += 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)) class SavePaperNowFileImporter(IngestFileResultImporter): """ This worker ingests from the same feed as IngestFileResultImporter, but only imports files from anonymous save-paper-now requests, and "submits" them for further human review (as opposed to accepting by default). """ def __init__(self, api, submit_mode=True, **kwargs): eg_desc = kwargs.pop('editgroup_description', None) or "Files crawled after a public 'Save Paper Now' request" eg_extra = kwargs.pop('editgroup_extra', dict()) eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.IngestFileSavePaperNow') kwargs['submit_mode'] = submit_mode kwargs['require_grobid'] = True kwargs['do_updates'] = False super().__init__(api, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs) 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 if row.get('hit') != True: self.counts['skip-hit'] += 1 return False if not row.get('file_meta'): self.counts['skip-file-meta'] += 1 return False if self.require_grobid and row.get('grobid', {}).get('status_code') != 200: self.counts['skip-grobid'] += 1 return False return True def insert_batch(self, batch): """ Usually running in submit_mode, so we can't use auto_batch method """ if self.submit_mode: eg = self.api.create_editgroup(fatcat_openapi_client.Editgroup( description=self.editgroup_description, extra=self.editgroup_extra)) for fe in batch: self.api.create_file(eg.editgroup_id, fe) self.api.update_editgroup(eg.editgroup_id, eg, submit=True) else: 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))