#!/usr/bin/env python3 import sys import json import base64 import datetime import fatcat_openapi_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_openapi_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_openapi_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_openapi_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_openapi_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_openapi_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_openapi_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_openapi_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_openapi_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_openapi_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_openapi_client.FileAutoBatch( editgroup=fatcat_openapi_client.Editgroup( description=self.editgroup_description, extra=self.editgroup_extra), entity_list=batch))