""" Importer for DOAJ article-level metadata, schema v1. DOAJ API schema and docs: https://doaj.org/api/v1/docs """ import datetime import warnings from typing import Any, Dict, List, Optional, Sequence import fatcat_openapi_client from fatcat_openapi_client import ApiClient, ReleaseEntity from fatcat_tools.importers.common import EntityImporter from fatcat_tools.normal import ( clean_doi, clean_orcid, clean_pmcid, clean_pmid, clean_str, detect_text_lang, parse_country_name, parse_lang_name, parse_month, ) # Cutoff length for abstracts. MAX_ABSTRACT_LENGTH = 2048 class DoajArticleImporter(EntityImporter): def __init__(self, api: ApiClient, issn_map_file: Sequence, **kwargs) -> None: eg_desc = kwargs.get( "editgroup_description", "Automated import of DOAJ article metadata, harvested from REST API or bulk dumps", ) eg_extra = kwargs.get("editgroup_extra", dict()) eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.DoajArticleImporter") # ensure default is to not do updates with this worker (override super() default) kwargs["do_updates"] = kwargs.get("do_updates", False) super().__init__( api, issn_map_file=issn_map_file, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs, ) self.this_year = datetime.datetime.now().year self.read_issn_map_file(issn_map_file) def want(self, raw_record: Dict[str, Any]) -> bool: return True def parse_record(self, obj: Dict[str, Any]) -> Optional[ReleaseEntity]: """ bibjson { abstract (string, optional), author (Array[bibjson.author], optional), identifier (Array[bibjson.identifier]), journal (bibjson.journal, optional), keywords (Array[string], optional), link (Array[bibjson.link], optional), month (string, optional), subject (Array[bibjson.subject], optional), title (string), year (string, optional) } bibjson.journal { country (string, optional), end_page (string, optional), language (Array[string], optional), license (Array[bibjson.journal.license], optional), number (string, optional), publisher (string, optional), start_page (string, optional), title (string, optional), volume (string, optional) } """ if not obj or not isinstance(obj, dict) or "bibjson" not in obj: self.counts["skip-empty"] += 1 return None bibjson = obj["bibjson"] title = clean_str(bibjson.get("title"), force_xml=True) if not title: self.counts["skip-title"] += 1 return False container_name = clean_str(bibjson["journal"]["title"]) container_id = None # NOTE: 'issns' not documented in API schema for issn in bibjson["journal"]["issns"]: issnl = self.issn2issnl(issn) if issnl: container_id = self.lookup_issnl(self.issn2issnl(issn)) if container_id: # don't store container_name when we have an exact match container_name = None break volume = clean_str(bibjson["journal"].get("volume")) # NOTE: this schema seems to use "number" as "issue number" issue = clean_str(bibjson["journal"].get("number")) publisher = clean_str(bibjson["journal"].get("publisher")) try: release_year: Optional[int] = int(bibjson.get("year")) except (TypeError, ValueError): release_year = None release_month = parse_month(clean_str(bibjson.get("month"))) # block bogus far-future years/dates if release_year is not None and ( release_year > (self.this_year + 5) or release_year < 1000 ): release_month = None release_year = None license_slug = self.doaj_license_slug(bibjson["journal"].get("license")) country = parse_country_name(bibjson["journal"].get("country")) language = None for raw in bibjson["journal"].get("language") or []: language = parse_lang_name(raw) if language: break # pages # NOTE: error in API docs? seems like start_page not under 'journal' object start_page = clean_str(bibjson["journal"].get("start_page")) or clean_str( bibjson.get("start_page") ) end_page = clean_str(bibjson["journal"].get("end_page")) or clean_str( bibjson.get("end_page") ) pages: Optional[str] = None if start_page and end_page: pages = f"{start_page}-{end_page}" elif start_page: pages = start_page doaj_article_id = obj["id"].lower() ext_ids = self.doaj_ext_ids(bibjson["identifier"], doaj_article_id) abstracts = self.doaj_abstracts(bibjson) contribs = self.doaj_contribs(bibjson.get("author") or []) # DOAJ-specific extra doaj_extra: Dict[str, Any] = dict() if bibjson.get("subject"): doaj_extra["subject"] = bibjson.get("subject") if bibjson.get("keywords"): doaj_extra["keywords"] = [ k for k in [clean_str(s) for s in bibjson.get("keywords")] if k ] # generic extra extra: Dict[str, Any] = dict() if country: extra["country"] = country if not container_id and container_name: extra["container_name"] = container_name if release_year and release_month: # TODO: schema migration extra["release_month"] = release_month if doaj_extra: extra["doaj"] = doaj_extra if not extra: extra = None re = fatcat_openapi_client.ReleaseEntity( work_id=None, container_id=container_id, release_type="article-journal", release_stage="published", title=title, release_year=release_year, # release_date, publisher=publisher, ext_ids=ext_ids, contribs=contribs, volume=volume, issue=issue, pages=pages, language=language, abstracts=abstracts, extra=extra, license_slug=license_slug, ) re = self.biblio_hacks(re) return re @staticmethod def biblio_hacks(re: ReleaseEntity) -> ReleaseEntity: """ This function handles known special cases. For example, publisher-specific or platform-specific workarounds. """ return re def try_update(self, re: ReleaseEntity) -> bool: # lookup existing release by DOAJ article id existing = None try: existing = self.api.lookup_release(doaj=re.ext_ids.doaj) except fatcat_openapi_client.rest.ApiException as err: if err.status != 404: raise err # then try other ext_id lookups if not existing: for extid_type in ("doi", "pmid", "pmcid"): extid_val = getattr(re.ext_ids, extid_type) if not extid_val: continue # print(f" lookup release type: {extid_type} val: {extid_val}") try: existing = self.api.lookup_release(**{extid_type: extid_val}) except fatcat_openapi_client.rest.ApiException as err: if err.status != 404: raise err if existing: if existing.ext_ids.doaj: warn_str = f"unexpected DOAJ ext_id match after lookup failed doaj={re.ext_ids.doaj} ident={existing.ident}" warnings.warn(warn_str) self.counts["skip-doaj-id-mismatch"] += 1 return False break if not existing and self.do_fuzzy_match: fuzzy_result = self.match_existing_release_fuzzy(re) # TODO: in the future, could assign work_id for clustering, or for # "EXACT" match, set existing and allow (optional) update code path # to run if fuzzy_result is not None: self.counts["exists-fuzzy"] += 1 return False # if no fuzzy existing match, create entity if not existing: return True # other logic could go here about skipping updates if not self.do_updates or existing.ext_ids.doaj: self.counts["exists"] += 1 return False # fields to copy over for update existing.ext_ids.doaj = existing.ext_ids.doaj or re.ext_ids.doaj existing.release_type = existing.release_type or re.release_type existing.release_stage = existing.release_stage or re.release_stage existing.container_id = existing.container_id or re.container_id existing.abstracts = existing.abstracts or re.abstracts existing.extra["doaj"] = re.extra["doaj"] existing.volume = existing.volume or re.volume existing.issue = existing.issue or re.issue existing.pages = existing.pages or re.pages existing.language = existing.language or re.language try: self.api.update_release(self.get_editgroup_id(), existing.ident, existing) self.counts["update"] += 1 except fatcat_openapi_client.rest.ApiException as err: # there is a code path where we try to update the same release # twice in a row; if that happens, just skip # NOTE: API behavior might change in the future? if "release_edit_editgroup_id_ident_id_key" in err.body: self.counts["skip-update-conflict"] += 1 return False else: raise err return False def insert_batch(self, batch: List[ReleaseEntity]) -> None: self.api.create_release_auto_batch( fatcat_openapi_client.ReleaseAutoBatch( editgroup=fatcat_openapi_client.Editgroup( description=self.editgroup_description, extra=self.editgroup_extra ), entity_list=batch, ) ) def doaj_abstracts(self, bibjson: dict) -> List[fatcat_openapi_client.ReleaseAbstract]: text = clean_str(bibjson.get("abstract")) if not text or len(text) < 10: return [] if len(text) > MAX_ABSTRACT_LENGTH: text = text[:MAX_ABSTRACT_LENGTH] + " [...]" lang = detect_text_lang(text) abstract = fatcat_openapi_client.ReleaseAbstract( mimetype="text/plain", content=text, lang=lang, ) return [ abstract, ] def doaj_contribs(self, authors: List[dict]) -> List[fatcat_openapi_client.ReleaseContrib]: """ bibjson.author { affiliation (string, optional), name (string), orcid_id (string, optional) } """ contribs = [] index = 0 for author in authors: if not author.get("name"): continue creator_id = None orcid = clean_orcid(author.get("orcid_id")) if orcid: creator_id = self.lookup_orcid(orcid) contribs.append( fatcat_openapi_client.ReleaseContrib( raw_name=author.get("name"), role="author", index=index, creator_id=creator_id, raw_affiliation=clean_str(author.get("affiliation")), ) ) index += 1 return contribs def doaj_ext_ids( self, identifiers: List[dict], doaj_article_id: str ) -> fatcat_openapi_client.ReleaseExtIds: """ bibjson.identifier { id (string), type (string) } """ assert doaj_article_id.isalnum() and len(doaj_article_id) == 32 doi: Optional[str] = None pmid: Optional[str] = None pmcid: Optional[str] = None for id_obj in identifiers: if not id_obj.get("id"): continue if id_obj["type"].lower() == "doi": doi = clean_doi(id_obj["id"]) elif id_obj["type"].lower() == "pmid": pmid = clean_pmid(id_obj["id"]) elif id_obj["type"].lower() == "pmcid": pmcid = clean_pmcid(id_obj["id"]) return fatcat_openapi_client.ReleaseExtIds( doaj=doaj_article_id, doi=doi, pmid=pmid, pmcid=pmcid, ) def doaj_license_slug(self, license_list: List[dict]) -> Optional[str]: """ bibjson.journal.license { open_access (boolean, optional), title (string, optional), type (string, optional), url (string, optional), version (string, optional) } """ if not license_list: return None for license in license_list: if not license.get("open_access"): continue slug = license.get("type") if slug and slug.startswith("CC "): slug = slug.replace("CC ", "cc-").lower() return slug return None