diff options
Diffstat (limited to 'python/fatcat_tools')
| -rw-r--r-- | python/fatcat_tools/importers/__init__.py | 1 | ||||
| -rw-r--r-- | python/fatcat_tools/importers/doaj_article.py | 289 |
2 files changed, 290 insertions, 0 deletions
diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py index c08e04c2..d2928d09 100644 --- a/python/fatcat_tools/importers/__init__.py +++ b/python/fatcat_tools/importers/__init__.py @@ -30,3 +30,4 @@ from .cdl_dash_dat import auto_cdl_dash_dat from .ingest import IngestFileResultImporter, SavePaperNowFileImporter, IngestWebResultImporter from .shadow import ShadowLibraryImporter from .file_meta import FileMetaImporter +from .doaj_article import DoajArticleImporter diff --git a/python/fatcat_tools/importers/doaj_article.py b/python/fatcat_tools/importers/doaj_article.py new file mode 100644 index 00000000..74ac9a0e --- /dev/null +++ b/python/fatcat_tools/importers/doaj_article.py @@ -0,0 +1,289 @@ +""" +Importer for DOAJ article-level metadata, schema v1. + +DOAJ API schema and docs: https://doaj.org/api/v1/docs +""" + +import collections +import datetime +import sys +from typing import List, Dict, Optional + +import langdetect + +import fatcat_openapi_client +from fatcat_tools.normal import clean_doi +from fatcat_tools.transforms import entity_to_dict +from fatcat_tools.importers.common import EntityImporter, clean + +# Cutoff length for abstracts. +MAX_ABSTRACT_LENGTH = 2048 + + +class DoajArticleImporter(EntityImporter): + + def __init__(self, + api, + issn_map_file, + debug=False, + insert_log_file=None, + **kwargs): + + 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') + 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, obj): + return True + + + def parse_record(self, obj): + """ + 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) + } + + TODO: + - release_date + - container_id + - issue (number?) + - license is article license; import as slug + - "open_access" flag in doaj_meta + - container lookup from issns ("issns" key) + """ + + if not obj or not isinstance(obj, dict) or not 'bibjson' in obj: + self.counts['skip-empty'] += 1 + return None + + bibjson = obj['bibjson'] + + title = clean(bibjson.get('title')) + if not title: + self.counts['skip-title'] += 1 + return False + + container_id = None + container_name = None + + volume = clean(bibjson['journal'].get('volume')) + number = clean(bibjson['journal'].get('number')) + publisher = clean(bibjson['journal'].get('publisher')) + + try: + release_year = int(bibjson.get('year')) + except (TypeError, ValueError): + release_year = None + # XXX: parse_month + release_month = clean(bibjson.get('year')) + + # 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 + + # country + country = None + # XXX: country = parse_country(bibjson['journal'].get('country')) + + # language + language = None + # XXX: language = parse_language(bibjson['journal'].get('language')) + + # pages + # TODO: error in API docs? seems like start_page not under 'journal' object + start_page = clean(bibjson['journal'].get('start_page')) or clean(bibjson.get('start_page')) + end_page = clean(bibjson['journal'].get('end_page')) or clean(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() + if bibjson.get('subject'): + doaj_extra['subject'] = bibjson.get('subject') + if bibjson.get('keywords'): + doaj_extra['keywords'] = [k for k in [clean(s) for s in bibjson.get('keywords')] if k] + + # generic extra + extra = 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, + number=number, # XXX + #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): + """ + This function handles known special cases. For example, + publisher-specific or platform-specific workarounds. + """ + return re + + def try_update(self, re): + + # lookup existing DOI (don't need to try other ext idents for crossref) + 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 + # doesn't exist, need to update + return True + + # eventually we'll want to support "updates", but for now just skip if + # entity already exists + if existing: + self.counts['exists'] += 1 + return False + + return True + + def insert_batch(self, batch): + 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(bibjson['abstract']) + if not text or len(text) < 10: + return [] + if len(text) > MAX_ABSTRACT_LENGTH: + text = text[:MAX_ABSTRACT_LENGTH] + " [...]" + + # Detect language. This is fuzzy and may be removed, if too unreliable. + lang = None + try: + lang = langdetect.detect(text) + except (langdetect.lang_detect_exception.LangDetectException, TypeError) as err: + #print('[{}] language detection failed with {} on {}'.format(doi, err, text), file=sys.stderr) + pass + + 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 = [] + # TODO: index? + for author in authors: + if not author.get('name'): + continue + contribs.append(fatcat_openapi_client.ReleaseContrib( + raw_name=author.get('name'), + # XXX: orcid_id=author.get('orcid_id') or None, + # XXX: affiliation=author.get('affiliation') or None, + )) + 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 id_obj['type'].lower() == 'doi': + doi = clean_doi(id_obj['id']) + elif id_obj['type'].lower() == 'pmid': + pmid = id_obj['id'] + elif id_obj['type'].lower() == 'pmcid': + pmcid = id_obj['id'] + + return fatcat_openapi_client.ReleaseExtIds( + doaj=doaj_article_id, + doi=doi, + pmid=pmid, + pmcid=pmcid, + ) |