import sys import json import sqlite3 import datetime import itertools import subprocess from bs4 import BeautifulSoup import fatcat_openapi_client from .common import EntityImporter, clean, is_cjk, DATE_FMT def parse_jalc_persons(raw_persons): """ For the most part, JALC DC names are in either japanese or english. The two common patterns are a list alternating between the two (in which case the names are translations), or all in one language or the other. Because dublin core is a projection tossing away a bunch of context, the other cases are hard to disambiguate. There are also some cases with Korean and other languages mixed in. This crude method doesn't handle everything right; it tries to just get the two common patterns correct. Sorry humans! Edge cases for this function: - 10.11316/jpsgaiyo.56.1.4.0_757_3 <= all english, some japanese, works - 10.14988/pa.2017.0000013531 <= complex, not japanese/english, mixed - 10.15036/arerugi.62.1407_1 <= one japanese, two english; fails - 10.14988/pa.2017.0000007327 <= ambiguous; translator in jpn/eng """ persons = [] # first parse out into language-agnostic dics for raw in raw_persons: name = raw.find('name') or None if name: name = clean(name.get_text().replace('\n', ' ')) surname = raw.find('familyName') or None if surname: surname = clean(surname.get_text().replace('\n', ' ')) given_name = raw.find('givenName') or None if given_name: given_name = clean(given_name.get_text().replace('\n', ' ')) lang = 'en' if is_cjk(name): lang = 'ja' if lang == 'en' and surname and given_name: # english names order is flipped name = "{} {}".format(given_name, surname) rc = fatcat_openapi_client.ReleaseContrib( raw_name=name, surname=surname, given_name=given_name, role="author") # add an extra hint field; won't end up in serialized object rc._lang = lang persons.append(rc) if not persons: return [] if all([p._lang == 'en' for p in persons]) or all([p._lang == 'ja' for p in persons]): # all english names, or all japanese names return persons # for debugging #if len([1 for p in persons if p._lang == 'en']) != len([1 for p in persons if p._lang == 'ja']): # print("INTERESTING: {}".format(persons[0])) start_lang = persons[0]._lang contribs = [] for p in persons: if p._lang == start_lang: contribs.append(p) else: if p._lang == 'en' and contribs[-1]._lang == 'ja': eng = p jpn = contribs[-1] elif p._lang == 'ja' and contribs[-1]._lang == 'en': eng = contribs[-1] jpn = p else: # give up and just add as another author contribs.append(p) continue eng.extra = { 'original_name': { 'lang': jpn._lang, 'raw_name': jpn.raw_name, 'given_name': jpn.given_name, 'surname': jpn.surname, }, } contribs[-1] = eng return contribs class JalcImporter(EntityImporter): """ Importer for JALC DOI metadata. NOTE: some JALC DOIs seem to get cross-registered with Crossref """ def __init__(self, api, issn_map_file, **kwargs): eg_desc = kwargs.get('editgroup_description', "Automated import of JALC DOI metadata") eg_extra = kwargs.get('editgroup_extra', dict()) eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.JalcImporter') super().__init__(api, issn_map_file=issn_map_file, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs) self.create_containers = kwargs.get('create_containers', True) extid_map_file = kwargs.get('extid_map_file') self.extid_map_db = None if extid_map_file: db_uri = "file:{}?mode=ro".format(extid_map_file) print("Using external ID map: {}".format(db_uri)) self.extid_map_db = sqlite3.connect(db_uri, uri=True) else: print("Not using external ID map") self.read_issn_map_file(issn_map_file) def lookup_ext_ids(self, doi): if self.extid_map_db is None: return dict(core_id=None, pmid=None, pmcid=None, wikidata_qid=None, arxiv_id=None, jstor_id=None) row = self.extid_map_db.execute("SELECT core, pmid, pmcid, wikidata FROM ids WHERE doi=? LIMIT 1", [doi.lower()]).fetchone() if row is None: return dict(core_id=None, pmid=None, pmcid=None, wikidata_qid=None, arxiv_id=None, jstor_id=None) row = [str(cell or '') or None for cell in row] return dict( core_id=row[0], pmid=row[1], pmcid=row[2], wikidata_qid=row[3], # TODO: arxiv_id=None, jstor_id=None, ) def want(self, obj): return True def parse_record(self, record): """ record is a beautiful soup object returns a ReleaseEntity, or None In JALC metadata, both English and Japanese records are given for most fields. """ extra = dict() extra_jalc = dict() titles = record.find_all("title") if not titles: return None title = titles[0].get_text().replace('\n', ' ').strip() original_title = None if title.endswith('.'): title = title[:-1] if len(titles) > 1: original_title = titles[1].get_text().replace('\n', ' ').strip() if original_title.endswith('.'): original_title = original_title[:-1] doi = None if record.doi: doi = record.doi.string.lower().strip() if doi.startswith('http://dx.doi.org/'): doi = doi.replace('http://dx.doi.org/', '') elif doi.startswith('https://dx.doi.org/'): doi = doi.replace('https://dx.doi.org/', '') elif doi.startswith('http://doi.org/'): doi = doi.replace('http://doi.org/', '') elif doi.startswith('https://doi.org/'): doi = doi.replace('https://doi.org/', '') if not (doi.startswith('10.') and '/' in doi): sys.stderr.write("bogus JALC DOI: {}\n".format(doi)) doi = None if not doi: return None people = record.find_all("Person") contribs = parse_jalc_persons(people) for i, contrib in enumerate(contribs): if contrib.raw_name != "et al.": contrib.index = i release_year = None release_date = None date = record.date or None if date: date = date.string if len(date) == 10: release_date = datetime.datetime.strptime(date['completed-date'], DATE_FMT).date() release_year = release_date.year release_date = release_date.isoformat() elif len(date) == 4 and date.isdigit(): release_year = int(date) pages = None if record.startingPage and record.startingPage.string.strip(): pages = record.startingPage.string.strip() if record.endingPage and record.endingPage.string.strip(): pages = "{}-{}".format(pages, record.endingPage.string.strip()) # double check to prevent "-" as pages if pages and pages.strip() == '-': pages = None volume = None if record.volume: volume = record.volume.string issue = None if record.number: # note: number/issue transform issue = record.number.string # container issn = None issn_list = record.find_all("issn") if issn_list: # if we wanted the other ISSNs, would also need to uniq the list. # But we only need one to lookup ISSN-L/container issn = issn_list[0].string issnl = self.issn2issnl(issn) container_id = None if issnl: container_id = self.lookup_issnl(issnl) publisher = None container_name = None container_extra = dict() if record.publicationName: pubs = [p.get_text().replace('\n', ' ').strip() for p in record.find_all("publicationName") if p.get_text()] pubs = [clean(p) for p in pubs if p] assert(pubs) if len(pubs) > 1 and pubs[0] == pubs[1]: pubs = [pubs[0]] if len(pubs) > 1 and is_cjk(pubs[0]): # eng/jpn ordering is not reliable pubs = [pubs[1], pubs[0]] container_name = clean(pubs[0]) if len(pubs) > 1: container_extra['original_name'] = clean(pubs[1]) if record.publisher: pubs = [p.get_text().replace('\n', ' ').strip() for p in record.find_all("publisher") if p.get_text()] pubs = [p for p in pubs if p] if len(pubs) > 1 and pubs[0] == pubs[1]: pubs = [pubs[0]] if len(pubs) > 1 and is_cjk(pubs[0]): # ordering is not reliable pubs = [pubs[1], pubs[0]] if pubs: publisher = clean(pubs[0]) if len(pubs) > 1: container_extra['publisher_aliases'] = pubs[1:] if (container_id is None and self.create_containers and (issnl is not None) and container_name): # name, type, publisher, issnl # extra: issnp, issne, original_name, languages, country container_extra['country'] = 'jp' container_extra['languages'] = ['ja'] ce = fatcat_openapi_client.ContainerEntity( name=container_name, container_type='journal', publisher=publisher, issnl=issnl, extra=(container_extra or None)) ce_edit = self.create_container(ce) container_id = ce_edit.ident # short-cut future imports in same batch self._issnl_id_map[issnl] = container_id # the vast majority of works are in japanese # TODO: any indication when *not* in japanese? lang = "ja" # reasonable default for this collection release_type = "article-journal" # external identifiers extids = self.lookup_ext_ids(doi=doi) # extra: # translation_of # aliases # container_name # group-title # always put at least an empty dict here to indicate the DOI registrar # (informally) extra['jalc'] = extra_jalc title = clean(title) if not title: return None re = fatcat_openapi_client.ReleaseEntity( work_id=None, title=title, original_title=clean(original_title), release_type="article-journal", release_stage='published', release_date=release_date, release_year=release_year, ext_ids=fatcat_openapi_client.ReleaseExtIds( doi=doi, pmid=extids['pmid'], pmcid=extids['pmcid'], wikidata_qid=extids['wikidata_qid'], core=extids['core_id'], arxiv=extids['arxiv_id'], jstor=extids['jstor_id'], ), volume=volume, issue=issue, pages=pages, publisher=publisher, language=lang, #license_slug container_id=container_id, contribs=contribs, extra=extra, ) return re def try_update(self, re): # lookup existing DOI existing = None try: existing = self.api.lookup_release(doi=re.ext_ids.doi) except fatcat_openapi_client.rest.ApiException as err: if err.status != 404: raise err # doesn't exist, need to insert 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 parse_file(self, handle): """ Helper for testing; can run this file stand-alone instead of using a pusher """ # 1. open with beautiful soup soup = BeautifulSoup(handle, "xml") # 2. iterate over articles, call parse_article on each for record in soup.find_all("Description"): resp = self.parse_record(record) #print(json.dumps(resp)) print(resp) #sys.exit(-1) if __name__=='__main__': parser = JalcImporter(None, None) parser.parse_file(open(sys.argv[1]))