""" Prototype Importer for datacite.org data. Example doc at: https://gist.github.com/miku/5610a2d64e3fee82d16f5d3f3a295fc8 """ from .common import EntityImporter import dateparser import datetime import fatcat_openapi_client import hashlib import json import pycountry import langdetect import sqlite3 import sys from fatcat_tools.transforms import entity_to_dict # Cutoff length for abstracts. MAX_ABSTRACT_LENGTH = 2048 # https://guide.fatcat.wiki/entity_container.html#container_type-vocabulary CONTAINER_TYPE_MAP = { 'Journal': 'journal', 'Series': 'journal', 'Book Series': 'book-series', } # The docs/guide should be the cannonical home for these mappings; update there # first. Map various datacite type types to CSL-ish types. None means TODO or # remove. DATACITE_TYPE_MAP = { 'ris': { 'THES': 'thesis', 'SOUND': None, 'CHAP': 'chapter', 'FIGURE': None, 'RPRT': 'report', 'JOUR': 'article-journal', 'MPCT': None, 'GEN': None, 'BOOK': 'book', 'DATA': 'dataset', 'COMP': None, }, 'schemaOrg': { 'Dataset': 'dataset', 'Book': 'book', 'ScholarlyArticle': 'article', 'ImageObject': 'graphic', 'Collection': None, 'MediaObject': None, 'Event': None, 'SoftwareSourceCode': None, 'Chapter': 'chapter', 'CreativeWork': None, 'PublicationIssue': 'article', 'AudioObject': None, 'Thesis': 'thesis', }, 'citeproc': { 'article': 'article', 'article-journal': 'article-journal', 'article-magazine': 'article-magazine', 'article-newspaper': 'article-newspaper', 'bill': 'bill', 'book': 'book', 'broadcast': 'broadcast', 'chapter': 'chapter', 'dataset': 'dataset', 'entry-dictionary': 'entry-dictionary', 'entry-encyclopedia': 'entry-encyclopedia', 'entry': 'entry', 'figure': 'figure', 'graphic': 'graphic', 'interview': 'interview', 'legal_case': 'legal_case', 'legislation': 'legislation', 'manuscript': 'manuscript', 'map': 'map', 'motion_picture': 'motion_picture', 'musical_score': 'musical_score', 'pamphlet': 'pamphlet', 'paper-conference': 'paper-conference', 'patent': 'patent', 'personal_communication': 'personal_communication', 'post': 'post', 'post-weblog': 'post-weblog', 'report': 'report', 'review-book': 'review-book', 'review': 'review', 'song': 'song', 'speech': 'speech', 'thesis': 'thesis', 'treaty': 'treaty', 'webpage': 'webpage', }, # https://docs.citationstyles.org/en/master/specification.html#appendix-iii-types 'bibtex': { 'phdthesis': 'thesis', 'inbook': 'chapter', 'misc': None, 'article': 'article-journal', 'book': 'book', }, 'resourceTypeGeneral': { 'Image': None, 'Dataset': 'dataset', 'PhysicalObject': None, 'Collection': None, 'Text': None, 'Sound': None, 'InteractiveResource': None, 'Event': None, 'Software': None, 'Other': None, 'Workflow': None, 'Audiovisual': None, } } # TODO(martin): merge this with other maps, maybe. LICENSE_SLUG_MAP = { "//creativecommons.org/licenses/by/2.0/": "CC-BY", "//creativecommons.org/licenses/by/2.0/uk/legalcode": "CC-BY", "//creativecommons.org/licenses/by/3.0/": "CC-BY", "//creativecommons.org/licenses/by/3.0/us": "CC-BY", "//creativecommons.org/licenses/by/4.0/": "CC-BY", "//creativecommons.org/licenses/by/4.0/deed.de/": "CC-BY", "//creativecommons.org/licenses/by/4.0/deed.en_US/": "CC-BY", "//creativecommons.org/licenses/by/4.0/legalcode/": "CC-BY", "//creativecommons.org/licenses/by-nc/2.0/": "CC-BY-NC", "//creativecommons.org/licenses/by-nc/3.0/": "CC-BY-NC", "//creativecommons.org/licenses/by-nc/4.0/": "CC-BY-NC", "//creativecommons.org/licenses/by-nc/4.0/legalcode": "CC-BY-NC", "//creativecommons.org/licenses/by-nc-nd/3.0/": "CC-BY-NC-ND", "//creativecommons.org/licenses/by-nc-nd/3.0/gr": "CC-BY-NC-ND", "//creativecommons.org/licenses/by-nc-nd/4.0/": "CC-BY-ND", "//creativecommons.org/licenses/by-nc-nd/4.0/legalcode": "CC-BY-ND", "//creativecommons.org/licenses/by-nc-sa/4.0/": "CC-BY-NC-SA", "//creativecommons.org/licenses/by-nd/4.0/": "CC-BY-ND", "//creativecommons.org/licenses/by-sa/3.0/de": "CC-BY-SA", "//creativecommons.org/licenses/by-sa/3.0/gr": "CC-BY-SA", "//creativecommons.org/licenses/by-sa/4.0/": "CC-BY-SA", "//creativecommons.org/licenses/by-sa/4.0/legalcode": "CC-BY-SA", "//creativecommons.org/licenses/CC-BY/4.0/": "CC-BY", "//creativecommons.org/licenses/publicdomain/zero/1.0/": "CC-0", "//creativecommons.org/publicdomain/zero/1.0/": "CC-0", "//creativecommons.org/publicdomain/zero/1.0/legalcode": "CC-0", "//opensource.org/licenses/MIT": "MIT", "//www.elsevier.com/open-access/userlicense/1.0": "ELSEVIER-USER-1.0", "//www.gnu.org/licenses/gpl-3.0.en.html": "GPLv3", "//www.gnu.org/licenses/old-licenses/gpl-2.0.en.html": "GPLv2", "//www.karger.com/Services/SiteLicenses": "KARGER", "//www.opensource.org/licenses/Apache-2.0": "Apache-2.0", "//www.opensource.org/licenses/BSD-3-Clause": "BSD-3-Clause", "//www.opensource.org/licenses/EUPL-1.1": "EUPL-1.1", # redirects to EUPL-1.2 "//www.opensource.org/licenses/MIT": "MIT", # "http://royalsocietypublishing.org/licence": "", # OA and "normal", https://royalsociety.org/journals/authors/licence-to-publish/ # "http://rsc.li/journals-terms-of-use": "RSC", # "http://www.fu-berlin.de/sites/refubium/rechtliches/Nutzungsbedingungen": "", # 53 UrhG. # "http://www.nrcresearchpress.com/page/about/CorporateTextAndDataMining": "", # "http://www.springer.com/tdm": "", # "https://cds.unistra.fr/vizier-org/licences_vizier.html": "", # Maybe try to "SPN" those: https://web.archive.org/web/*/https://cds.unistra.fr/vizier-org/licences_vizier.html # "https://link.aps.org/licenses/aps-default-accepted-manuscript-license": "", # "https://oparu.uni-ulm.de/xmlui/license_opod_v1": "", # "https://publikationen.bibliothek.kit.edu/kitopen-lizenz": "", # "https://rightsstatements.org/page/InC/1.0?language=en": "", # "https://services.ceda.ac.uk/cedasite/register/info": "", # "https://wdc.dlr.de/ndmc/userfiles/file/NDMC-Data_Sharing_Principles.pdf": "", # 404 # "https://www.cambridge.org/core/terms": "", # "https://www.elsevier.com/tdm/userlicense/1.0", # "info:eu-repo/semantics/closedAccess": "", # https://wiki.surfnet.nl/display/standards/info-eu-repo/#info-eu-repo-AccessRights # "info:eu-repo/semantics/embargoedAccess": "", # "info:eu-repo/semantics/openAccess": "", # Note: Some URLs pointing to licensing terms are not in WB yet (but would be nice). } class DataciteImporter(EntityImporter): """ Importer for datacite records. """ def __init__(self, api, issn_map_file, debug=False, lang_detect=False, insert_log_file=None, **kwargs): eg_desc = kwargs.get( 'editgroup_description', "Automated import of Datacite DOI metadata, harvested from REST API" ) eg_extra = kwargs.get('editgroup_extra', dict()) eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.DataciteImporter') 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), file=sys.stderr) self.extid_map_db = sqlite3.connect(db_uri, uri=True) else: print("Not using external ID map", file=sys.stderr) self.read_issn_map_file(issn_map_file) self.debug = debug self.lang_detect = lang_detect self.insert_log_file = insert_log_file print('datacite with debug={}, lang_detect={}'.format( self.debug, self.lang_detect), file=sys.stderr) def lookup_ext_ids(self, doi): """ Return dictionary of identifiers refering to the same things as the given 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 parse_record(self, obj): """ Mapping datacite JSON to ReleaseEntity. """ if not obj or not isinstance(obj, dict): return None if 'attributes' not in obj: return None attributes = obj['attributes'] # Contributors. Many nameIdentifierSchemes, we do not use (yet): # "attributes.creators[].nameIdentifiers[].nameIdentifierScheme": # ["LCNA", "GND", "email", "NAF", "OSF", "RRID", "ORCID", # "SCOPUS", "NRCPID", "schema.org", "GRID", "MGDS", "VIAF", "JACoW-ID"]. contribs = [] for i, c in enumerate(attributes['creators']): nameType = c.get('nameType', '') or '' if nameType == 'Personal': creator_id = None for nid in c.get('nameIdentifiers', []): if not nid.get('nameIdentifierScheme').lower() == "orcid": continue orcid = nid.get('nameIdentifier', '').replace('https://orcid.org/', '') if not orcid: continue creator_id = self.lookup_orcid(orcid) # TODO(martin): If creator_id is None, should we create creators? # If there are multiple affiliation strings, use the first one. affiliations = c.get('affiliation', []) or [] raw_affiliation = None if len(affiliations) == 0: raw_affiliation = None else: raw_affiliation = affiliations[0] contribs.append( fatcat_openapi_client.ReleaseContrib( creator_id=creator_id, index=i, raw_name=c.get('name'), given_name=c.get('givenName'), surname=c.get('familyName'), role='author', raw_affiliation=raw_affiliation, )) elif nameType == 'Organizational': name = c.get('name', '') or '' if name == 'NN': continue if len(name) < 3: continue extra = {'organization': name} contribs.append(fatcat_openapi_client.ReleaseContrib( index=i, extra=extra)) else: print('unknown name type: {}'.format(nameType), file=sys.stderr) # Title, may come with "attributes.titles[].titleType", like # "AlternativeTitle", "Other", "Subtitle", "TranslatedTitle" titles = attributes.get('titles', []) or [] title, original_language_title, subtitle = parse_datacite_titles( titles) if not title: print('skipping record w/o title: {}'.format(obj), file=sys.stderr) return False if not subtitle: subtitle = None # Dates. A few internal dates (registered, created, updated) and # published (0..2554). We try to work with typed date list, in # "attributes.dates[].dateType", values: "Accepted", "Available" # "Collected", "Copyrighted", "Created", "Issued", "Submitted", # "Updated", "Valid". release_date, release_year = parse_datacite_dates( attributes.get('dates', [])) # Publisher. A few NA values. A few bogus values. publisher = attributes.get('publisher') if publisher in ('(:unav)', 'Unknown', 'n.a.', '[s.n.]', '(:unap)', '(:none)'): publisher = None if publisher is not None and len(publisher) > 80: # Arbitrary magic value max length. TODO(martin): better heuristic, # but factored out; first we have to log misses. Example: # "ETH-Bibliothek Zürich, Bildarchiv / Fotograf: Feller, # Elisabeth, Empfänger, Unbekannt, Fotograf / Fel_041033-RE / # Unbekannt, Nutzungsrechte müssen durch den Nutzer abgeklärt # werden" publisher = None # Container. For the moment, only ISSN as container. container_id = None container = attributes.get('container', {}) or {} if container.get('type') in CONTAINER_TYPE_MAP.keys(): container_type = CONTAINER_TYPE_MAP.get(container['type']) if container.get('identifier') and container.get( 'identifierType') == 'ISSN': issn = container.get('identifier') if len(issn) == 8: issn = issn[:4] + "-" + issn[4:] issnl = self.issn2issnl(issn) if issnl is not None: container_id = self.lookup_issnl(issnl) if container_id is None and container.get('title'): container_title = container.get('title') if isinstance(container_title, list): if len(container_title) > 0: print('too many container titles: {}'.format( len(container_title))) container_title = container_title[0] assert isinstance(container_title, str) ce = fatcat_openapi_client.ContainerEntity( issnl=issnl, container_type=container_type, name=container_title, ) ce_edit = self.create_container(ce) container_id = ce_edit.ident self._issnl_id_map[issnl] = container_id # Volume and issue. volume = container.get('volume') issue = container.get('issue') # Pages. pages = None first_page = container.get('firstPage') last_page = container.get('lastPage') if first_page and last_page: try: int(first_page) < int(last_page) pages = '{}-{}'.format(first_page, last_page) except ValueError as err: print(err, file=sys.stderr) pass if not pages and first_page: pages = first_page # License. license_slug = None license_extra = [] for l in attributes.get('rightsList', []): slug = lookup_license_slug(l.get('rightsUri')) if slug: license_slug = slug license_extra.append(l) # Release type. Try to determine the release type from a variety of # types supplied in datacite. The "attributes.types.resourceType" # contains too many (176 in sample) things for now; citeproc may be the # closest, but not always supplied. for typeType in ('citeproc', 'resourceTypeGeneral', 'schemaOrg', 'bibtex', 'ris'): value = attributes.get('types', {}).get(typeType) release_type = DATACITE_TYPE_MAP.get(typeType, {}).get(value) if release_type is not None: break if release_type is None: print("no mapped type: {}".format(value), file=sys.stderr) # Language values are varied ("ger", "es", "English", "ENG", "en-us", # "other", ...). Try to crush it with langcodes: "It may sound to you # like langcodes solves a pretty boring problem. At one level, that's # right. Sometimes you have a boring problem, and it's great when a # library solves it for you." -- TODO(martin): We need more of these. language = None value = attributes.get('language', '') or '' try: language = pycountry.languages.lookup(value).alpha_2 except (LookupError, AttributeError) as err: print('language lookup miss for {}: {}'.format(value, err), file=sys.stderr) # Abstracts appear in "attributes.descriptions[].descriptionType", some # of the observed values: "Methods", "TechnicalInfo", # "SeriesInformation", "Other", "TableOfContents", "Abstract". The # "Other" fields might contain references or related articles (with # DOI). TODO(martin): maybe try to parse out some of those refs. abstracts = [] descs = attributes.get('descriptions', []) or [] for desc in descs: if not desc.get('descriptionType') == 'Abstract': continue if len(desc.get('description', '')) < 10: continue text = desc.get('description') if len(text) > MAX_ABSTRACT_LENGTH: text = text[:MAX_ABSTRACT_LENGTH] + " [...]" lang = None if self.lang_detect: try: lang = langdetect.detect(text) except langdetect.lang_detect_exception.LangDetectException as err: print('language detection failed: {}'.format(err), file=sys.stderr) abstracts.append( fatcat_openapi_client.ReleaseAbstract( mimetype="text/plain", content=text, lang=lang, )) # References and relations. Datacite include many relation types in # "attributes.relatedIdentifiers[].relationType", e.g. # "IsPartOf", "IsPreviousVersionOf", "Continues", "IsVariantFormOf", # "IsSupplementTo", "Cites", "IsSupplementedBy", "IsDocumentedBy", "HasVersion", # "IsCitedBy", "IsMetadataFor", "IsNewVersionOf", "IsIdenticalTo", "HasPart", # "References", "Reviews", "HasMetadata", "IsContinuedBy", "IsVersionOf", # "IsDerivedFrom", "IsSourceOf". # # For the moment, we only care about References. refs, ref_index = [], 0 relIds = attributes.get('relatedIdentifiers', []) or [] for rel in relIds: if not rel.get('relationType') == 'References': continue ref_extra = dict() if rel.get('relatedIdentifierType') == 'DOI': ref_extra['doi'] = rel.get('relatedIdentifier') if not ref_extra: ref_extra = None refs.append( fatcat_openapi_client.ReleaseRef( index=ref_index, extra=ref_extra, )) ref_index += 1 # Start with clear stages, e.g. published. TODO(martin): we could # probably infer a bit more from the relations, e.g. # "IsPreviousVersionOf" or "IsNewVersionOf". release_stage = None if attributes.get( 'state') == 'findable' or attributes.get('isActive') is True: release_stage = 'published' # Extra information. extra_datacite = dict() if license_extra: extra_datacite['license'] = license_extra if attributes.get('subjects'): extra_datacite['subjects'] = attributes['subjects'] # Include certain relations from relatedIdentifiers. Keeping the # original structure of data here, which is a list of dicts, with # relation type, identifer and identifier type (mostly). relations = [] for rel in relIds: if rel.get('relationType') in ('IsPartOf', 'Reviews', 'Continues', 'IsVariantFormOf', 'IsSupplementTo', 'HasVersion', 'IsMetadataFor', 'IsNewVersionOf', 'IsIdenticalTo', 'IsVersionOf', 'IsDerivedFrom', 'IsSourceOf'): relations.append(rel) if relations: extra_datacite['relations'] = relations extra = dict() if extra_datacite: extra['datacite'] = extra_datacite doi = attributes.get('doi', '').lower() extids = self.lookup_ext_ids(doi=doi) # Assemble release. re = fatcat_openapi_client.ReleaseEntity( work_id=None, container_id=container_id, release_type=release_type, release_stage=release_stage, title=title, subtitle=subtitle, original_title=original_language_title, release_year=release_year, release_date=release_date, publisher=publisher, 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'], ), contribs=contribs, volume=volume, issue=issue, pages=pages, language=language, abstracts=abstracts, refs=refs, extra=extra, license_slug=license_slug, ) return re def try_update(self, re): """ When debug is true, write the RE to stdout, not to the database. Might hide schema mismatch bugs. """ if self.debug is True: print(json.dumps(entity_to_dict(re, api_client=None))) return False # lookup existing DOI (don't need to try other ext idents for crossref) 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 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): print('inserting batch ({})'.format(len(batch)), file=sys.stderr) if self.insert_log_file: with open(self.insert_log_file, 'a') as f: for doc in batch: json.dump(entity_to_dict(re, api_client=None), f) f.write('\n') 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 lookup_license_slug(raw): """ TODO(martin): reuse from or combine with crossref, maybe. """ if not raw: return None raw = raw.strip().replace('http://', '//').replace('https://', '//') if 'creativecommons.org' in raw.lower(): raw = raw.lower() raw = raw.replace('/legalcode', '/').replace('/uk', '') if not raw.endswith('/'): raw = raw + '/' return LICENSE_SLUG_MAP.get(raw) def find_original_language_title(item, min_length=4, max_questionmarks=3): """ Perform a few checks before returning a potential original language title. """ if not 'original_language_title' in item: return None title = item.get('title') if not title: return None original_language_title = item.get('original_language_title') if isinstance(original_language_title, str) and title != original_language_title: if len(original_language_title) < min_length: return None if original_language_title.count('?') > max_questionmarks: return None return original_language_title if isinstance(original_language_title, dict): content = original_language_title.get('__content__', '') or '' if content and content != title and not content.count( '?') > max_questionmarks: return content return None def parse_datacite_titles(titles): """ Given a list of title items from datacite, return 3-tuple (title, original_language_title, subtitle). Example input: [ { "title": "Meeting Heterogeneity in Consumer Demand" } ] """ title, original_language_title, subtitle = None, None, None if titles is None: return title, original_language_title, subtitle if len(titles) == 0: return title, original_language_title, subtitle elif len(titles) == 1: original_language_title = find_original_language_title(titles[0]) title = titles[0].get('title', '') or '' title = title.strip() if not title: title = None return title, original_language_title, subtitle else: for entry in titles: if not title and ('titleType' not in entry or not entry.get('titleType')): title = entry.get('title').strip() if not subtitle and entry.get('titleType') == 'Subtitle': subtitle = entry.get('title', '').strip() if not original_language_title: original_language_title = find_original_language_title(entry) return title, original_language_title, subtitle def parse_datacite_dates(dates): """ Given a list of date fields (under .dates), return tuple, (release_date, release_year). """ release_date, release_year = None, None if not dates: return release_date, release_year if not isinstance(dates, list): raise ValueError('expected a list of date items') # Ignored: Collected, Issued. date_type_prio = ( 'Valid', 'Available', 'Accepted', 'Submitted', 'Copyrighted', 'Created', 'Updated', ) # Before using (expensive) dateparser, try a few common patterns. common_patterns = ('%Y-%m-%d', '%Y-%m', '%Y-%m-%dT%H:%M:%SZ', '%Y-%m-%dT%H:%M:%S', '%Y') def parse_item(item): result, value, year_only = None, item.get('date', ''), False release_date, release_year = None, None for pattern in common_patterns: try: result = datetime.datetime.strptime(value, pattern) except ValueError: continue else: if pattern == '%Y': year_only = True break if result is None: print('fallback for {}'.format(value), file=sys.stderr) try: result = dateparser.parse(value) except TypeError as err: print("{} date parsing failed with: {}".format(value, err), file=sys.stderr) return result_date, result_year if result is None: # Unparsable date. return release_date, release_year if not year_only: release_date = result.date() release_year = result.year return release_date, release_year for prio in date_type_prio: for item in dates: if not item.get('dateType') == prio: continue release_date, release_year = parse_item(item) if release_date is None and release_year is None: continue if release_year < 1000 or release_year > datetime.date.today( ).year + 5: # Skip possibly bogus dates. release_year = None continue break else: continue break if release_date is None and release_year is None: for item in dates: release_date, release_year = parse_item(item) if release_year or release_date: break return release_date, release_year