#!/usr/bin/env python3 """ Count Chocula - online serials metadata and stats "one, two, three, un-preserved web-native open-access long-tail indie journals, hah, hah, hah!" (yeah, I know, this name isn't very good) (see also: https://teamyacht.com/ernstchoukula.com/Ernst-Choukula.html) Commands: everything init_db summarize export export_fatcat index_doaj index_road index_crossref index_entrez index_norwegian index_szczepanski index_ezb index_wikidata index_openapc load_fatcat load_fatcat_stats export_urls update_url_status Future commands: index_jurn index_datacite preserve_kbart --keeper SLUG preserve_sim See TODO.md for more work-in-progress """ import sys, csv, json from collections import Counter import sqlite3 import argparse import ftfy import urlcanon import surt import tldextract import pycountry import stdnum.issn ################### File Config ISSNL_FILE = 'data/20200323.ISSN-to-ISSN-L.txt' ENTREZ_FILE = 'data/entrez-journals.csv' ROAD_FILE = 'data/road-2018-01-24.tsv' ROAD_DATE = '2018-01-24' DOAJ_FILE = 'data/journalcsv__doaj_20191221_0135_utf8.csv' DOAJ_DATE = '2019-12-21' CROSSREF_FILE = 'data/doi_titles_file_2019-12-20.csv' SHERPA_ROMEO_JOURNAL_FILE = 'data/romeo-journals.csv' SHERPA_ROMEO_POLICY_FILE = 'data/romeo-policies.csv' NORWEGIAN_FILE = 'data/2019-12-21 Norwegian Register for Scientific Journals and Series.csv' NORWEGIAN_DATE = '2019-12-21' LOCKSS_FILE = 'data/kbart_LOCKSS.txt' CLOCKSS_FILE = 'data/kbart_CLOCKSS.txt' PORTICO_FILE = 'data/Portico_Holding_KBart.txt' JSTOR_FILE = 'data/JSTOR_Global_AllArchiveTitles_2019-12-21.txt' SIM_FILE = 'data/MASTER TITLE_METADATA_LIST_20171019.converted.csv' SZCZEPANSKI_DATE = '2018' SZCZEPANSKI_FILE = 'data/Jan-Szczepanski-Open-Access-Journals-2018_0.fixed.json' EZB_FILE = 'data/ezb_metadata.json' GOLD_OA_FILE = 'data/ISSN_Gold-OA_3.0.csv' WIKIDATA_SPARQL_FILE = 'data/wikidata_journals_sparql.2019-12-20.tsv' OPENAPC_FILE = 'data/apc_de.2019-12-20.csv' FATCAT_CONTAINER_FILE = 'data/container_export.2019-12-13.json' IA_CRAWL_FILE = 'data/url_status.20191223.json' FATCAT_STATS_FILE = 'data/container_stats.20191213.json' ################### Utilities # NOTE: this is a partial list, focusing on non-publisher hosted platforms and # software frameworks PLATFORM_MAP = { 'OJS': 'ojs', 'BMC': 'bmc', 'SciELO Brazil': 'scielo', 'SciELO Argentina': 'scielo', 'SciELO': 'scielo', 'SciELO Mexico': 'scielo', 'SciELO Spain': 'scielo', 'SciELO Portugal': 'scielo', 'WordPress': 'wordpress', 'Sciendo': 'sciendo', 'Drupal': 'drupal', 'revues.org': 'openedition', } MIMETYPE_MAP = { 'PDF': 'application/pdf', 'HTML': 'text/html', 'XML': 'application/xml', } BIG5_PUBLISHERS = [ 'Elsevier', 'Informa UK (Taylor & Francis)', 'Springer-Verlag', 'SAGE Publications', 'Wiley (Blackwell Publishing)', 'Wiley (John Wiley & Sons)', 'Springer (Biomed Central Ltd.)', 'Springer Nature', ] COMMERCIAL_PUBLISHERS = [ 'Peter Lang International Academic Publishers', 'Walter de Gruyter GmbH', 'Oldenbourg Wissenschaftsverlag', 'Georg Thieme Verlag KG', # not springer 'Emerald (MCB UP )', 'Medknow Publications', 'Inderscience Enterprises Ltd', 'Bentham Science', 'Ovid Technologies (Wolters Kluwer) - Lippincott Williams & Wilkins', 'Scientific Research Publishing, Inc', 'MDPI AG', 'S. Karger AG', 'Pleiades Publishing', 'Science Publishing Group', 'IGI Global', 'The Economist Intelligence Unit', 'Maney Publishing', 'Diva Enterprises Private Limited', 'World Scientific', 'Mary Ann Liebert', 'Trans Tech Publications', ] OA_PUBLISHERS = [ 'Hindawi Limited', 'OMICS Publishing Group', 'De Gruyter Open Sp. z o.o.', 'OpenEdition', 'Hindawi (International Scholarly Research Network)', 'Public Library of Science', 'Frontiers Media SA', 'eLife Sciences Publications, Ltd', 'MDPI AG', 'Hindawi (International Scholarly Research Network)', 'Dove Medical Press', 'Open Access Text', ] SOCIETY_PUBLISHERS = [ 'Institute of Electrical and Electronics Engineers', 'Institution of Electrical Engineers', 'Association for Computing Machinery', 'American Psychological Association', 'IOS Press', 'IOP Publishing', 'American Chemical Society', 'Royal Society of Chemistry (RSC)', 'American Geophysical Union', 'American College of Physicians', 'New England Journal of Medicine', 'BMJ', 'RCN Publishing', 'International Union of Crystallography', 'Portland Press', 'ASME International', ] UNI_PRESS_PUBLISHERS = [ 'Cambridge University Press', 'Oxford University Press', 'The University of Chicago Press', 'MIT Press', ] ARCHIVE_PUBLISHERS = [ 'JSTOR', 'Portico', ] REPOSITORY_PUBLISHERS = [ 'PERSEE Program', 'Social Science Electronic Publishing', 'CAIRN', 'CSIRO Publishing', ] OTHER_PUBLISHERS = [ 'African Journals Online', 'Smithsonian Institution Biodiversity Heritage Library', 'Canadian Science Publishing', 'Philosophy Documentation Center', 'Project MUSE', ] def unquote(s): if s.startswith('"'): s = s[1:] if s.endswith('"'): s = s[:-1] if s.endswith('.'): s = s[:-1] return s.strip() def parse_lang(s): if not s or s in ('Not applicable', 'Multiple languages', 'Unknown'): return None try: if len(s) == 2: lang = pycountry.languages.get(alpha2=s.lower()) elif len(s) == 3: lang = pycountry.languages.get(alpha3=s.lower()) else: lang = pycountry.languages.get(name=s) return lang.alpha2.lower() except KeyError: return None except AttributeError: return None def parse_country(s): if not s or s in ('Unknown'): return None try: if len(s) == 2: country = pycountry.countries.get(alpha2=s.lower()) else: country = pycountry.countries.get(name=s) except KeyError: return None if country: return country.alpha_2.lower() else: return None def parse_mimetypes(val): # XXX: multiple mimetypes? if not val: return mimetype = None if '/' in val: mimetype = val else: mimetype = MIMETYPE_MAP.get(val) if not mimetype: return None return [mimetype] def gaps_to_spans(first, last, gaps): if not gaps: return [[first, last]] if not (last >= first and max(gaps) < last and min(gaps) > first): # mangled print("mangled years: {}".format((first, last, gaps))) return [] full = list(range(first, last+1)) for missing in gaps: full.remove(missing) spans = [] low = None last = None for year in full: if not low: low = year last = year continue if year != last+1: spans.append([low, last]) low = year last = year last = year if low: spans.append([low, last]) return spans def test_gaps(): assert gaps_to_spans(1900, 1900, None) == \ [[1900, 1900]] assert gaps_to_spans(1900, 1903, None) == \ [[1900, 1903]] assert gaps_to_spans(1900, 1902, [1901]) == \ [[1900, 1900], [1902, 1902]] assert gaps_to_spans(1950, 1970, [1955, 1956, 1965]) == \ [[1950, 1954], [1957, 1964], [1966, 1970]] def merge_spans(old, new): if not new: return old if not old: old = [] old.extend(new) years = set() for span in old: for y in range(span[0], span[1]+1): years.add(y) if not years: return [] spans = [] start = None last = None todo = False for y in sorted(list(years)): if start == None: # very first start = y last = y todo = True continue if y == last + 1: # span continues last = y todo = True continue # a gap just happened! spans.append([start, last]) start = y last = y todo = True if todo: spans.append([start, last]) return spans def test_merge_spans(): assert merge_spans([[5, 10]], [[10, 20]]) == \ [[5, 20]] assert merge_spans([[5, 9]], [[10, 20]]) == \ [[5, 20]] assert merge_spans([[5, 11]], [[10, 20]]) == \ [[5, 20]] assert merge_spans([], []) == \ [] assert merge_spans([[9, 11]], []) == \ [[9,11]] assert merge_spans([[2000, 2000]], [[1450, 1900]]) == \ [[1450, 1900], [2000, 2000]] def parse_url(url): """ Parses/cleans URLs. Returns a dict with: url: str, cleaned/normalized URL url_surt: str, "sortable url" (a web-archiving format) host: str, full hostname registered_domain: "primary domain", eg "google.com" or "thing.co.uk" suffix: str, eg "com" or "co.uk" Returns None if url is really bad (not a URL). """ if not url or 'mailto:' in url.lower() or url.lower() in ('http://n/a', 'http://na/', 'http://na'): return None if url.startswith('www.'): url = "http://" + url if url.startswith('ttp://') or url.startswith('ttps://'): url = "h" + url url.replace('Http://', 'http://') url = str(urlcanon.semantic_precise(url)) if url == 'http://na/': # sort of redundant with above, but some only match after canonicalization return None url_surt = surt.surt(url) tld = tldextract.extract(url) host = '.'.join(tld) if host.startswith('.'): host = host[1:] return dict(url=url, url_surt=url_surt or None, host=host or None, registered_domain=tld.registered_domain or None, suffix=tld.suffix or None) def test_parse_url(): assert parse_url("http://thing.core.ac.uk")['registered_domain'] == 'core.ac.uk' assert parse_url("http://thing.core.ac.uk")['host'] == 'thing.core.ac.uk' assert parse_url("http://thing.core.ac.uk")['suffix'] == 'ac.uk' assert parse_url("google.com")['suffix'] == 'com' assert parse_url("google.com")['host'] == 'google.com' assert parse_url("mailto:bnewbold@bogus.com") == None assert parse_url("thing.com")['url'] == 'http://thing.com/' assert parse_url("Http://thing.com///")['url'] == 'http://thing.com/' ################### Main Class class ChoculaDatabase(): def __init__(self, db_file): self._issn_issnl_map = dict() self.db = sqlite3.connect(db_file, isolation_level='EXCLUSIVE') self.data = dict() self.c = None def read_issn_map_file(self, issn_map_path): print("##### Loading ISSN-L map file...") with open(issn_map_path, 'r') as issn_map_file: self._issn_issnl_map = dict() for line in issn_map_file: if line.startswith("ISSN") or len(line) == 0: continue (issn, issnl) = line.split()[0:2] self._issn_issnl_map[issn] = issnl # double mapping makes lookups easy self._issn_issnl_map[issnl] = issnl print("Got {} ISSN-L mappings.".format(len(self._issn_issnl_map))) def issn2issnl(self, issn): if issn is None: return None return self._issn_issnl_map.get(issn) def add_issn(self, index_slug, raw_issn=None, issne=None, issnp=None, identifier=None, name=None, publisher=None, extra=None): # do ISSN => ISSN-L mappings for any raw ISSNs issnl = None if not (raw_issn or issne or issnp): return None, 'no-issn' for lookup in (issnp, issne, raw_issn): if not lookup: continue lookup = lookup.strip().upper() #if not (len(lookup) == 9 and lookup[4] == '-'): # print(lookup) # print(len(lookup)) # print(lookup[4]) # return None, 'invalid-issn' #assert len(lookup) == 9 and lookup[4] == '-' issnl = self.issn2issnl(lookup) if issnl: break if not issnl: return None, 'unknown-issnl' #print((raw_issn, issne, issnp)) # UGH. #issnl = issne or issnp or raw_issn #if not issnl: #issnl = issnl.strip().upper() #assert len(issnl) == 9 and issnl[4] == '-' #status = 'found-munge' else: status = 'found' if extra == None: extra = dict() if issne: extra['issne'] = issne if issnp: extra['issnp'] = issnp if publisher: publisher = unquote(ftfy.fix_text(publisher)) if publisher: extra['publisher'] = publisher if extra: extra = json.dumps(extra) else: extra = None try: self.c.execute("INSERT INTO directory VALUES (?,?,?,?,?)", (issnl, index_slug, identifier, name, extra)) status = 'inserted' except sqlite3.IntegrityError as ie: if str(ie).startswith("UNIQUE"): return None, "duplicate-issnl" raise ie return issnl, status def add_url(self, issnl, url): if not (issnl and url): return meta = parse_url(url) if not meta: return self.c.execute("INSERT OR REPLACE INTO homepage (issnl, surt, url, host, domain, suffix) VALUES (?,?,?,?,?,?)", (issnl, meta['url_surt'], meta['url'], meta['host'], meta['registered_domain'], meta['suffix'] )) def index_entrez(self, args): path = args.input_file or ENTREZ_FILE print("##### Loading Entrez...") # JrId,JournalTitle,MedAbbr,"ISSN (Print)","ISSN (Online)",IsoAbbr,NlmId reader = csv.DictReader(open(path)) counts = Counter() self.c = self.db.cursor() for row in reader: if not (row.get('ISSN (Online)') or row.get('ISSN (Print)')): counts['skipped'] += 1 continue extra = dict() if row['IsoAbbr']: extra['abbrev'] = row['IsoAbbr'].strip() issnl, status = self.add_issn( 'entrez', issne=row.get('ISSN (Online)'), issnp=row.get('ISSN (Print)'), name=row['JournalTitle'], extra=extra, ) counts[status] += 1 self.c.close() self.db.commit() print(counts) def index_road(self, args): path = args.input_file or ROAD_FILE print("##### Loading ROAD...") reader = csv.DictReader(open(path), delimiter='\t', fieldnames=("ISSN", "ISSN-L", "Short Title", "Title", "Publisher", "URL1", "URL2", "Region", "Lang1", "Lang2") ) counts = Counter() self.c = self.db.cursor() for row in reader: extra = dict() if row['Lang1']: extra['langs'] = [row['Lang1']] if row['Lang2']: extra['langs'].append(row['Lang2']) # TODO: region mapping: "Europe and North America" # TODO: lang mapping: already alpha-3 issnl, status = self.add_issn( 'road', raw_issn=row['ISSN-L'], name=row['Short Title'], publisher=row['Publisher'], ) counts[status] += 1 if not issnl: continue if row['URL1']: self.add_url(issnl, row['URL1']) if row['URL2']: self.add_url(issnl, row['URL2']) self.c.close() self.db.commit() print(counts) def index_doaj(self, args): path = args.input_file or DOAJ_FILE print("##### Loading DOAJ...") #Journal title,Journal URL,Alternative title,Journal ISSN (print version),Journal EISSN (online version),Publisher,Society or institution,"Platform, host or aggregator",Country of publisher,Journal article processing charges (APCs),APC information URL,APC amount,Currency,Journal article submission fee,Submission fee URL,Submission fee amount,Submission fee currency,Number of articles publish in the last calendar year,Number of articles information URL,Journal waiver policy (for developing country authors etc),Waiver policy information URL,Digital archiving policy or program(s),Archiving: national library,Archiving: other,Archiving infomation URL,Journal full-text crawl permission,Permanent article identifiers,Journal provides download statistics,Download statistics information URL,First calendar year journal provided online Open Access content,Full text formats,Keywords,Full text language,URL for the Editorial Board page,Review process,Review process information URL,URL for journal's aims & scope,URL for journal's instructions for authors,Journal plagiarism screening policy,Plagiarism information URL,Average number of weeks between submission and publication,URL for journal's Open Access statement,Machine-readable CC licensing information embedded or displayed in articles,URL to an example page with embedded licensing information,Journal license,License attributes,URL for license terms,Does this journal allow unrestricted reuse in compliance with BOAI?,Deposit policy directory,Author holds copyright without restrictions,Copyright information URL,Author holds publishing rights without restrictions,Publishing rights information URL,DOAJ Seal,Tick: Accepted after March 2014,Added on Date,Subjects # TODO: Subjects, Permanent article identifiers, work_level stuff reader = csv.DictReader(open(path)) counts = Counter() self.c = self.db.cursor() for row in reader: extra = dict(as_of=DOAJ_DATE) extra['mimetypes'] = parse_mimetypes(row['Full text formats']) platform = PLATFORM_MAP.get(row['Platform, host or aggregator']) if platform: extra['platform'] = platform if row['DOAJ Seal']: extra['seal'] = {"no": False, "yes": True}[row['DOAJ Seal'].lower()] if row['Country of publisher']: extra['country'] = parse_country(row['Country of publisher']) row['lang'] = parse_lang(row['Full text language']) if row['Digital archiving policy or program(s)']: extra['archive'] = [a.strip() for a in row['Digital archiving policy or program(s)'].split(',') if a.strip()] elif row['Archiving: national library']: extra['archive'] = ['national-library'] crawl_permission = row['Journal full-text crawl permission'] if crawl_permission: extra['crawl-permission'] = dict(Yes=True, No=False)[crawl_permission] default_license = row['Journal license'] if default_license and default_license.startswith('CC'): extra['default_license'] = default_license.replace('CC ', 'CC-').strip() issnl, status = self.add_issn( 'doaj', issnp=row['Journal ISSN (print version)'], issne=row['Journal EISSN (online version)'], name=row['Journal title'], publisher=row['Publisher'], extra=extra, ) if row['Journal URL']: self.add_url(issnl, row['Journal URL']) counts[status] += 1 self.c.close() self.db.commit() print(counts) def index_sherpa_romeo(self, args): journal_path = args.input_file or SHERPA_ROMEO_JOURNAL_FILE policy_path = SHERPA_ROMEO_POLICY_FILE # first load policies print("##### Loading SHERPA/ROMEO policies...") #RoMEO Record ID,Publisher,Policy Heading,Country,RoMEO colour,Published Permission,Published Restrictions,Published Max embargo,Accepted Prmission,Accepted Restrictions,Accepted Max embargo,Submitted Permission,Submitted Restrictions,Submitted Max embargo,Open Access Publishing,Record Status,Updated policies = dict() fixed_policy_file = ftfy.fix_file(open(policy_path, 'rb')) policy_reader = csv.DictReader(fixed_policy_file) for row in policy_reader: policies[row['RoMEO Record ID']] = row print("##### Loading SHERPA/ROMEO journal metadata...") #Journal Title,ISSN,ESSN,URL,RoMEO Record ID,Updated # super mangled :( raw_file = open(journal_path, 'rb').read().decode(errors='replace') fixed_file = ftfy.fix_text(raw_file) reader = csv.DictReader(fixed_file.split('\n')) counts = Counter() self.c = self.db.cursor() for row in reader: #row['Journal Title'] = row.pop('\ufeffJournal Title') row.update(policies[row['RoMEO Record ID']]) extra = dict() if row['RoMEO colour']: extra['color'] = row['RoMEO colour'] # row['Open Access Publishing'] if row['Country']: extra['country'] = parse_country(row['Country']) issnl, status = self.add_issn( 'sherpa_romeo', issnp=row['ISSN'], issne=row['ESSN'], name=row['Journal Title'], publisher=row['Publisher'], extra=extra, ) counts[status] += 1 if not issnl: continue self.c.close() self.db.commit() print(counts) def index_norwegian(self, args): path = args.input_file or NORWEGIAN_FILE print("##### Loading Norwegian Registry...") #pandas.read_csv(NORWEGIAN_FILE, sep=';', encoding="ISO-8859-1") # Old: NSD tidsskrift_id;Original title;International title;Present Level (2018);Print ISSN;Online ISSN;Open Access;NPI Scientific Field;NPI Academic Discipline;URL;Publishing Company;Publisher;Country of publication;Language;Level 2019;Level 2018;Level 2017;Level 2016;Level 2015;Level 2014;Level 2013;Level 2012;Level 2011;Level 2010;Level 2009;Level 2008;Level 2007;Level 2006;Level 2005;Level 2004;itar_id # New: NSD tidsskrift_id;Original title;International title;Print ISSN;Online ISSN;Open Access;NPI Academic Discipline;NPI Scientific Field;Level 2020;Level 2019;Level 2018;Level 2017;Level 2016;Level 2015;Level 2014;Level 2013;Level 2012;Level 2011;Level 2010;Level 2009;Level 2008;Level 2007;Level 2006;Level 2005;Level 2004;itar_id;NSD forlag_id;Publishing Company;Publisher;Country of publication;Language;Conference Proceedings;Established;Ceased;URL reader = csv.DictReader(open(path, encoding="ISO-8859-1"), delimiter=";") counts = Counter() self.c = self.db.cursor() for row in reader: issnp = row['Print ISSN'] issne = row['Online ISSN'] if issne and len(issne.strip()) != 9: issne = None if issnp and len(issnp.strip()) != 9: issnp = None if not (issnp or issne): counts['no-issn'] += 1 continue extra = dict(as_of=NORWEGIAN_DATE) if row['Level 2019']: extra['level'] = int(row['Level 2019']) if row['Original title'] != row['International title']: extra['original_name'] = row['Original title'] if row['Country of publication']: extra['country'] = parse_country(row['Country of publication']) if row['Language']: extra['lang'] = parse_lang(row['Language']) issnl, status = self.add_issn( 'norwegian', issnp=issnp, issne=issne, identifier=row['NSD tidsskrift_id'], name=row['International title'], publisher=row['Publisher'], extra=extra, ) counts[status] += 1 if not issnl: continue if row['URL']: self.add_url(issnl, row['URL']) self.c.close() self.db.commit() print(counts) def index_szczepanski(self, args): path = args.input_file or SZCZEPANSKI_FILE print("##### Loading Szczepanski...") # JSON json_file = open(path, 'r') counts = Counter() self.c = self.db.cursor() for row in json_file: if not row: continue row = json.loads(row) if not (row.get('issne') or row.get('issnp') or row.get('issn')): #print(row) counts['no-issn'] += 1 continue extra = dict(as_of=SZCZEPANSKI_DATE) if row.get('extra'): extra['notes'] = row.get('extra') for k in ('other_titles', 'year_spans', 'ed'): if row.get(k): extra[k] = row[k] issnl, status = self.add_issn( 'szczepanski', issne=row.get('issne'), issnp=row.get('issnp'), raw_issn=row.get('issn'), name=row['title'], publisher=row.get('ed'), extra=extra, ) counts[status] += 1 if not issnl: continue for url in row.get('urls', []): self.add_url(issnl, url['url']) self.c.close() self.db.commit() print(counts) def index_ezb(self, args): path = args.input_file or EZB_FILE print("##### Loading EZB...") # JSON json_file = open(path, 'r') counts = Counter() self.c = self.db.cursor() for row in json_file: if not row: continue row = json.loads(row) if not (row.get('issne') or row.get('issnp')): #print(row) counts['no-issn'] += 1 continue extra = dict() for k in ('ezb_color', 'subjects', 'keywords', 'zdb_id', 'first_volume', 'first_issue', 'first_year', 'appearance', 'costs'): if row.get(k): extra[k] = row[k] issnl, status = self.add_issn( 'ezb', issne=row.get('issne'), issnp=row.get('issnp'), identifier=row['ezb_id'], name=row['title'], publisher=row.get('publisher'), extra=extra, ) counts[status] += 1 if not issnl: continue if row.get('url'): self.add_url(issnl, row['url']) self.c.close() self.db.commit() print(counts) def index_gold_oa(self, args): path = args.input_file or GOLD_OA_FILE print("##### Loading GOLD OA...") # "ISSN","ISSN_L","ISSN_IN_DOAJ","ISSN_IN_ROAD","ISSN_IN_PMC","ISSN_IN_OAPC","ISSN_IN_WOS","ISSN_IN_SCOPUS","JOURNAL_IN_DOAJ","JOURNAL_IN_ROAD","JOURNAL_IN_PMC","JOURNAL_IN_OAPC","JOURNAL_IN_WOS","JOURNAL_IN_SCOPUS","TITLE","TITLE_SOURCE" reader = csv.DictReader(open(path, encoding="ISO-8859-1")) counts = Counter() self.c = self.db.cursor() for row in reader: if not (row.get('ISSN_L') and row.get('TITLE')): counts['skipped'] += 1 continue extra = dict() for ind in ('DOAJ', 'ROAD', 'PMC', 'OAPC', 'WOS', 'SCOPUS'): extra['in_' + ind.lower()] = bool(int(row['JOURNAL_IN_' + ind])) issnl, status = self.add_issn( 'gold_oa', raw_issn=row['ISSN_L'], name=row['TITLE'], extra=extra, ) counts[status] += 1 # also add for other non-direct indices for ind in ('WOS', 'SCOPUS'): issnl, status = self.add_issn( ind.lower(), raw_issn=row['ISSN_L'], name=row['TITLE'], ) self.c.close() self.db.commit() print(counts) def index_wikidata(self, args): path = args.input_file or WIKIDATA_SPARQL_FILE print("##### Loading Wikidata...") reader = csv.DictReader(open(path), delimiter='\t') counts = Counter() self.c = self.db.cursor() for row in reader: if not (row.get('issn') and row.get('title')): counts['skipped'] += 1 continue publisher = row['publisher_name'] if (publisher.startswith('Q') and publisher[1].isdigit()) or publisher.startswith('t1') or not publisher: publisher = None wikidata_qid = row['item'].strip().split('/')[-1] extra = dict() extra['start_year'] = row.get('start_year') issnl, status = self.add_issn( 'wikidata', raw_issn=row['issn'], name=row['title'], identifier=wikidata_qid, publisher=publisher, extra=extra, ) counts[status] += 1 if not issnl: continue if row.get('websiteurl'): self.add_url(issnl, row['websiteurl']) self.c.close() self.db.commit() print(counts) def index_openapc(self, args): path = args.input_file or OPENAPC_FILE print("##### Loading OpenAPC...") # "institution","period","euro","doi","is_hybrid","publisher","journal_full_title","issn","issn_print","issn_electronic","issn_l","license_ref","indexed_in_crossref","pmid","pmcid","ut","url","doaj" reader = csv.DictReader(open(path)) counts = Counter() self.c = self.db.cursor() for row in reader: if not row.get('issn'): counts['skipped'] += 1 continue extra = dict(is_hybrid=bool(row['is_hybrid'])) issnl, status = self.add_issn( 'openapc', issne=row['issn_electronic'], issnp=row['issn_print'], raw_issn=row['issn_l'] or row['issn'], name=row['journal_full_title'], publisher=row['publisher'], extra=extra, ) counts[status] += 1 if not issnl: continue if row.get('url'): self.add_url(issnl, row['url']) self.c.close() self.db.commit() print(counts) def parse_kbart(self, name, path): """ Transforms a KBART file into a dict of dicts; but basically a list of JSON objects, one per journal. KBART files can have multiple rows per journal (eg, different year spans), which is why this pass is needed. """ print("##### Parsing KBART file for {}...".format(name)) #publication_title print_identifier online_identifier date_first_issue_online num_first_vol_online num_first_issue_online date_last_issue_online num_last_vol_online num_last_issue_online title_url first_author title_id embargo_info coverage_depth coverage_notes publisher_name kbart_dict = dict() raw_file = open(path, 'rb').read().decode(errors='replace') fixed_file = ftfy.fix_text(raw_file) reader = csv.DictReader(fixed_file.split('\n'), delimiter='\t') counts = Counter() for row in reader: if not row['print_identifier'] and not row['online_identifier']: counts['no-issn'] += 1 continue issnl, status = self.lookup_issnl( issnp=row['print_identifier'], issne=row['online_identifier'], ) counts[status] += 1 if not issnl: continue info = dict( title=row['publication_title'] or None, publisher=row['publisher_name'] or None, url=row['title_url'] or None, embargo_info=row['embargo_info'] or None, ) d = kbart_dict.get(issnl, info) old_spans = d.get('year_spans', []) if row['date_first_issue_online'] and row['date_last_issue_online']: start = int(row['date_first_issue_online'][:4]) end = int(row['date_last_issue_online'][:4]) if not start <= end: print("{}: {} not before {}! er, mangling".format( issnl, row['date_first_issue_online'], row['date_last_issue_online'])) new_spans = [[end, start]] else: new_spans = [[start, end]] d['year_spans'] = merge_spans(old_spans, new_spans) print(counts) return kbart_dict def index_crossref(self, args): path = args.input_file or CROSSREF_FILE print("##### Loading Crossref...") #"JournalTitle","JournalID","Publisher","pissn","eissn","additionalIssns","doi","(year1)[volume1]issue1,issue2,issue3(year2)[volume2]issue4,issues5" reader = csv.DictReader(open(path)) counts = Counter() self.c = self.db.cursor() for row in reader: if row['pissn'] and len(row['pissn']) == 8: row['pissn'] = row['pissn'][:4] + '-' + row['pissn'][4:] if row['eissn'] and len(row['eissn']) == 8: row['eissn'] = row['eissn'][:4] + '-' + row['eissn'][4:] if row['additionalIssns'] and len(row['additionalIssns']) == 8: row['additionalIssns'] = row['additionalIssns'][:4] + '-' + row['additionalIssns'][4:] if not (row['pissn'] or row['eissn'] or row['additionalIssns']): #print(row) counts['no-issn'] += 1 continue extra = dict() issnl, status = self.add_issn( 'crossref', issnp=row['pissn'], issne=row['eissn'], raw_issn=row['additionalIssns'], identifier=row.get('doi'), name=row['JournalTitle'], publisher=row['Publisher'], extra=extra, ) counts[status] += 1 self.c.close() self.db.commit() print(counts) def index_sim(self, args): path = args.input_file or SIM_FILE print("##### Loading SIM Metadata...") #NA Pub Cat ID,Title,Publisher,ISSN,Impact Rank,Total Cities,Journal Impact Factor,Eigenfact or Score,First Volume,Last Volume,NA Gaps,"Scholarly / Peer-\n Reviewed","Peer-\n Reviewed",Pub Type,Pub Language,Subjects reader = csv.DictReader(open(path)) counts = Counter() self.c = self.db.cursor() for row in reader: if not row['ISSN'] or row['ISSN'] == "NULL": counts['no-issn'] += 1 continue issnl, status = self.add_issn( 'ia_sim', raw_issn=row['ISSN'][:9], name=row['Title'], publisher=row['Publisher'], extra=extra, ) counts[status] += 1 if not issnl: continue d = self.data[issnl] sim = dict() sim['id'] = row['NA Pub Cat ID'] first_year = row['First Volume'] if first_year: first_year = int(first_year) sim['first_year'] = int(row['First Volume']) else: first_year = None last_year = row['Last Volume'] if last_year: last_year = int(last_year) sim['last_year'] = last_year else: last_year = None gaps = [int(g) for g in row['NA Gaps'].split(';') if g.strip()] if gaps: sim['gaps'] = gaps if first_year and last_year: sim['year_spans'] = gaps_to_spans(first_year, last_year, gaps) if row['Pub Language']: self.add_lang(issnl, row['Pub Language']) # TODO: 'Pub Type' all_keys = list(sim.keys()) for k in all_keys: if not sim[k]: sim.pop(k) self.data[issnl]['sim'] = sim self.c.close() self.db.commit() print(counts) def update_url_status(self, args): path = args.input_file or IA_CRAWL_FILE print("##### Loading IA Homepage Crawl Results...") counts = Counter() self.c = self.db.cursor() for row in open(path, 'r'): if not row.strip(): continue row = json.loads(row) counts['total'] += 1 url = row['url'] assert(url) if row.get('gwb_url_success_dt') == 'error': row['gwb_url_success_dt'] = None if row.get('gwb_terminal_url_success_dt') == 'error': row['gwb_terminal_url_success_dt'] = None self.c.execute("UPDATE homepage SET status_code=?, crawl_error=?, terminal_url=?, terminal_status_code=?, platform_software=?, issnl_in_body=?, blocked=?, gwb_url_success_dt=?, gwb_terminal_url_success_dt=? WHERE url=?", (row['status_code'], row.get('crawl_error'), row.get('terminal_url'), row.get('terminal_status_code'), row.get('platform_software'), row.get('issnl_in_body'), row.get('blocked'), row.get('gwb_url_success_dt'), row.get('gwb_terminal_url_success_dt'), url)) counts['updated'] += 1 self.c.close() self.db.commit() print(counts) def load_fatcat(self, args): path = args.input_file or FATCAT_CONTAINER_FILE print("##### Loading Fatcat Container Entities...") # JSON json_file = open(path, 'r') counts = Counter() self.c = self.db.cursor() for row in json_file: if not row: continue row = json.loads(row) if row['state'] != 'active': continue counts['total'] += 1 extra = row.get('extra', dict()) issne = extra.get('issne') issnp = extra.get('issnp') country = extra.get('country') languages = extra.get('languages', []) lang = None if languages: lang = languages[0] try: self.c.execute("INSERT OR REPLACE INTO fatcat_container (issnl, ident, revision, issne, issnp, wikidata_qid, name, container_type, publisher, country, lang) VALUES (?,?,?,?,?,?,?,?,?,?,?)", (row.get('issnl'), row['ident'], row['revision'], issne, issnp, row.get('wikidata_qid'), row['name'], row.get('container_type'), extra.get('publisher'), country, lang, )) except sqlite3.IntegrityError as ie: if str(ie).startswith("UNIQUE"): return None, "duplicate-issnl" raise ie counts['inserted'] += 1 if row.get('issnl'): urls = extra.get('urls', []) for url in urls: self.add_url(row['issnl'], url) self.c.close() self.db.commit() print(counts) def load_fatcat_stats(self, args): path = args.input_file or FATCAT_STATS_FILE print("##### Loading Fatcat Container Stats...") # JSON json_file = open(path, 'r') counts = Counter() self.c = self.db.cursor() for row in json_file: if not row: continue row = json.loads(row) total = int(row['total']) if total > 0: ia_frac = float(row['in_web'])/total preserved_frac = float(row['is_preserved'])/total else: ia_frac = None preserved_frac = None self.c.execute("UPDATE fatcat_container SET release_count = ?, ia_count = ?, ia_frac = ?, preserved_count = ?, preserved_frac = ? WHERE issnl = ?", (total, row['in_web'], ia_frac, row['is_preserved'], preserved_frac, row['issnl'])) counts['updated'] += 1 self.c.close() self.db.commit() print(counts) def export_urls(self, args): self.c = self.db.cursor() self.db.row_factory = sqlite3.Row cur = self.db.execute("SELECT issnl, url FROM homepage;") for hrow in cur: assert(hrow['url']) assert(len(hrow['url'].split()) == 1) print('\t'.join((hrow['issnl'], hrow['url']))) def summarize(self, args): print("##### Summarizing Everything...") counts = Counter() self.c = self.db.cursor() self.db.row_factory = sqlite3.Row index_issnls = list(self.c.execute('SELECT DISTINCT issnl FROM directory')) fatcat_issnls = list(self.c.execute('SELECT DISTINCT issnl FROM fatcat_container WHERE issnl IS NOT null')) all_issnls = set([i[0] for i in index_issnls + fatcat_issnls]) print("{} total ISSN-Ls".format(len(all_issnls))) for issnl in list(all_issnls): #print(issnl) counts['total'] += 1 out = dict() # check if ISSN-L is good. this is here because of fatcat import out['known_issnl'] = (self.issn2issnl(issnl) == issnl) if not out['known_issnl']: counts['unknown-issnl'] += 1 out['valid_issnl'] = stdnum.issn.is_valid(issnl) if not out['valid_issnl']: counts['invalid-issnl'] += 1 fatcat_row = list(self.db.execute("SELECT * FROM fatcat_container WHERE issnl = ?;", [issnl])) if fatcat_row: frow = fatcat_row[0] out['fatcat_ident'] = frow['ident'] for k in ('name', 'publisher', 'issne', 'issnp', 'wikidata_qid', 'lang', 'country', 'release_count', 'ia_count', 'ia_frac', 'kbart_count', 'kbart_frac', 'preserved_count', 'preserved_frac'): if not out.get(k) and frow[k] != None: out[k] = frow[k] cur = self.db.execute("SELECT * FROM directory WHERE issnl = ?;", [issnl]) for irow in cur: if irow['slug'] in ('crossref',): out['has_dois'] = True # TODO: other DOI registrars (japan, datacite) if irow['slug'] == 'wikidata': out['wikidata_qid'] = irow['identifier'] for k in ('name',): if not out.get(k) and irow[k]: out[k] = irow[k] if irow['extra']: extra = json.loads(irow['extra']) for k in ('country', 'lang', 'issne', 'issnp', 'publisher'): if not out.get(k) and extra.get(k): out[k] = extra[k] if irow['slug'] in ('doaj','road','szczepanski', 'gold_oa'): out['is_oa'] = True if irow['slug'] == 'ezb': ezb_extra = json.loads(irow['extra']) if ezb_extra['ezb_color'] == 'green': out['is_oa'] = True if irow['slug'] == 'sherpa_romeo': extra = json.loads(irow['extra']) out['sherpa_color'] = extra['color'] if extra['color'] == 'green': out['is_oa'] = True # filter out "NA" ISSNs for k in ('issne', 'issnp'): if out.get(k) and (len(out[k]) != 9 or out[k][4] != '-'): out.pop(k) cur = self.db.execute("SELECT * FROM homepage WHERE issnl = ?;", [issnl]) for hrow in cur: out['any_homepage'] = True if hrow['terminal_status_code'] == 200 and hrow['host'] != 'web.archive.org': out['any_live_homepage'] = True if hrow['gwb_url_success_dt'] or hrow['gwb_terminal_url_success_dt']: out['any_gwb_homepage'] = True if out.get('wikidata_qid'): assert out['wikidata_qid'].startswith('Q') assert out['wikidata_qid'][1].isdigit() assert out['wikidata_qid'][-1].isdigit() # define publisher types publisher = out.get('publisher') pl = out.get('publisher', '').lower().strip() if publisher in BIG5_PUBLISHERS or 'elsevier' in pl or 'springer' in pl or 'wiley' in pl: out['publisher_type'] = 'big5' elif publisher in OA_PUBLISHERS: out['publisher_type'] = 'oa' elif publisher in COMMERCIAL_PUBLISHERS or 'wolters kluwer' in pl or 'wolters-kluwer' in pl: out['publisher_type'] = 'commercial' elif publisher in ARCHIVE_PUBLISHERS: out['publisher_type'] = 'archive' elif publisher in REPOSITORY_PUBLISHERS: out['publisher_type'] = 'repository' elif publisher in OTHER_PUBLISHERS: out['publisher_type'] = 'other' elif publisher in SOCIETY_PUBLISHERS or 'society' in pl or 'association' in pl or 'academy of ' in pl or 'institute of' in pl: out['publisher_type'] = 'society' elif publisher in UNI_PRESS_PUBLISHERS or 'university ' in pl: out['publisher_type'] = 'unipress' elif 'scielo' in pl: out['publisher_type'] = 'scielo' elif out.get('is_oa') and (not out.get('has_dois') or out.get('lang') not in (None, 'en', 'de', 'fr', 'ja') or out.get('country') not in (None, 'us', 'gb', 'nl', 'cn', 'jp', 'de')): # current definition of longtail out['publisher_type'] = 'longtail' out['is_longtail'] = True self.c.execute("INSERT OR REPLACE INTO journal (issnl, issne, issnp, wikidata_qid, fatcat_ident, name, publisher, country, lang, is_oa, sherpa_color, is_longtail, is_active, publisher_type, has_dois, any_homepage, any_live_homepage, any_gwb_homepage, known_issnl, valid_issnl, release_count, ia_count, ia_frac, kbart_count, kbart_frac, preserved_count, preserved_frac) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)", (issnl, out.get('issne'), out.get('issnp'), out.get('wikidata_qid'), out.get('fatcat_ident'), out.get('name'), out.get('publisher'), out.get('country'), out.get('lang'), out.get('is_oa', False), out.get('sherpa_color'), out.get('is_longtail', False), out.get('is_active'), out.get('publisher_type'), out.get('has_dois', False), out.get('any_homepage', False), out.get('any_live_homepage', False), out.get('any_gwb_homepage', False), out.get('known_issnl'), out.get('valid_issnl'), out.get('release_count'), out.get('ia_count'), out.get('ia_frac'), out.get('kbart_count'), out.get('kbart_frac'), out.get('preserved_count'), out.get('preserved_frac'), )) self.c.close() self.db.commit() print(counts) def everything(self, args): self.init_db(args) self.index_doaj(args) self.index_norwegian(args) self.index_crossref(args) self.index_sherpa_romeo(args) self.index_road(args) self.index_entrez(args) self.index_ezb(args) self.index_szczepanski(args) self.index_gold_oa(args) self.index_openapc(args) self.index_wikidata(args) self.load_fatcat(args) self.load_fatcat_stats(args) #self.preserve_kbart('lockss', LOCKSS_FILE) #self.preserve_kbart('clockss', CLOCKSS_FILE) #self.preserve_kbart('portico', PORTICO_FILE) #self.preserve_kbart('jstor', JSTOR_FILE) #self.preserve_sim(args) self.update_url_status(args) self.summarize(args) print("### Done with everything!") def export(self, args): def dict_factory(cursor, row): d = {} for idx, col in enumerate(cursor.description): d[col[0]] = row[idx] return d counts = Counter() self.db.row_factory = dict_factory self.c = self.db.cursor() for row in self.c.execute('SELECT * FROM journal'): print(json.dumps(row)) counts['total'] += 1 def export_fatcat(self, args): counts = Counter() self.db.row_factory = sqlite3.Row self.c = self.db.cursor() for row in self.c.execute('SELECT * FROM journal WHERE valid_issnl = 1'): counts['total'] += 1 name = row['name'] if name: name = name.strip() if not row['name']: counts['empty-name'] += 1 continue if len(name) <= 2: counts['short-name'] += 1 continue publisher = row['publisher'] if publisher: publisher = publisher.strip() or None out = dict( issnl=row['issnl'], wikidata_qid=row['wikidata_qid'], ident=row['fatcat_ident'], publisher=publisher, name=name, _known_issnl=row['known_issnl']) extra = dict( issnp=row['issnp'], issne=row['issne'], country=row['country'], ) if row['lang']: extra['languages'] = [row['lang'],] if row['sherpa_color']: extra['sherpa_romeo'] = dict(color=row['sherpa_color']) urls = [] webarchive_urls = [] cur = self.db.execute("SELECT * FROM homepage WHERE issnl = ?;", [row['issnl']]) for hrow in cur: if '://doaj.org/' in hrow['url'] or '://www.doaj.org/' in hrow['url']: continue if '://www.ncbi.nlm.nih.gov/' in hrow['url']: continue if 'web.archive.org/web' in hrow['url']: webarchive_urls.append(hrow['url']) urls.append(hrow['url']) continue if hrow['host'] in ('www.google.com', 'books.google.com'): # individual books or google searches, not journal/conference homepages continue if '/oai/request' in hrow['url']: # OAI-PMH endpoints, not homepages continue if not row['any_live_homepage'] and hrow['gwb_url_success_dt'] and hrow['gwb_url_success_dt'] != 'error': webarchive_urls.append("https://web.archive.org/web/{}/{}".format(hrow['gwb_url_success_dt'], hrow['url'])) continue if hrow['blocked']: urls.append(hrow['url']) continue if hrow['terminal_status_code'] == 200: if hrow['terminal_url'] == hrow['url'].replace('http://', 'https://') or hrow['terminal_url'] == hrow['url'] + "/": # check for trivial redirects; use post-redirect URL in those cases urls.append(hrow['terminal_url']) else: urls.append(hrow['url']) continue # didn't even crawl and no match? add anyways as a pass-through if not hrow['status_code']: urls.append(hrow['url']) continue extra['webarchive_urls'] = webarchive_urls extra['urls'] = urls cur = self.db.execute("SELECT * FROM directory WHERE issnl = ?;", [row['issnl']]) for drow in cur: if drow['slug'] == 'ezb': ezb = json.loads(drow['extra']) extra['ezb'] = dict(ezb_id=drow['identifier'], color=ezb['ezb_color']) if drow['slug'] == 'szczepanski': extra['szczepanski'] = dict(as_of=SZCZEPANSKI_DATE) if drow['slug'] == 'doaj': extra['doaj'] = json.loads(drow['extra']) out['extra'] = extra print(json.dumps(out)) def init_db(self, args): print("### Creating Database...") self.db.executescript(""" PRAGMA main.page_size = 4096; PRAGMA main.cache_size = 20000; PRAGMA main.locking_mode = EXCLUSIVE; PRAGMA main.synchronous = OFF; """) with open('chocula_schema.sql', 'r') as fschema: self.db.executescript(fschema.read()) print("Done!") def main(): parser = argparse.ArgumentParser( formatter_class=argparse.ArgumentDefaultsHelpFormatter) subparsers = parser.add_subparsers() parser.add_argument("--db-file", help="run in mode that considers only terminal HTML success", default='chocula.sqlite', type=str) parser.add_argument("--input-file", help="override default input file path", default=None, type=str) sub = subparsers.add_parser('everything', help="run all the commands") sub.set_defaults(func='everything') sub = subparsers.add_parser('init_db', help="create sqlite3 output file and tables") sub.set_defaults(func='init_db') sub = subparsers.add_parser('summarize', help="aggregate metadata from all tables into 'journals' table") sub.set_defaults(func='summarize') sub = subparsers.add_parser('export', help="dump JSON output") sub.set_defaults(func='export') sub = subparsers.add_parser('export_fatcat', help="dump JSON output in a format that can load into fatcat") sub.set_defaults(func='export_fatcat') # TODO: 'jurn' for ind in ('doaj', 'road', 'crossref', 'entrez', 'norwegian', 'szczepanski', 'ezb', 'gold_oa', 'wikidata', 'openapc'): sub = subparsers.add_parser('index_{}'.format(ind), help="load metadata from {}".format(ind)) sub.set_defaults(func='index_{}'.format(ind)) sub = subparsers.add_parser('load_fatcat', help="load fatcat container metadata") sub.set_defaults(func='load_fatcat') sub = subparsers.add_parser('load_fatcat_stats', help="update container-level stats from JSON file") sub.set_defaults(func='load_fatcat_stats') sub = subparsers.add_parser('export_urls', help="dump homepage URLs (eg, to crawl for status)") sub.set_defaults(func='export_urls') sub = subparsers.add_parser('update_url_status', help="import homepage URL crawl status") sub.set_defaults(func='update_url_status') args = parser.parse_args() if not args.__dict__.get("func"): print("tell me what to do! (try --help)") sys.exit(-1) cdb = ChoculaDatabase(args.db_file) if args.func.startswith('index_') or args.func in ('everything','summarize',): cdb.read_issn_map_file(ISSNL_FILE) func = getattr(cdb, args.func) func(args) if __name__ == '__main__': main()