start refactoring files into module

1 files changed, 0 insertions, 1469 deletions

diff --git a/chocula.py b/chocula.py
deleted file mode 100755
index f34a4e2..0000000
--- a/chocula.py
+++ /dev/null
@@ -1,1469 +0,0 @@
-#!/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()
-