diff options
| -rw-r--r-- | extra/journal_metadata/Pipfile | 16 | ||||
| -rw-r--r-- | extra/journal_metadata/Pipfile.lock | 115 | ||||
| -rwxr-xr-x | extra/journal_metadata/chocula.py | 798 | ||||
| -rw-r--r-- | extra/journal_metadata/chocula_schema.sql | 80 |
4 files changed, 1009 insertions, 0 deletions
diff --git a/extra/journal_metadata/Pipfile b/extra/journal_metadata/Pipfile new file mode 100644 index 00000000..c078ec11 --- /dev/null +++ b/extra/journal_metadata/Pipfile @@ -0,0 +1,16 @@ +[[source]] +name = "pypi" +url = "https://pypi.org/simple" +verify_ssl = true + +[dev-packages] + +[packages] +ftfy = "*" +urlcanon = "*" +surt = "*" +tldextract = "*" +pycountry = "*" + +[requires] +python_version = "3.5" diff --git a/extra/journal_metadata/Pipfile.lock b/extra/journal_metadata/Pipfile.lock new file mode 100644 index 00000000..723085a7 --- /dev/null +++ b/extra/journal_metadata/Pipfile.lock @@ -0,0 +1,115 @@ +{ + "_meta": { + "hash": { + "sha256": "ed04855e4e25cce6663fecc042c2421ca429af32caa8527a1d4a9137a74e7c27" + }, + "pipfile-spec": 6, + "requires": { + "python_version": "3.5" + }, + "sources": [ + { + "name": "pypi", + "url": "https://pypi.org/simple", + "verify_ssl": true + } + ] + }, + "default": { + "certifi": { + "hashes": [ + "sha256:046832c04d4e752f37383b628bc601a7ea7211496b4638f6514d0e5b9acc4939", + "sha256:945e3ba63a0b9f577b1395204e13c3a231f9bc0223888be653286534e5873695" + ], + "version": "==2019.6.16" + }, + "chardet": { + "hashes": [ + "sha256:84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae", + "sha256:fc323ffcaeaed0e0a02bf4d117757b98aed530d9ed4531e3e15460124c106691" + ], + "version": "==3.0.4" + }, + "ftfy": { + "hashes": [ + "sha256:84a1614190173bb447ac9d581e50185c6aa35b538754b6bedaba0cc0f83d8e80", + "sha256:fa74757fb7cb444366fa6a79c2feabd40281a44dfbf6eaed492a804764ee26b2" + ], + "index": "pypi", + "version": "==5.5.1" + }, + "idna": { + "hashes": [ + "sha256:c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407", + "sha256:ea8b7f6188e6fa117537c3df7da9fc686d485087abf6ac197f9c46432f7e4a3c" + ], + "version": "==2.8" + }, + "pycountry": { + "hashes": [ + "sha256:104a8ca94c700898c42a0172da2eab5a5675c49637b729a11db9e1dac2d983cd", + "sha256:8ec4020b2b15cd410893d573820d42ee12fe50365332e58c0975c953b60a16de" + ], + "index": "pypi", + "version": "==18.12.8" + }, + "requests": { + "hashes": [ + "sha256:11e007a8a2aa0323f5a921e9e6a2d7e4e67d9877e85773fba9ba6419025cbeb4", + "sha256:9cf5292fcd0f598c671cfc1e0d7d1a7f13bb8085e9a590f48c010551dc6c4b31" + ], + "version": "==2.22.0" + }, + "requests-file": { + "hashes": [ + "sha256:75c175eed739270aec3c5279ffd74e6527dada275c5c0d76b5817e9c86bb7dea", + "sha256:8f04aa6201bacda0567e7ac7f677f1499b0fc76b22140c54bc06edf1ba92e2fa" + ], + "version": "==1.4.3" + }, + "six": { + "hashes": [ + "sha256:3350809f0555b11f552448330d0b52d5f24c91a322ea4a15ef22629740f3761c", + "sha256:d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73" + ], + "version": "==1.12.0" + }, + "surt": { + "hashes": [ + "sha256:1e6a2f3e626b45d6c2aa278f7d5b176e8a06586870453045e6f5f2cfe5cc62a3" + ], + "index": "pypi", + "version": "==0.3.0" + }, + "tldextract": { + "hashes": [ + "sha256:2c1c5d9d454f79734b4f3da0d603856dd9f820753410a3e9abf0a0c9fde33e97", + "sha256:b72bef6013de67c7fa181250bc2c2e089a994d259c09ca95a9771f2f97e29ed1" + ], + "index": "pypi", + "version": "==2.2.1" + }, + "urlcanon": { + "hashes": [ + "sha256:30f5bf0e2e4a0feb6dd9ee139a4180a5d493117e8a1448569da3d73c18b92b62" + ], + "index": "pypi", + "version": "==0.3.1" + }, + "urllib3": { + "hashes": [ + "sha256:b246607a25ac80bedac05c6f282e3cdaf3afb65420fd024ac94435cabe6e18d1", + "sha256:dbe59173209418ae49d485b87d1681aefa36252ee85884c31346debd19463232" + ], + "version": "==1.25.3" + }, + "wcwidth": { + "hashes": [ + "sha256:3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e", + "sha256:f4ebe71925af7b40a864553f761ed559b43544f8f71746c2d756c7fe788ade7c" + ], + "version": "==0.1.7" + } + }, + "develop": {} +} diff --git a/extra/journal_metadata/chocula.py b/extra/journal_metadata/chocula.py new file mode 100755 index 00000000..6e32a3af --- /dev/null +++ b/extra/journal_metadata/chocula.py @@ -0,0 +1,798 @@ +#!/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 + + index_doaj + index_road + index_crossref + index_szczepanski + index_jurn + index_norwegian + + fatcat_load + fatcat_stats + + export_urls + update_url_status + +TODO: + + index_ezb + index_wikidata + index_datacite + preserve_kbart --keeper SLUG + preserve_sim + +""" + +import sys, csv, json +from collections import Counter +import sqlite3 +import argparse + +import ftfy +import urlcanon +import surt +import tldextract +import pycountry + + +################### File Config + +ISSNL_FILE = 'data/20190220.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/doaj_20190124.csv' +DOAJ_DATE = '2019-01-24' +CROSSREF_FILE = 'data/doi_titles_file_2019-01-24.csv' +SHERPA_ROMEO_JOURNAL_FILE = 'data/romeo-journals.csv' +SHERPA_ROMEO_POLICY_FILE = 'data/romeo-policies.csv' +NORWEGIAN_FILE = 'data/2018-03-02 Norwegian Register for Scientific Journals and Series.csv' +NORWEGIAN_DATE = '2018-03-02' +LOCKSS_FILE = 'data/kbart_LOCKSS.txt' +CLOCKSS_FILE = 'data/kbart_CLOCKSS.txt' +PORTICO_FILE = 'data/Portico_Holding_KBart.txt' +JSTOR_FILE = 'data/jstor_all-archive-titles.txt' +SIM_FILE = 'data/MASTER TITLE_METADATA_LIST_20171019.converted.csv' +IA_CRAWL_FILE = 'data/journal_homepage_results.partial.tsv' + + +################### 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', +} + +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 + return country.alpha_2.lower() + +def parse_mimetypes(val): + # XXX: multiple mimetypes? + if not (val and issnl): + 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]] + + +################### Main Class + +class ChoculaDatabase(): + """ + Top-level fields we'd like to fill in if possible: + + issnp: string + issne: string + first_year: year (integer) + last_year: if publishing has stopped + languages: array of ISO codes; first is the "primary" language + country: ISO shortcode of country published from + urls: homepage links + abbrev: string + default_license: slug + original_name: native name (if name is translated) + platform: hosting platform: OJS, wordpress, scielo, etc + mimetypes: array of strings (eg, 'application/pdf', 'text/html') + aliases: array of "also known as" + + Lower priority (TODO/later): + coden: string + oclc_id: string (lookup?) + lccn_id: string (lookup?) + dblb_id: string + region: TODO: continent/world-region + discipline: TODO: highest-level subject; "life science", "humanities", etc + field: TODO: narrower description of field + subjects: TODO? + + TODO: so many missing ISSN/ISSN-L + TODO: abbrev + """ + + 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 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, 'no-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 + + publisher = unquote(ftfy.fix_text(publisher)) + if publisher: + extra['publisher'] = publisher + + if extra: + extra = json.dumps(extra) + else: + extra = None + + self.c.execute("INSERT INTO journal_index VALUES (?,?,?,?,?,?)", + (issnl, index_slug, identifier, name, None, extra)) + + return issnl, status + + def add_url(self, issnl, url): + if not (url and issnl) or 'mailto:' in url.lower() or url in ('http://n/a', 'http://N/A'): + return + if url.startswith('www.'): + url = "http://" + url + url.replace('Http://', 'http://') + + url = str(urlcanon.semantic_precise(url)) + surt = surt.surt(url) + tld = tldextract.extract(url) + domain = '.'.join(tld[:]) + + self.c.execute("INSERT OR REPLACE INTO homepage (issnl, surt, url, host, domain, suffix) VALUES (?,?,?,?,?,?)", + (issnl, surt, url, tld.domain, tld.registered_domain, tld.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() + 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() + 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 + 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']: + print(row['Country of publisher']) + extra['country'] = parse_country(row['Country of publisher']) + row['lang'] = parse_lang(row['Full text language']) + # TODO: work_level: bool (are work-level publications deposited with DOAJ?) + + 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] + # TODO: Permanent article identifiers + default_license = row['Journal license'] + if default_license and default_license.startswith('CC'): + extra[issnl]['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 + + # TODO: Subjects + self.c.close() + 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() + 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") + #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 + 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 + issnl, status = self.add_issn( + 'norwegian', + issnp=issnp, + issne=issne, + name=row['International title'], + publisher=row['Publisher'], + extra=extra, + ) + counts[status] += 1 + if not issnl: + continue + d = self.data[issnl] + norwegian = dict(as_of=NORWEGIAN_DATE) + norwegian['level'] = int(row['Present Level (2018)']) + norwegian['id'] = int(row['NSD tidsskrift_id']) + + if row['Original title'] != row['International title'] and not 'original_name' in d: + self.data[issnl]['original_name'] = row['Original title'] + if row['Country of publication']: + self.add_country(issnl, row['Country of publication']) + if row['Language']: + self.add_lang(issnl, row['Language']) + if row['URL']: + self.add_url(issnl, row['URL']) + self.data[issnl]['norwegian'] = norwegian + self.c.close() + print(counts) + + def index_kbart(self, name, path): + print("##### Loading 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 + 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() + self.c = self.db.cursor() + for row in reader: + if not row['print_identifier'] and not row['online_identifier']: + counts['no-issn'] += 1 + continue + issnl, status = self.add_issn( + issnp=row['print_identifier'], + issne=row['online_identifier'], + name=row['publication_title'], + publisher=row['publisher_name'], + extra=extra, + ) + counts[status] += 1 + if not issnl: + continue + d = self.data[issnl] + if not 'kbart' in d: + self.data[issnl]['kbart'] = dict() + d = self.data[issnl] + if not name in d['kbart']: + self.data[issnl]['kbart'][name] = dict() + old_spans = self.data[issnl]['kbart'].get(name, dict()).get('year_spans', []) + kbart = dict() + 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]] + self.data[issnl]['kbart'][name]['year_spans'] = merge_spans(old_spans, new_spans) + self.c.close() + print(counts) + + 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 not (row['pissn'] or row['eissn']): + counts['no-issn'] += 1 + continue + issnl, status = self.add_issn( + 'crossref', + issnp=row['pissn'], + issne=row['eissn'], + name=row['JournalTitle'], + publisher=row['Publisher'], + extra=extra, + ) + counts[status] += 1 + if not issnl: + continue + d = self.data[issnl] + crossref = dict() + if row['doi']: + crossref['doi'] = row['doi'] + crossref['any'] = True + self.data[issnl]['crossref'] = crossref + self.c.close() + 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() + print(counts) + + def load_homepage_crawl(self, path): + print("##### Loading IA Homepage Crawl Results...") + reader = csv.DictReader(open(path), delimiter='\t', + fieldnames=("ISSN", "first_url", "first_status", "last_status", "last_url") + ) + counts = Counter() + self.c = self.db.cursor() + for row in reader: + issnl, status = self.add_issn( + raw_issn=row['ISSN'], + ) + counts[status] += 1 + if not issnl: + continue + d = self.data[issnl] + ia = d.get('ia', dict()) + ia['homepage_status'] = int(row['last_status']) + if ia['homepage_status'] == 200: + ia['homepage_url'] = row['last_url'] + else: + ia['homepage_url'] = row['first_url'] + self.data[issnl]['ia'] = ia + self.c.close() + print(counts) + + def everything(self, 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.load_kbart('lockss', LOCKSS_FILE) + #self.load_kbart('clockss', CLOCKSS_FILE) + #self.load_kbart('portico', PORTICO_FILE) + #self.load_kbart('jstor', JSTOR_FILE) + self.index_sim(args) + #self.load_homepage_crawl(IA_CRAWL_FILE) + self.summarize(args) + print("### Done with everything!") + + 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 summarize(self, args): + pass + +def main(): + parser = argparse.ArgumentParser() + 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') + sub.set_defaults(func='everything') + + sub = subparsers.add_parser('init_db') + sub.set_defaults(func='init_db') + + sub = subparsers.add_parser('summarize') + sub.set_defaults(func='summarize') + + + #index_doaj + #index_road + #index_crossref + #index_szczepanski + #index_jurn + #index_norwegian + + #fatcat_load + #fatcat_stats + + #export_urls + #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 not in ('init_db', 'summarize'): + cdb.read_issn_map_file(ISSNL_FILE) + func = getattr(cdb, args.func) + func(args) + +if __name__ == '__main__': + main() + diff --git a/extra/journal_metadata/chocula_schema.sql b/extra/journal_metadata/chocula_schema.sql new file mode 100644 index 00000000..e03907ac --- /dev/null +++ b/extra/journal_metadata/chocula_schema.sql @@ -0,0 +1,80 @@ + + +CREATE TABLE IF NOT EXISTS journal_summary + (issnl TEXT NOT NULL PRIMARY KEY, + issne TEXT, + issnp TEXT, + country TEXT, + lang TEXT, + langs TEXT, + publisher_type TEXT, + is_active BOOLEAN, + is_oa BOOLEAN default false, + is_longtail BOOLEAN default false, + vor_pdf BOOLEAN, + vor_html BOOLEAN, + vor_jats BOOLEAN, + has_dois BOOLEAN, + any_live_homepage BOOLEAN, + any_preservation BOOLEAN, + any_ia BOOLEAN + ); + +CREATE TABLE IF NOT EXISTS journal_index + (issnl TEXT NOT NULL, + slug TEXT NOT NULL, + identifier TEXT, + name TEXT, + work_count INTEGER, + extra TEXT, + PRIMARY KEY(issnl, slug) + ); + +CREATE TABLE IF NOT EXISTS fatcat_container + (issnl TEXT NOT NULL PRIMARY KEY, + ident TEXT NOT NULL, + revision TEXT NOT NULL, + name TEXT, + container_type TEXT, + publisher TEXT, + country TEXT, + lang TEXT, + release_count INTEGER, + ia_count INTEGER, + ia_frac float, + kbart_count INTEGER, + kbart_frac float + ); + +CREATE TABLE IF NOT EXISTS homepage + (id INTEGER PRIMARY KEY, + issnl TEXT NOT NULL, + surt TEXT NOT NULL, + url TEXT NOT NULL, + host TEXT NOT NULL, + domain TEXT NOT NULL, + suffix TEXT NOT NULL, + status_code INTEGER, + terminal_url TEXT, + terminal_status_code INTEGER, + platform_software TEXT, + scope TEXT, + has_issn BOOLEAN, + blocked BOOLEAN, + UNIQUE(issnl, surt) + ); + +CREATE TABLE IF NOT EXISTS fulltext_pattern + (id INTEGER PRIMARY KEY, + issnl TEXT NOT NULL, + surt_glob TEXT, + mimetype TEXT, + state_date TEXT, + end_date TEXT + ); + +CREATE TABLE IF NOT EXISTS title + (id INTEGER PRIMARY KEY, + issnl TEXT NOT NULL, + title TEXT NOT NULL + ); |