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#!/usr/bin/env python3
"""
This file must be moved to the fatcat:python/ directory (aka, not in
fatcat:extra/fixups) to run. It's a "one-off", so probably will bitrot pretty
quickly. There are no tests.
Example invocation:
zcat /srv/fatcat/datasets/2018-09-23-0405.30-dumpgrobidmetainsertable.longtail_join.filtered.tsv.gz | ./fixup_longtail_issnl_unique.py /srv/fatcat/datasets/single_domain_issnl.tsv -
See also:
- bnewbold/scratch:mellon/201904_longtail_issn.md
- aitio:/rapida/OA-JOURNAL-TESTCRAWL-TWO-2018
- https://archive.org/details/OA-JOURNAL-TESTCRAWL-TWO-2018-extra
= https://archive.org/download/ia_longtail_dumpgrobidmetainsertable_2018-09-23/2018-09-23-0405.30-dumpgrobidmetainsertable.longtail_join.filtered.tsv.gz
QA notes:
- everything on revistas.uv.mx linked to 2395-9495, which is only one journal
on that domain. blacklist 'revistas' in the domain?
- afjg3yjdjbf2dad47t5jq7nlbe => 2305-7254 ok match but not perfect (wrong year
of conference). probably better than nothing.
- elib.mi.sanu.ac.rs has several journals on domain. container_name was correct.
- revistavirtual.ucn.edu.co has 2x journals
- lpchkxkp5jecdgrab33fxodd7y bad match
- k36web33jvf25by64gop4yil7q an IR, not a journal (ok)
- hvxercwasjhotpewb5xfadyyle good match, though only an abstract (in URL). full
articles get DOIs
- release_epkiok6y3zhsnp3no2lkljznza not a paper; journal match batch (cato, wtf)
- release_b3jolh25mbg4djrqotgosyeike jfr.unibo.it good
- release_bzr35evb4bdd3mxex6gxn6dcyy conf.ostis.net good?
- uzspace.uzulu.ac.za IR, not a container
- release_5lt36yy3vre2nnig46toy67kdi wrong, multiple journals
- release_54hmv5gvtjghjk7rpcbp2pn2ky good
- release_6h7doxfaxnao3jm7f6jkfdpdwm good
- release_6pio5hz6bvawfnodhkvmfk4jei correct but stub
- release_7oobqygqczapbgdvvgbxfyvqli correct
- release_tsljmbevpzfpxiezzv7puwbilq good
general notes:
- GROBID works pretty well. references look pretty good, should match. there is
a non-trivial fraction of non-journal content, but it isn't too bad
- this "single-journal domain" premise doesn't work
- could probably do a subset based on "is the journal name in the domain name",
or "is domain acronym of journal name"
- surprising number of IRs with ISSNs in here
- might have better luck blacklisting out latin american TLDs, which tend to
host many journals?
"""
import os, sys, argparse
import json
import sqlite3
import itertools
import fatcat_client
from fatcat_tools import authenticated_api
from fatcat_tools.importers.common import EntityImporter, clean, LinePusher
from fatcat_tools.importers.arabesque import b32_hex
class LongtailIssnlSingleDomainFixup(EntityImporter):
"""
Fixup script for bootstrap longtail OA release entities which don't have a
container but are confidently associated with an ISSN-L based on file
domain.
Expected to be a one-time fixup impacting about 600k entities (around half
the longtail OA batch).
Reads in a mapping of unique domain-ISSNL mappings, and then iterates over
the original matched import batch file. For each line in the later:
- checks if in-scope based on domain-ISSNL map
- uses API to lookup file (by SHA-1) and confirm domain in URL list
- look up releases for file and retain the longtail-oa ones (an extra flag)
- if release is longtail-oa and no container, set the container based on
ISSN-L (using cached lookup)
- use EntityImporter stuff to manage update/editgroup queue
"""
def __init__(self, api, domain_issnl_tsv_file, **kwargs):
eg_desc = kwargs.pop('editgroup_description',
"Fixup for longtail OA releases that can be matched to specific container by file domain / ISSN-L mapping")
eg_extra = kwargs.pop('editgroup_extra', dict())
eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.LongtailIssnlSingleDomainFixup')
super().__init__(api,
editgroup_description=eg_desc,
editgroup_extra=eg_extra,
**kwargs)
self._domain_issnl_map = self.load_domain_issnl(domain_issnl_tsv_file)
self._issnl_container_map = dict()
def load_domain_issnl(self, tsv_file):
print("Loading domain ISSN-L file...")
m = dict()
for l in tsv_file:
l = l.strip().split('\t')
assert len(l) == 2
domain = l[0].lower()
issnl = l[1]
assert len(issnl) == 9 and issnl[4] == '-'
m[domain] = issnl
print("Got {} matchings.".format(len(m)))
return m
def want(self, raw_record):
# do it all in parse_record()
return True
def parse_record(self, row):
"""
TSV rows:
- sha1 b32 key
- JSON string: CDX-ish
- surt
- url
- <etc>
- mime
- size (?)
- JSON string: grobid metadata
"""
# parse row
row = row.split('\t')
assert len(row) == 5
sha1 = b32_hex(row[0][5:])
cdx_dict = json.loads(row[1])
url = cdx_dict['url']
domain = url.split('/')[2].lower()
if not domain:
self.counts['skip-domain-blank'] += 1
return None
# domain in scope?
issnl = self._domain_issnl_map.get(domain)
if not issnl:
self.counts['skip-domain-scope'] += 1
return None
if 'revistas' in domain.lower().split('.'):
self.counts['skip-domain-revistas'] += 1
return None
# lookup file
#print(sha1)
try:
file_entity = self.api.lookup_file(sha1=sha1, expand="releases")
except fatcat_client.rest.ApiException as err:
if err.status == 404:
self.counts['skip-file-not-found'] += 1
return None
else:
raise err
# container ident
container_id = self.lookup_issnl(issnl)
if not container_id:
self.counts['skip-container-not-found'] += 1
return None
# confirm domain
url_domain_match = False
for furl in file_entity.urls:
fdomain = furl.url.split('/')[2].lower()
if domain == fdomain:
url_domain_match = True
break
if not url_domain_match:
self.counts['skip-no-domain-match'] += 1
return None
# fetch releases
releases = [r for r in file_entity.releases if (r.extra.get('longtail_oa') == True and r.container_id == None)]
if not releases:
#print(file_entity.releases)
self.counts['skip-no-releases'] += 1
return None
# fetch full release objects (need abstract, etc, for updating)
releases = [self.api.get_release(r.ident) for r in releases]
# set container_id
for r in releases:
r.container_id = container_id
return releases
def try_update(self, re_list):
for re in re_list:
self.api.update_release(self.get_editgroup_id(), re.ident, re)
self.counts['update'] += 1
return False
def insert_batch(self, batch):
raise NotImplementedError
def run_fixup(args):
fmi = LongtailIssnlSingleDomainFixup(args.api,
args.domain_issnl_tsv_file,
edit_batch_size=args.batch_size)
LinePusher(fmi, args.insertable_tsv_file).run()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--api-host-url',
default="http://localhost:9411/v0",
help="connect to this host/port")
parser.add_argument('--batch-size',
help="size of batch to send",
default=50, type=int)
parser.add_argument('domain_issnl_tsv_file',
help="domain/ISSNL mapping TSV file",
type=argparse.FileType('r'))
parser.add_argument('insertable_tsv_file',
help="dumpgrobidmetainsertable TSV file to work over",
default=sys.stdin, type=argparse.FileType('r'))
auth_var = "FATCAT_AUTH_SANDCRAWLER"
args = parser.parse_args()
args.api = authenticated_api(
args.api_host_url,
# token is an optional kwarg (can be empty string, None, etc)
token=os.environ.get(auth_var))
run_fixup(args)
if __name__ == '__main__':
main()
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