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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
"""
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()
# domain in scope?
issnl = self._domain_issnl_map.get(domain)
if not issnl:
self.counts['skip-domain-scope'] += 1
return None
# lookup file
#print(sha1)
try:
file_entity = self.api.lookup_file(sha1=sha1)
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 = self.api.get_file_releases(file_entity.ident)
releases = [r for r in releases if (r.extra.get('longtail-oa') == True and r.container_id == None)]
if not releases:
self.counts['skip-no-releases'] += 1
return None
# 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(re.ident, re, editgroup_id=self.get_editgroup_id())
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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