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authorBryan Newbold <bnewbold@robocracy.org>2019-05-07 17:26:28 -0700
committerBryan Newbold <bnewbold@robocracy.org>2019-06-24 19:46:06 -0700
commitc2928f8f973be85fc74419e7d574905168937b0a (patch)
tree508193ed60a518cb2c17cf08e89fb2d041d6a4d7 /extra/fixups/fixup_longtail_issnl_unique.py
parentd00271db5a56d0b0bbcdfc8337e8a949972acb5f (diff)
downloadfatcat-c2928f8f973be85fc74419e7d574905168937b0a.tar.gz
fatcat-c2928f8f973be85fc74419e7d574905168937b0a.zip
initial work on longtail_issnl_unique.py
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diff --git a/extra/fixups/fixup_longtail_issnl_unique.py b/extra/fixups/fixup_longtail_issnl_unique.py
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+++ b/extra/fixups/fixup_longtail_issnl_unique.py
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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 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
+ # TODO: memoize these issnl/container lookups
+ container_id = self.lookup_container(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()