initial work on longtail_issnl_unique.py

1 files changed, 192 insertions, 0 deletions

diff --git a/extra/fixups/fixup_longtail_issnl_unique.py b/extra/fixups/fixup_longtail_issnl_unique.py
new file mode 100755
index 00000000..7c492fc3
--- /dev/null
+++ b/extra/fixups/fixup_longtail_issnl_unique.py
@@ -0,0 +1,192 @@
+#!/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()