diff options
Diffstat (limited to 'python')
| -rwxr-xr-x | python/deliver_dumpgrobid_to_s3.py | 124 | ||||
| -rwxr-xr-x | python/grobid2json.py | 10 | ||||
| -rw-r--r-- | python/tests/files/small.json | 6 |
3 files changed, 134 insertions, 6 deletions
diff --git a/python/deliver_dumpgrobid_to_s3.py b/python/deliver_dumpgrobid_to_s3.py new file mode 100755 index 0000000..ac0949c --- /dev/null +++ b/python/deliver_dumpgrobid_to_s3.py @@ -0,0 +1,124 @@ +#!/usr/bin/env python3 +""" +Tool for bulk uploading GROBID TEI-XML output from a local filesystem dump +(from HBase) to AWS S3. + +See unpaywall delivery README (in bnewbold's scratch repo) for notes on running +this script for that specific use-case. + +Script takes: +- input TSV: `sha1_hex, json (including grobid0:tei_xml)` + => usually from dumpgrobid, with SHA-1 key transformed to hex, and filtered + down (eg, by join by SHA-1) to a specific manifest +- AWS S3 bucket and prefix + +AWS S3 credentials are passed via environment variables (AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY) + +Output: +- errors/stats to stderr +- log to stdout (redirect to file), prefixed by sha1 + +Requires: +- raven (sentry) +- boto3 (AWS S3 client library) +""" + +import os +import sys +import json +import base64 +import hashlib +import argparse +from collections import Counter + +import boto3 +import raven + +# Yep, a global. Gets DSN from `SENTRY_DSN` environment variable +sentry_client = raven.Client() + + +def b32_hex(s): + """copy/pasta from elsewhere""" + s = s.strip().split()[0].lower() + if s.startswith("sha1:"): + s = s[5:] + if len(s) != 32: + return s + return base64.b16encode(base64.b32decode(s.upper())).lower().decode('utf-8') + + +class DeliverDumpGrobidS3(): + + def __init__(self, s3_bucket, **kwargs): + self.rstore = None + self.count = Counter() + self.s3_bucket = s3_bucket + self.s3_prefix = kwargs.get('s3_prefix', 'grobid/') + self.s3_suffix = kwargs.get('s3_suffix', '.tei.xml') + self.s3_storage_class = kwargs.get('s3_storage_class', 'STANDARD') + self.s3 = boto3.resource('s3') + self.bucket = self.s3.Bucket(self.s3_bucket) + + def run(self, dump_file): + sys.stderr.write("Starting...\n") + for line in dump_file: + line = line.strip().split('\t') + if len(line) != 2: + self.count['skip-line'] += 1 + continue + sha1_hex, grobid_json = line[0], line[1] + if len(sha1_hex) != 40: + sha1_hex = b32_hex(sha1_hex) + assert len(sha1_hex) == 40 + grobid = json.loads(grobid_json) + tei_xml = grobid.get('tei_xml') + if not tei_xml: + print("{}\tskip empty".format(sha1_hex)) + self.count['skip-empty'] += 1 + continue + tei_xml = tei_xml.encode('utf-8') + # upload to AWS S3 + obj = self.bucket.put_object( + Key="{}{}/{}{}".format( + self.s3_prefix, + sha1_hex[0:4], + sha1_hex, + self.s3_suffix, + StorageClass=self.s3_storage_class), + Body=tei_xml) + print("{}\tsuccess\t{}\t{}".format(sha1_hex, obj.key, len(tei_xml))) + self.count['success-s3'] += 1 + sys.stderr.write("{}\n".format(self.count)) + +@sentry_client.capture_exceptions +def main(): + + parser = argparse.ArgumentParser() + parser.add_argument('--s3-bucket', + required=True, + type=str, + help='AWS S3 bucket to upload into') + parser.add_argument('--s3-prefix', + type=str, + default="grobid/", + help='key prefix for items created in bucket') + parser.add_argument('--s3-suffix', + type=str, + default=".tei.xml", + help='file suffix for created objects') + parser.add_argument('--s3-storage-class', + type=str, + default="STANDARD", + help='AWS S3 storage class (redundancy) to use') + parser.add_argument('dump_file', + help="TSV/JSON dump file", + default=sys.stdin, + type=argparse.FileType('r')) + args = parser.parse_args() + + worker = DeliverDumpGrobidS3(**args.__dict__) + worker.run(args.dump_file) + +if __name__ == '__main__': # pragma: no cover + main() diff --git a/python/grobid2json.py b/python/grobid2json.py index ca460f8..d438d48 100755 --- a/python/grobid2json.py +++ b/python/grobid2json.py @@ -31,9 +31,13 @@ import xml.etree.ElementTree as ET ns = "http://www.tei-c.org/ns/1.0" def all_authors(elem): - names = [' '.join([e.findtext('./{%s}forename' % ns) or '', e.findtext('./{%s}surname' % ns) or '']).strip() - for e in elem.findall('.//{%s}author/{%s}persName' % (ns, ns))] - return [dict(name=n) for n in names] + names = [] + for e in elem.findall('.//{%s}author/{%s}persName' % (ns, ns)): + given_name = e.findtext('./{%s}forename' % ns) or None + surname = e.findtext('./{%s}surname' % ns) or None + full_name = '{} {}'.format(given_name or '', surname or '').strip() + names.append(dict(name=full_name, given_name=given_name, surname=surname)) + return names def journal_info(elem): diff --git a/python/tests/files/small.json b/python/tests/files/small.json index 208fb49..49a5671 100644 --- a/python/tests/files/small.json +++ b/python/tests/files/small.json @@ -1,8 +1,8 @@ { "title": "Dummy Example File", "authors": [ - {"name": "Brewster Kahle"}, - {"name": "J Doe"} + {"name": "Brewster Kahle", "given_name": "Brewster", "surname": "Kahle"}, + {"name": "J Doe", "given_name": "J", "surname": "Doe"} ], "journal": { "name": "Dummy Example File. Journal of Fake News. pp. 1-2. ISSN 1234-5678", @@ -15,7 +15,7 @@ "date": "2000", "doi": null, "citations": [ - { "authors": [{"name": "A Seaperson"}], + { "authors": [{"name": "A Seaperson", "given_name": "A", "surname": "Seaperson"}], "date": "2001", "id": "b0", "index": 0, |