diff options
Diffstat (limited to 'extraction/extraction_cdx_grobid.py')
| -rwxr-xr-x | extraction/extraction_cdx_grobid.py | 248 |
1 files changed, 248 insertions, 0 deletions
diff --git a/extraction/extraction_cdx_grobid.py b/extraction/extraction_cdx_grobid.py new file mode 100755 index 0000000..54d8b71 --- /dev/null +++ b/extraction/extraction_cdx_grobid.py @@ -0,0 +1,248 @@ +#!/usr/bin/env python3 +""" +Streaming Hadoop script to import extract metadata and body from fulltext (eg, +PDF) files using GROBID. Input is a CDX file; results primarly go to HBase, +with status written to configurable output stream. + +Fulltext files are loaded directly from WARC files in petabox, instead of going +through the wayback replay. + +Requires: +- happybase +- mrjob +- wayback/GWB libraries +""" + +import io +import sys +import struct +import requests +import happybase +import mrjob +from mrjob.job import MRJob +from wayback.resource import Resource +from wayback.resource import ArcResource +from wayback.resourcestore import ResourceStore +from gwb.loader import CDXLoaderFactory + + +def parse_cdx_line(raw_cdx): + + cdx = raw_cdx.split() + if len(cdx) < 11: + return None + + surt = cdx[0] + dt = cdx[1] + url = cdx[2] + mime = normalize_mime(cdx[3]) + http_status = cdx[4] + key = cdx[5] + c_size = cdx[8] + offset = cdx[9] + warc = cdx[10] + + if not (key.isalnum() and c_size.isdigit() and offset.isdigit() + and http_status == "200" and len(key) == 32 and dt.isdigit()): + return None + + if '-' in (surt, dt, url, mime, http_status, key, c_size, offset, warc): + return None + + key = "sha1:{}".format(key) + + info = dict(surt=surt, dt=dt, url=url, c_size=int(c_size), + offset=int(offset), warc=warc) + + warc_file = warc.split('/')[-1] + dt_iso = datetime.strptime(dt, "%Y%m%d%H%M%S").isoformat() + try: + dt_iso = datetime.strptime(dt, "%Y%m%d%H%M%S").isoformat() + except: + return None + + # 'i' intentionally not set + heritrix = dict(u=url, d=dt_iso, f=warc_file, o=int(offset), c=1) + return {'key': key, 'file:mime': mime, 'file:cdx': info, 'f:c': heritrix} + + +class MRExtractCdxGrobid(MrJob): + + # CDX lines in; JSON status out + INPUT_PROTOCOL = mrjob.protocol.RawValueProtocol + OUTPUT_PROTOCOL = mrjob.protocol.JSONValueProtocol + + def configure_args(self): + super(MRExtractCdxGrobid, self).configure_args() + + self.add_passthru_arg('--hbase-table', + type=str, + default='wbgrp-journal-extract-0-qa', + help='HBase table to backfill into (must exist)') + self.add_passthru_arg('--hbase-host', + type=str, + default='localhost', + help='HBase thrift API host to connect to') + self.add_passthru_arg('--grobid-uri', + type=str, + default='http://localhost:8070', + help='URI of GROBID API Server') + + def __init__(self, *args, **kwargs): + + # Allow passthrough for tests + if 'hb_table' in kwargs: + self.hb_table = kwargs.pop('hb_table') + else: + self.hb_table = None + + super(MRExtractCdxGrobid, self).__init__(*args, **kwargs) + self.mime_filter = ['application/pdf'] + + def grobid_fulltext(self, content): + r = requests.post(self.options.grobid_uri + "/api/processFulltextDocument", + files={'input': content}) + if r.status_code is not 200: + # XXX: + print("FAIL (Grobid: {}): {}".format(r.content.decode('utf8'))) + else: + # XXX: + print("SUCCESS: " + debug_line) + return r.json() + + def mapper_init(self): + + if self.hb_table is None: + try: + host = self.options.hbase_host + # TODO: make these configs accessible from... mrconf.cfg? + hb_conn = happybase.Connection(host=host, transport="framed", + protocol="compact") + except Exception as err: + raise Exception("Couldn't connect to HBase using host: {}".format(host)) + self.hb_table = hb_conn.table(self.options.hbase_table) + + def parse_line(self, raw_cdx): + + if (raw_cdx.startswith(' ') or raw_cdx.startswith('filedesc') or + raw_cdx.startswith('#')): + return None, dict(status="invalid", reason="line prefix") + + info = parse_cdx_line(raw_cdx) + if info is None: + return None, dict(status="invalid", reason="CDX parse") + + if info['file:mime'] not in self.mime_filter: + self.increment_counter('lines', 'skip') + return None, dict(status="skip", reason="mimetype") + + # If warc is not item/file.(w)arc.gz form, skip it + if len(info['file:cdx']['warc'].split('/')) != 2: + self.increment_counter('lines', 'skip') + return None, dict(status="skip", reason="WARC path not petabox item/file") + + return info, None + + def extract(self, info): + + # Fetch data from WARCs in petabox + try: + rstore = ResourceStore(loaderfactory=CDXLoaderFactory()) + gwb_record = rstore.load_resource( + info['file:cdx']['warc'], + info['file:cdx']['offset'], + info['file:cdx']['c_size']) + except IOError as ioe: + # XXX: catch correct error + self.increment_counter('lines', 'existing') + return _, dict(status="existing") + + if gwb_record.get_status()[0] != 200: + self.increment_counter('lines', 'error') + return _, dict(status="error", reason="non-HTTP-200 WARC content") + + # Submit to GROBID + content = gwb_record.open_raw_content() + try: + grobid_result = self.grobid_fulltext(gwb_record.open_raw_content()) + except IOError as ioe: + # XXX: catch correct error + self.increment_counter('lines', 'existing') + return _, dict(status="existing") + + info['file:size'] = len(resource_data) + + info['grobid0:status_code'] = None + info['grobid0:quality'] = None + info['grobid0:status'] = {} + info['grobid0:tei_xml'] = None + info['grobid0:tei_json'] = {} + info['grobid0:metadata'] = {} + + # Convert TEI XML to JSON + # TODO + + # Determine extraction "quality" + # TODO + + return info, None + + def mapper(self, _, raw_cdx): + """ + 1. parse CDX line + 2. check what is already in hbase + 3. fetch data from wayback + 4. submit to GROBID + 5. convert GROBID response to JSON (and metadata) + 6. determine "quality" + 7. push results to hbase + """ + + self.increment_counter('lines', 'total') + + # Parse line and filter down + info, status = self.parse_line(raw_cdx) + if info is None: + self.increment_counter('lines', status['status']) + return _, status + + # Check if we've already processed this line + oldrow = self.hb_table.get(info['key'], columns=['f', 'file', + 'grobid:status_code']) + if row.get('grobid0:status', None): + # This file has already been processed; skip it + self.increment_counter('lines', 'existing') + return _, dict(status="existing") + + # Do the extraction + info, status = self.extract(info) + if info is None: + self.increment_counter('lines', status['status']) + return _, status + + # Decide what to bother inserting back into HBase + # Particularly: ('f:c', 'file:mime', 'file:size', 'file:cdx') + grobid_status = info.get('grobid0:status_code', None) + for k in info.keys(): + if k in oldrow: + info.pop(k) + + # Convert fields to binary + for k in info.keys(): + if k in ('f:c', 'file:cdx', 'grobid0:status', 'grobid0:tei_json', + 'grobid0:metadata'): + assert type(info[k]) == dict + info[k] = json.dumps(info[k], sort_keys=True, indent=None) + if k in ('file:size', 'grobid0:status_code'): + # encode as int64 in network byte order + info[k] = struct.pack('!q', info[k]) + + key = info.pop('key') + self.hb_table.put(key, info) + self.increment_counter('lines', 'success') + + yield _, dict(status="success", grobid_status=grobid_status) + +if __name__ == '__main__': + MRExtractCdxGrobid.run() + |