diff options
Diffstat (limited to 'python')
| -rw-r--r-- | python/common.py | 26 | ||||
| -rwxr-xr-x | python/extraction_ungrobided.py | 268 | ||||
| -rw-r--r-- | python/tests/files/example_ungrobided.tsv | 20 | ||||
| -rw-r--r-- | python/tests/test_extraction_ungrobided.py | 176 |
4 files changed, 490 insertions, 0 deletions
diff --git a/python/common.py b/python/common.py index 6710044..e596b35 100644 --- a/python/common.py +++ b/python/common.py @@ -1,4 +1,5 @@ +import json from datetime import datetime NORMAL_MIME = ( @@ -71,3 +72,28 @@ def parse_cdx_line(raw_cdx): # '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} + +def parse_ungrobided_line(raw_line): + + line = raw_line.strip().split("\t") + if len(line) != 4: + return None + + key = line[0] + mime = normalize_mime(line[2]) + try: + f_c = json.loads(line[1]) + cdx = json.loads(line[3]) + except json.JSONDecodeError: + return None + + if not (key[5:].isalnum() and len(key) == 37 and mime != None): + print(mime) + print(key) + print("FAIL") + return None + + if '-' in (key, mime, f_c, cdx): + return None + + return {'key': key, 'file:mime': mime, 'file:cdx': cdx, 'f:c': f_c} diff --git a/python/extraction_ungrobided.py b/python/extraction_ungrobided.py new file mode 100755 index 0000000..4074112 --- /dev/null +++ b/python/extraction_ungrobided.py @@ -0,0 +1,268 @@ +#!/usr/bin/env python3 +""" +Variant of extraction_cdx_grobid which takes a partial metadata list as input +instead of CDX. + +This task list is dumped by another Hadoop job which scans over the HBase table +quickly, which allows this job to skip a (relatively) expensive HBase read +per-row. + +Requires: +- happybase +- mrjob +- wayback/GWB libraries +""" + +# XXX: some broken MRO thing going on in here due to python3 object wrangling +# in `wayback` library. Means we can't run pylint. +# pylint: skip-file + +import xml +import json +import raven +import struct +import requests +import happybase +import mrjob +from mrjob.job import MRJob +import wayback.exception +from wayback.resource import Resource +from wayback.resource import ArcResource +from wayback.resourcestore import ResourceStore +from gwb.loader import CDXLoaderFactory +from common import parse_ungrobided_line +from grobid2json import teixml2json + +# Yep, a global. Gets DSN from `SENTRY_DSN` environment variable +sentry_client = raven.Client() + +# Specific poison-pill rows we should skip +KEY_BLACKLIST = ( + 'sha1:DLCCSMMVTCCIR6LRXHEQLZ4PWO6NG2YT', # "failed to guess ARC header format" +) + +class MRExtractUnGrobided(MRJob): + + # "ungrobided" TSV lines in; JSON status out + #HADOOP_INPUT_FORMAT = 'org.apache.hadoop.mapred.lib.NLineInputFormat' + #INPUT_PROTOCOL = mrjob.protocol.RawProtocol + INPUT_PROTOCOL = mrjob.protocol.RawValueProtocol + OUTPUT_PROTOCOL = mrjob.protocol.JSONValueProtocol + + def configure_args(self): + super(MRExtractUnGrobided, 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') + self.add_passthru_arg('--warc-uri-prefix', + type=str, + default='https://archive.org/serve/', + help='URI where WARCs can be found') + + def __init__(self, *args, **kwargs): + super(MRExtractUnGrobided, self).__init__(*args, **kwargs) + self.mime_filter = ['application/pdf'] + self.hb_table = None + + def grobid_process_fulltext(self, content): + r = requests.post(self.options.grobid_uri + "/api/processFulltextDocument", + files={'input': content}) + return r + + def mapper_init(self): + + if self.hb_table: + return + + sentry_client.tags_context(dict(hbase_table=self.options.hbase_table)) + 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: + raise Exception("Couldn't connect to HBase using host: {}".format(host)) + self.hb_table = hb_conn.table(self.options.hbase_table) + + def parse_ungrobided_line(self, raw_line): + """Line should be TSV and have non-null fields: + + - key (string) + - f:c (string, json) + - file:mime (string) + - file:cdx (string, json) + """ + + if (raw_line.startswith(' ') or raw_line.startswith('#')): + return None, dict(status="invalid", reason="line prefix", input=raw_line) + + info = parse_ungrobided_line(raw_line) + if info is None: + return None, dict(status="invalid", reason="ungrobided parse") + + if info['file:mime'] not in self.mime_filter: + return None, dict(status="skip", reason="mimetype", mimetype=info['file:mime']) + + # If warc is not item/file.(w)arc.gz form, skip it + if len(info['file:cdx']['warc'].split('/')) != 2: + return None, dict(status="skip", reason="WARC path not petabox item/file", path=info['file:cdx']['warc']) + + return info, None + + def fetch_warc_content(self, warc_path, offset, c_size): + warc_uri = self.options.warc_uri_prefix + warc_path + try: + rstore = ResourceStore(loaderfactory=CDXLoaderFactory()) + gwb_record = rstore.load_resource(warc_uri, offset, c_size) + except wayback.exception.ResourceUnavailable: + return None, dict(status="error", + reason="failed to load file contents from wayback/petabox") + + if gwb_record.get_status()[0] != 200: + return None, dict(status="error", + reason="archived HTTP response (WARC) was not 200", + warc_status=gwb_record.get_status()[0]) + return gwb_record.open_raw_content().read(), None + + def extract(self, info): + + # Fetch data from WARCs in petabox + original_content, status = self.fetch_warc_content( + info['file:cdx']['warc'], + info['file:cdx']['offset'], + info['file:cdx']['c_size']) + if status: + return None, status + + info['file:size'] = len(original_content) + + # Submit to GROBID + try: + grobid_response = self.grobid_process_fulltext(original_content) + except requests.exceptions.ConnectionError: + return None, dict(status="error", reason="connection to GROBID worker") + + info['grobid0:status_code'] = grobid_response.status_code + + # 4 MByte XML size limit; don't record GROBID status on this path + if len(grobid_response.content) > 4000000: + info['grobid0:status'] = {'status': 'oversize'} + return info, dict(status="oversize", reason="TEI response was too large") + + if grobid_response.status_code != 200: + # response.text is .content decoded as utf-8 + info['grobid0:status'] = dict(status='error', description=grobid_response.text) + return info, dict(status="error", reason="non-200 GROBID HTTP status", + extra=grobid_response.text) + + info['grobid0:status'] = {'status': 'partial'} + info['grobid0:tei_xml'] = grobid_response.content + + # Convert TEI XML to JSON + try: + info['grobid0:tei_json'] = teixml2json(info['grobid0:tei_xml'], encumbered=True) + except xml.etree.ElementTree.ParseError: + info['grobid0:status'] = dict(status="fail", reason="GROBID 200 XML parse error") + return info, info['grobid0:status'] + except ValueError: + info['grobid0:status'] = dict(status="fail", reason="GROBID 200 XML non-TEI content") + return info, info['grobid0:status'] + + tei_metadata = info['grobid0:tei_json'].copy() + for k in ('body', 'annex'): + # Remove fulltext (copywritted) content + tei_metadata.pop(k, None) + info['grobid0:metadata'] = tei_metadata + + # Determine extraction "quality" + # TODO: + + info['grobid0:quality'] = None + info['grobid0:status'] = {'status': 'success'} + + return info, None + + @sentry_client.capture_exceptions + def mapper(self, _, raw_line): + """ + 1. parse filtered line + 2. fetch data from wayback + 3. submit to GROBID + 4. convert GROBID response to JSON (and metadata) + 6. determine "quality" + 6. push results to hbase + """ + + self.increment_counter('lines', 'total') + + # Parse line and filter down + info, status = self.parse_ungrobided_line(raw_line) + if info is None: + self.increment_counter('lines', status['status']) + yield _, status + return + key = info['key'] + if key in KEY_BLACKLIST: + self.increment_counter('lines', 'blacklist') + yield _, dict(status='blacklist', key=key) + return + + # Note: this may not get "cleared" correctly + sentry_client.extra_context(dict(row_key=key)) + + # Do the extraction + info, status = self.extract(info) + if info is None: + self.increment_counter('lines', status['status']) + status['key'] = key + yield _, status + return + extraction_status = status + + # Decide what to bother inserting back into HBase + # Basically, don't overwrite backfill fields. + grobid_status_code = info.get('grobid0:status_code', None) + for k in list(info.keys()): + if k.encode('utf-8') in ('f:c', 'file:mime', 'file:cdx'): + info.pop(k) + + # Convert fields to binary + for k in list(info.keys()): + if info[k] is None: + info.pop(k) + # NOTE: we're not actually sending these f:*, file:* keys... + elif 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) + elif k in ('file:size', 'grobid0:status_code'): + # encode as int64 in network byte order + if info[k] != {} and info[k] != None: + info[k] = struct.pack('!q', info[k]) + + key = info.pop('key') + self.hb_table.put(key, info) + self.increment_counter('lines', 'success') + + if extraction_status is not None: + yield _, dict(status="partial", key=key, + grobid_status_code=grobid_status_code, + reason=extraction_status['reason']) + else: + yield _, dict(status="success", + grobid_status_code=grobid_status_code, key=key, + extra=extraction_status) + + +if __name__ == '__main__': # pragma: no cover + MRExtractUnGrobided.run() diff --git a/python/tests/files/example_ungrobided.tsv b/python/tests/files/example_ungrobided.tsv new file mode 100644 index 0000000..9263b6f --- /dev/null +++ b/python/tests/files/example_ungrobided.tsv @@ -0,0 +1,20 @@ +sha1:23LOSW2QVMKUYXPFZBXQHBBNQR45WTMU {"c": 1, "d": "2017-10-27T22:21:13", "f": "PDFS-20171027214658-00155.warc.gz", "o": 984263791, "u": 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"2010-10-28T09:03:57", "f": "WIDE-20101028084449158-00409-23450~ia360921.us.archive.org~9443.warc.gz", "o": 756726028, "u": "http://cdacnoida.in/ASCNT-2010/Language%20Technology/Paper/Reducing%20Errors%20in%20Translation%20using%20Pre-editor%20for%20Indian%20English%20Sentences.pdf"} application/pdf {"c_size": 98408, "dt": "20101028090357", "offset": 756726028, "surt": "in,cdacnoida)/ascnt-2010/language%20technology/paper/reducing%20errors%20in%20translation%20using%20pre-editor%20for%20indian%20english%20sentences.pdf", "url": "http://cdacnoida.in/ASCNT-2010/Language%20Technology/Paper/Reducing%20Errors%20in%20Translation%20using%20Pre-editor%20for%20Indian%20English%20Sentences.pdf", "warc": "WIDE-20101028063239344-00397-00415-ia360921/WIDE-20101028084449158-00409-23450~ia360921.us.archive.org~9443.warc.gz"} diff --git a/python/tests/test_extraction_ungrobided.py b/python/tests/test_extraction_ungrobided.py new file mode 100644 index 0000000..366d392 --- /dev/null +++ b/python/tests/test_extraction_ungrobided.py @@ -0,0 +1,176 @@ + +import io +import json +import mrjob +import pytest +import struct +import responses +import happybase_mock +import wayback.exception +from unittest import mock +from common import parse_ungrobided_line +from extraction_ungrobided import MRExtractUnGrobided + + +FAKE_PDF_BYTES = b"%PDF SOME JUNK" + struct.pack("!q", 112853843) +OK_UNGROBIDED_LINE = b"\t".join(( + b"sha1:3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ", + b"""{"c": 1, "d": "2017-07-06T07:54:11", "f": "CITESEERX-CRAWL-2017-06-20-20170706075012840-00388-3671~wbgrp-svc285.us.archive.org~8443.warc.gz", "o": 914718776, "u": "http://www.ibc7.org/article/file_down.php?mode%3Darticle_print%26pid%3D250"}""", + b"application/pdf", + b"""{"c_size": 501, "dt": "20170706075411", "offset": 914718776, "surt": "org,ibc7)/article/file_down.php?mode=article_print&pid=250", "url": "http://www.ibc7.org/article/file_down.php?mode%3Darticle_print%26pid%3D250", "warc": "CITESEERX-CRAWL-2017-06-20-20170706074206206-00379-00388-wbgrp-svc285/CITESEERX-CRAWL-2017-06-20-20170706075012840-00388-3671~wbgrp-svc285.us.archive.org~8443.warc.gz"}""", +)) + +with open('tests/files/23b29ea36382680716be08fc71aa81bd226e8a85.xml', 'r') as f: + REAL_TEI_XML = f.read() + +@pytest.fixture +def job(): + """ + Note: this mock only seems to work with job.run_mapper(), not job.run(); + the later results in a separate instantiation without the mock? + """ + job = MRExtractUnGrobided(['--no-conf', '-']) + + conn = happybase_mock.Connection() + conn.create_table('wbgrp-journal-extract-test', + {'file': {}, 'grobid0': {}, 'f': {}}) + job.hb_table = conn.table('wbgrp-journal-extract-test') + + return job + + +@mock.patch('extraction_ungrobided.MRExtractUnGrobided.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None)) +@responses.activate +def test_mapper_single_line(mock_fetch, job): + + responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=200, + body=REAL_TEI_XML, content_type='text/xml') + + raw = io.BytesIO(OK_UNGROBIDED_LINE) + + output = io.BytesIO() + job.sandbox(stdin=raw, stdout=output) + + job.run_mapper() + + # for debugging tests + #print(output.getvalue().decode('utf-8')) + #print(list(job.hb_table.scan())) + + # wayback gets FETCH 1x times + mock_fetch.assert_called_once_with( + "CITESEERX-CRAWL-2017-06-20-20170706074206206-00379-00388-wbgrp-svc285/CITESEERX-CRAWL-2017-06-20-20170706075012840-00388-3671~wbgrp-svc285.us.archive.org~8443.warc.gz", + 914718776, + 501) + + # grobid gets POST 1x times + assert len(responses.calls) == 1 + + # HBase + assert job.hb_table.row(b'1') == {} + + # Saved extraction info + row = job.hb_table.row(b'sha1:3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ') + + assert struct.unpack("!q", row[b'file:size'])[0] == len(FAKE_PDF_BYTES) + assert row[b'file:mime'] == b"application/pdf" + assert struct.unpack("!q", row[b'grobid0:status_code'])[0] == 200 + # TODO: assert row[b'grobid0:quality'] == None + status = json.loads(row[b'grobid0:status'].decode('utf-8')) + assert type(status) == type(dict()) + assert row[b'grobid0:tei_xml'].decode('utf-8') == REAL_TEI_XML + tei_json = json.loads(row[b'grobid0:tei_json'].decode('utf-8')) + metadata = json.loads(row[b'grobid0:metadata'].decode('utf-8')) + assert tei_json['title'] == metadata['title'] + assert 'body' in tei_json + assert 'body' not in metadata + +@mock.patch('extraction_ungrobided.MRExtractUnGrobided.fetch_warc_content', return_value=(FAKE_PDF_BYTES, None)) +@responses.activate +def test_mapper_lines(mock_fetch, job): + + responses.add(responses.POST, 'http://localhost:8070/api/processFulltextDocument', status=200, + body=REAL_TEI_XML, content_type='text/xml') + + raw = io.BytesIO(b"""sha1:23PTUXWSNSVE4HS5J7ELDUUG63J2FPCI\t{"c": 1, "d": "2016-06-09T00:27:36", "f": "WIDE-20160609001810-06993.warc.gz", "o": 287880616, "u": "http://www.case-research.eu/sites/default/files/publications/18092393_E-brief_Dabrowski_Monetary_Policy_final_0.pdf"}\tapplication/pdf\t{"c_size": 68262, "dt": "20160609002736", "offset": 287880616, "surt": "eu,case-research)/sites/default/files/publications/18092393_e-brief_dabrowski_monetary_policy_final_0.pdf", "url": "http://www.case-research.eu/sites/default/files/publications/18092393_E-brief_Dabrowski_Monetary_Policy_final_0.pdf", "warc": "WIDE-20160609000312-crawl427/WIDE-20160609001810-06993.warc.gz"} +sha1:23PW2APYHNBPIBRIVNQ6TMKUNY53UL3D\t{"c": 1, "d": "2016-01-07T03:29:03", "f": "MUSEUM-20160107025230-02354.warc.gz", "o": 413484441, "u": "http://www.portlandoregon.gov/fire/article/363695"}\tapplication/pdf\t{"c_size": 44600, "dt": "20160107032903", "offset": 413484441, "surt": "gov,portlandoregon)/fire/article/363695", "url": "http://www.portlandoregon.gov/fire/article/363695", "warc": "MUSEUM-20160107004301-crawl891/MUSEUM-20160107025230-02354.warc.gz"} +sha1:23RJIHUIOYY5747CR6YYCTMACXDCFYTT\t{"c": 1, "d": "2014-06-07T18:00:56", "f": "ARCHIVEIT-219-QUARTERLY-20047-20140607125555378-00017-wbgrp-crawl051.us.archive.org-6442.warc.gz", "o": 720590380, "u": "https://www.indiana.edu/~orafaq/faq/pdf.php?cat=36&id=264&artlang=en"}\tapplication/pdf\t{"c_size": 3727, "dt": "20140607180056", "offset": 720590380, "surt": "edu,indiana)/~orafaq/faq/pdf.php?artlang=en&cat=36&id=264", "url": "https://www.indiana.edu/~orafaq/faq/pdf.php?cat=36&id=264&artlang=en", "warc": "ARCHIVEIT-219-QUARTERLY-20047-00001/ARCHIVEIT-219-QUARTERLY-20047-20140607125555378-00017-wbgrp-crawl051.us.archive.org-6442.warc.gz"}""") + + + output = io.BytesIO() + job.sandbox(stdin=raw, stdout=output) + + job.run_mapper() + + # for debugging tests + #print(output.getvalue().decode('utf-8')) + #print(list(job.hb_table.scan())) + + # grobid gets POST 3x times + assert len(responses.calls) == 3 + + # wayback gets FETCH 3x times + mock_fetch.assert_has_calls(( + mock.call("WIDE-20160609000312-crawl427/WIDE-20160609001810-06993.warc.gz", 287880616, 68262), + mock.call("MUSEUM-20160107004301-crawl891/MUSEUM-20160107025230-02354.warc.gz", 413484441, 44600), + mock.call("ARCHIVEIT-219-QUARTERLY-20047-00001/ARCHIVEIT-219-QUARTERLY-20047-20140607125555378-00017-wbgrp-crawl051.us.archive.org-6442.warc.gz", 720590380, 3727), + )) + + # Saved extraction info + assert job.hb_table.row(b'sha1:3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ') == {} + assert job.hb_table.row(b'sha1:23PTUXWSNSVE4HS5J7ELDUUG63J2FPCI') != {} + assert job.hb_table.row(b'sha1:23PW2APYHNBPIBRIVNQ6TMKUNY53UL3D') != {} + assert job.hb_table.row(b'sha1:23RJIHUIOYY5747CR6YYCTMACXDCFYTT') != {} + + row = job.hb_table.row(b'sha1:23RJIHUIOYY5747CR6YYCTMACXDCFYTT') + assert struct.unpack("!q", row[b'file:size'])[0] == len(FAKE_PDF_BYTES) + assert row[b'file:mime'] == b"application/pdf" + assert struct.unpack("!q", row[b'grobid0:status_code'])[0] == 200 + status = json.loads(row[b'grobid0:status'].decode('utf-8')) + assert type(status) == type(dict()) + assert row[b'grobid0:tei_xml'].decode('utf-8') == REAL_TEI_XML + tei_json = json.loads(row[b'grobid0:tei_json'].decode('utf-8')) + metadata = json.loads(row[b'grobid0:metadata'].decode('utf-8')) + assert tei_json['title'] == metadata['title'] + assert 'body' in tei_json + assert 'body' not in metadata + +def test_parse_ungrobided_invalid(job): + + print("space-prefixed line") + raw = " com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf application/pdf 200 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz" + info, status = job.parse_ungrobided_line(raw) + assert info is None + assert status['status'] == "invalid" + assert 'prefix' in status['reason'] + + print("commented line") + raw = "#com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf application/pdf 200 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz" + info, status = job.parse_ungrobided_line(raw) + assert info is None + assert status['status'] == "invalid" + assert 'prefix' in status['reason'] + + print("wrong column count") + raw = "a b c d e" + info, status = job.parse_ungrobided_line(raw) + assert info is None + assert status['status'] == "invalid" + assert 'parse' in status['reason'] + + print("CDX line, somehow") + raw = "com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf - 200 3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ - - 401 313356621 CITESEERX-CRAWL-2017-06-20-20170705061647307-00039-00048-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705062052659-00043-31209~wbgrp-svc284.us.archive.org~8443.warc.gz" + info, status = job.parse_ungrobided_line(raw) + assert info is None + print(status) + assert status['status'] == "invalid" + assert 'parse' in status['reason'] + +def test_parse_ungrobided_valid(): + + parsed = parse_ungrobided_line(OK_UNGROBIDED_LINE.decode('utf-8')) + assert parsed['key'] == "sha1:3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ" + assert parsed['f:c']['u'] == "http://www.ibc7.org/article/file_down.php?mode%3Darticle_print%26pid%3D250" + assert parsed['file:mime'] == "application/pdf" + assert parsed['file:cdx']['c_size'] == 501 + assert parsed['file:cdx']['dt'] == "20170706075411" |