diff options
Diffstat (limited to 'extraction')
| -rw-r--r-- | extraction/README.md | 24 | ||||
| -rw-r--r-- | extraction/TODO | 4 | ||||
| -rwxr-xr-x | extraction/backfill_hbase_from_cdx.py | 195 | ||||
| -rw-r--r-- | extraction/mrjob.conf | 4 | ||||
| -rw-r--r-- | extraction/pytest.ini | 8 | ||||
| -rw-r--r-- | extraction/tests/files/example.cdx | 20 | ||||
| -rw-r--r-- | extraction/tests/test_backfill_hbase_from_cdx.py | 54 |
7 files changed, 308 insertions, 1 deletions
diff --git a/extraction/README.md b/extraction/README.md index 1da1454..b063fba 100644 --- a/extraction/README.md +++ b/extraction/README.md @@ -1,5 +1,4 @@ - ## Development and Testing Requires (eg, via `apt`): @@ -17,3 +16,26 @@ Run the tests with: TODO: GROBID and HBase during development? +## Backfill + +An example actually connecting to HBase from a local machine, with thrift +running on a devbox: + + ./backfill_hbase_from_cdx.py tests/files/example.cdx \ + --hbase-table wbgrp-journal-extract-0-qa \ + --hbase-host bnewbold-dev.us.archive.org + +Actual invocation to run on Hadoop cluster (running on an IA devbox, where +hadoop environment is configured): + + # Create tarball of virtualenv + pipenv shell + tar -czf backfill-4OmRI0zZ.tar.gz -C /home/bnewbold/.local/share/virtualenvs/backfill-4OmRI0zZ . + + ./backfill_hbase_from_cdx.py \ + -r hadoop \ + --hbase-host bnewbold-dev.us.archive.org \ + --hbase-table wbgrp-journal-extract-0-qa \ + -c mrjob.conf \ + --archive backfill-4OmRI0zZ.tar.gz#venv \ + hdfs:///user/bnewbold/journal_crawl_cdx/citeseerx_crawl_2017.cdx diff --git a/extraction/TODO b/extraction/TODO index ed10834..3459752 100644 --- a/extraction/TODO +++ b/extraction/TODO @@ -1,2 +1,6 @@ +- better test coverage (actually check coverage!) +- use pre-mapper command to filter down, eg, by status type? +- automation/docs for bundling virtualenv along +- think about speedups - abstract CDX line reading and HBase stuff out into a common library - actual GROBID_SERVER="http://wbgrp-svc096.us.archive.org:8070" diff --git a/extraction/backfill_hbase_from_cdx.py b/extraction/backfill_hbase_from_cdx.py new file mode 100755 index 0000000..fe37bd5 --- /dev/null +++ b/extraction/backfill_hbase_from_cdx.py @@ -0,0 +1,195 @@ +#!/usr/bin/env python3 +""" +Streaming Hadoop script to import CDX metadata into the HBase fulltext table, +primarily for URL-agnostic crawl de-duplication. Takes only "fulltext" file +formats. + +Requires: +- happybase +- mrjob + +TODO: +- argparse +- refactor into an object +- tests in separate file +- nose tests +- sentry integration for error reporting +""" + +import sys +import json +from datetime import datetime +import happybase +import mrjob +from mrjob.job import MRJob + +NORMAL_MIME = ( + 'application/pdf', + 'application/postscript', + 'text/html', + 'text/xml', +) + +def normalize_mime(raw): + raw = raw.lower() + for norm in NORMAL_MIME: + if raw.startswith(norm): + return norm + + # Special cases + if raw.startswith('application/xml'): + return 'text/xml' + if raw.startswith('application/x-pdf'): + return 'application/pdf' + return None + +def test_normalize_mime(): + assert normalize_mime("asdf") == None + assert normalize_mime("application/pdf") == "application/pdf" + assert normalize_mime("application/pdf+journal") == "application/pdf" + assert normalize_mime("Application/PDF") == "application/pdf" + assert normalize_mime("application/p") == None + assert normalize_mime("application/xml+stuff") == "text/xml" + +def transform_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} + +def test_transform_line(): + + raw = "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf 20170828233154 https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf application/pdf 200 WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G - - 210251 931661233 SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz" + correct = { + 'key': "sha1:WL3FEA62TEU4F52Y5DOVQ62VET4QJW7G", + 'file:mime': "application/pdf", + 'file:cdx': { + 'surt': "edu,upenn,ldc)/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf", + 'url': "https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf", + 'dt': "20170828233154", + 'warc': "SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828231135742-00000-00009-wbgrp-svc284/SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz", + 'offset': 931661233, + 'c_size': 210251, + }, + 'f:c': { + 'u': "https://www.ldc.upenn.edu/sites/www.ldc.upenn.edu/files/medar2009-large-arabic-broadcast-collection.pdf", + 'd': "2017-08-28T23:31:54", + 'f': "SEMSCHOLAR-PDF-CRAWL-2017-08-04-20170828232253025-00005-3480~wbgrp-svc284.us.archive.org~8443.warc.gz", + 'o': 931661233, + 'c': 1, + } + } + + assert transform_line(raw) == correct + assert transform_line(raw + "\n") == correct + assert transform_line(raw + " extra_field") == correct + + +class MRCDXBackfillHBase(MRJob): + + # CDX lines in; JSON status out + INPUT_PROTOCOL = mrjob.protocol.RawValueProtocol + OUTPUT_PROTOCOL = mrjob.protocol.JSONValueProtocol + + def configure_args(self): + super(MRCDXBackfillHBase, 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') + + 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(MRCDXBackfillHBase, self).__init__(*args, **kwargs) + self.mime_filter = ['application/pdf'] + + 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 mapper(self, _, raw_cdx): + + self.increment_counter('lines', 'total') + + if (raw_cdx.startswith(' ') or raw_cdx.startswith('filedesc') or + raw_cdx.startswith('#')): + + # Skip line + # XXX: tests don't cover this path; need coverage! + self.increment_counter('lines', 'invalid') + return _, dict(status="invalid") + + info = transform_line(raw_cdx) + if info is None: + self.increment_counter('lines', 'invalid') + return _, dict(status="invalid") + + if info['file:mime'] not in self.mime_filter: + self.increment_counter('lines', 'skip') + return _, dict(status="skip") + + key = info.pop('key') + info['f:c'] = json.dumps(info['f:c'], sort_keys=True, indent=None) + info['file:cdx'] = json.dumps(info['file:cdx'], sort_keys=True, + indent=None) + + self.hb_table.put(key, info) + self.increment_counter('lines', 'success') + + yield _, dict(status="success") + +if __name__ == '__main__': + MRCDXBackfillHBase.run() + diff --git a/extraction/mrjob.conf b/extraction/mrjob.conf new file mode 100644 index 0000000..cb286f1 --- /dev/null +++ b/extraction/mrjob.conf @@ -0,0 +1,4 @@ +runners: + hadoop: + setup: + - export PYTHONPATH=$PYTHONPATH:venv/lib/python3.5/site-packages/ diff --git a/extraction/pytest.ini b/extraction/pytest.ini new file mode 100644 index 0000000..0a5e921 --- /dev/null +++ b/extraction/pytest.ini @@ -0,0 +1,8 @@ + +[pytest] + +# allow imports from files in current directory +python_paths = . + +# search for 'test_*' functions in all python files, not just under tests +python_files = *.py diff --git a/extraction/tests/files/example.cdx b/extraction/tests/files/example.cdx new file mode 100644 index 0000000..84e3271 --- /dev/null +++ b/extraction/tests/files/example.cdx @@ -0,0 +1,20 @@ +edu,cmu,cs,adm,reports-archive)/anon/usr0/ftp/usr0/anon/2002/cmu-cs-02-119.pdf 20170706005950 http://reports-archive.adm.cs.cmu.edu/anon/usr0/ftp/usr0/anon/2002/CMU-CS-02-119.pdf application/pdf 200 MQHD36X5MNZPWFNMD5LFOYZSFGCHUN3V - - 361006 17120058 CITESEERX-CRAWL-2017-06-20-20170706004100259-00924-00932-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170706005946792-00926-31209~wbgrp-svc284.us.archive.org~8443.warc.gz +fi,tkk,lib)/diss/2001/isbn951225459x/isbn951225459x.pdf 20170705074926 http://lib.tkk.fi/Diss/2001/isbn951225459X/isbn951225459X.pdf application/pdf 200 KJBCOT7LGBNIAVGEGPUELK5OK6RTFORR - 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- 643 119398161 CITESEERX-CRAWL-2017-06-20-20170706014800946-00020-00029-wbgrp-svc285/CITESEERX-CRAWL-2017-06-20-20170706014907678-00022-3671~wbgrp-svc285.us.archive.org~8443.warc.gz diff --git a/extraction/tests/test_backfill_hbase_from_cdx.py b/extraction/tests/test_backfill_hbase_from_cdx.py new file mode 100644 index 0000000..1a13e5b --- /dev/null +++ b/extraction/tests/test_backfill_hbase_from_cdx.py @@ -0,0 +1,54 @@ +""" +TODO: could probably refactor to use unittest.mock.patch('happybase') +""" + +import io +import json +import pytest +import mrjob +import happybase_mock +from backfill_hbase_from_cdx import MRCDXBackfillHBase + +@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? + """ + conn = happybase_mock.Connection() + conn.create_table('wbgrp-journal-extract-test', + {'file': {}, 'grobid0': {}, 'f': {}}) + table = conn.table('wbgrp-journal-extract-test') + + job = MRCDXBackfillHBase(['--no-conf', '-'], hb_table=table) + return job + + +def test_some_lines(job): + + raw = io.BytesIO(b""" +com,sagepub,cep)/content/28/9/960.full.pdf 20170705062200 http://cep.sagepub.com/content/28/9/960.full.pdf application/pdf 301 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 +eu,eui,cadmus)/bitstream/handle/1814/36635/rscas_2015_03.pdf;jsessionid=761393014319a39f40d32ae3eb3a853f?sequence=1 20170705062202 http://cadmus.eui.eu/bitstream/handle/1814/36635/RSCAS_2015_03.pdf%3Bjsessionid%3D761393014319A39F40D32AE3EB3A853F?sequence%3D1 application/PDF 200 MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J - - 854156 328850624 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 +com,pbworks,educ333b)/robots.txt 20170705063311 http://educ333b.pbworks.com/robots.txt text/plain 200 6VAUYENMOU2SK2OWNRPDD6WTQTECGZAD - - 638 398190140 CITESEERX-CRAWL-2017-06-20-20170705062707827-00049-00058-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705063158203-00053-31209~wbgrp-svc284.us.archive.org~8443.warc.gz +""") + + job.sandbox(stdin=raw) + job.run_mapper() + + assert job.hb_table.row(b'1') == {} + # HTTP 301 + assert job.hb_table.row(b'sha1:3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ') == {} + # valid + assert job.hb_table.row(b'sha1:MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J') != {} + # text/plain + assert job.hb_table.row(b'sha1:6VAUYENMOU2SK2OWNRPDD6WTQTECGZAD') == {} + + row = job.hb_table.row(b'sha1:MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J') + assert row[b'file:mime'] == b"application/pdf" + + file_cdx = json.loads(row[b'file:cdx'].decode('utf-8')) + assert int(file_cdx['offset']) == 328850624 + + f_c = json.loads(row[b'f:c'].decode('utf-8')) + assert f_c['u'] == "http://cadmus.eui.eu/bitstream/handle/1814/36635/RSCAS_2015_03.pdf%3Bjsessionid%3D761393014319A39F40D32AE3EB3A853F?sequence%3D1" + assert b'i' not in f_c |