diff options
Diffstat (limited to 'backfill')
-rw-r--r-- | backfill/Pipfile | 17 | ||||
-rw-r--r-- | backfill/Pipfile.lock | 604 | ||||
-rw-r--r-- | backfill/README.md | 26 | ||||
-rw-r--r-- | backfill/TODO | 5 | ||||
-rwxr-xr-x | backfill/backfill_hbase_from_cdx.py | 195 | ||||
-rw-r--r-- | backfill/mrjob.conf | 4 | ||||
-rw-r--r-- | backfill/pytest.ini | 8 | ||||
-rw-r--r-- | backfill/tests/files/example.cdx | 20 | ||||
-rw-r--r-- | backfill/tests/test_backfill_hbase_from_cdx.py | 54 |
9 files changed, 0 insertions, 933 deletions
diff --git a/backfill/Pipfile b/backfill/Pipfile deleted file mode 100644 index 817a7ff..0000000 --- a/backfill/Pipfile +++ /dev/null @@ -1,17 +0,0 @@ -[[source]] -url = "https://pypi.python.org/simple" -verify_ssl = true -name = "pypi" - -[dev-packages] - -[packages] -happybase = "*" -happybase-mock = "*" -pytest = "*" -mrjob = "*" -pytest-pythonpath = "*" -setuptools = "*" - -[requires] -python_version = "3.5" diff --git a/backfill/Pipfile.lock b/backfill/Pipfile.lock deleted file mode 100644 index a14bdf6..0000000 --- a/backfill/Pipfile.lock +++ /dev/null @@ -1,604 +0,0 @@ -{ - "_meta": { - "hash": { - "sha256": "e056ad067114ae0f442c375ab12446d9fed77bbeda349a3461a161b0df7d01dc" - }, - "pipfile-spec": 6, - "requires": { - "python_version": "3.5" - }, - "sources": [ - { - "name": "pypi", - "url": "https://pypi.python.org/simple", - "verify_ssl": true - } - ] - }, - "default": { - "attrs": { - "hashes": [ - "sha256:1c7960ccfd6a005cd9f7ba884e6316b5e430a3f1a6c37c5f87d8b43f83b54ec9", - "sha256:a17a9573a6f475c99b551c0e0a812707ddda1ec9653bed04c13841404ed6f450" - 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-Run tests: - - pipenv run python -m pytest - -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/backfill/TODO b/backfill/TODO deleted file mode 100644 index e4023de..0000000 --- a/backfill/TODO +++ /dev/null @@ -1,5 +0,0 @@ -- 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 -- refactor into extraction folder diff --git a/backfill/backfill_hbase_from_cdx.py b/backfill/backfill_hbase_from_cdx.py deleted file mode 100755 index fe37bd5..0000000 --- a/backfill/backfill_hbase_from_cdx.py +++ /dev/null @@ -1,195 +0,0 @@ -#!/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/backfill/mrjob.conf b/backfill/mrjob.conf deleted file mode 100644 index cb286f1..0000000 --- a/backfill/mrjob.conf +++ /dev/null @@ -1,4 +0,0 @@ -runners: - hadoop: - setup: - - export PYTHONPATH=$PYTHONPATH:venv/lib/python3.5/site-packages/ diff --git a/backfill/pytest.ini b/backfill/pytest.ini deleted file mode 100644 index 0a5e921..0000000 --- a/backfill/pytest.ini +++ /dev/null @@ -1,8 +0,0 @@ - -[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/backfill/tests/files/example.cdx b/backfill/tests/files/example.cdx deleted file mode 100644 index 84e3271..0000000 --- a/backfill/tests/files/example.cdx +++ /dev/null @@ -1,20 +0,0 @@ -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 - - 344175 255650124 CITESEERX-CRAWL-2017-06-20-20170705074433815-00129-00138-wbgrp-svc284/CITESEERX-CRAWL-2017-06-20-20170705074843696-00134-31209~wbgrp-svc284.us.archive.org~8443.warc.gz -org,oxfordjournals,nar)/cgi/reprint/gkl1060v1.pdf 20170706035441 http://nar.oxfordjournals.org/cgi/reprint/gkl1060v1.pdf text/html 301 OX6MLVDFURLT2KSYCXUYW2PZNOVFSEVF - 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-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 |