refactor backfill for mrjob

4 files changed, 145 insertions, 64 deletions

diff --git a/backfill/README.md b/backfill/README.md
new file mode 100644
index 0000000..90b4ba7
--- /dev/null
+++ b/backfill/README.md
@@ -0,0 +1,8 @@
+
+Run tests:
+
+    pipenv run python -m pytest
+
+Run locally on a file:
+
+    ./backfill_hbase_from_cdx.py tests/files/example.cdx
diff --git a/backfill/backfill_hbase_from_cdx.py b/backfill/backfill_hbase_from_cdx.py
index 757794a..92a6d32 100755
--- a/backfill/backfill_hbase_from_cdx.py
+++ b/backfill/backfill_hbase_from_cdx.py
@@ -6,6 +6,7 @@ formats.
 
 Requires:
 - happybase
+- mrjob
 
 TODO:
 - argparse
@@ -18,6 +19,8 @@ TODO:
 import sys
 import json
 import happybase
+import mrjob
+from mrjob.job import MRJob
 
 NORMAL_MIME = (
     'application/pdf',
@@ -90,80 +93,75 @@ def test_transform_line():
     assert transform_line(raw + " extra_field") == correct
 
 
-def run(in_lines, out_lines, status_lines, table, mime_filter=None):
+class MRCDXBackfillHBase(MRJob):
 
-    if mime_filter is None:
-        mime_filter = ['application/pdf']
-    count_skip = count_invalid = count_fail = count_success = 0
+    # CDX lines in
+    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)
+
+    def mapper_init(self):
+
+        if self.hb_table is None:
+            try:
+                host = self.options.hbase_host
+                hb_conn = happybase.Connection(host=host)
+            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)
+
+        self.mime_filter = ['application/pdf']
+
+    def mapper(self, _, raw_cdx):
+
+        self.increment_counter('lines', 'total')
 
-    for raw_cdx in in_lines.readlines():
         if (raw_cdx.startswith(' ') or raw_cdx.startswith('filedesc') or
                 raw_cdx.startswith('#')):
+
             # Skip line
-            count_skip += 1
-            continue
+            self.increment_counter('lines', 'invalid')
+            return _, status
 
         info = transform_line(raw_cdx)
         if info is None:
-            count_invalid += 1
-            continue
-        if info['file:mime'] not in mime_filter:
-            count_skip += 1
-            continue
+            self.increment_counter('lines', 'invalid')
+            return
+
+        if info['file:mime'] not in self.mime_filter:
+            self.increment_counter('lines', 'skip')
+            return
 
         key = info.pop('key')
         info['file:cdx'] = json.dumps(info['file:cdx'], sort_keys=True,
             indent=None)
-        try:
-            table.put(key, info)
-            count_success += 1
-        except:
-            status_lines.write("ERROR\n") # TODO:
-            count_fail += 1
-
-    status_lines.write('\n')
-    status_lines.write('skip\t{}\n'.format(count_skip))
-    status_lines.write('invalid\t{}\n'.format(count_invalid))
-    status_lines.write('fail\t{}\n'.format(count_fail))
-    status_lines.write('success\t{}\n'.format(count_success))
-
-
-def test_run():
-    
-    import io 
-    import happybase_mock
-
-    out = io.StringIO()
-    status = io.StringIO()
-    raw = io.StringIO("""
-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
-""")
-
-    conn = happybase_mock.Connection()
-    conn.create_table('wbgrp-journal-extract-test', {'file': {}, 'grobid0': {}})
-
-    table = conn.table('wbgrp-journal-extract-test')
-    run(raw, out, status, table)
-
-    print(status.getvalue())
-
-    assert table.row(b'1') == {}
-    # HTTP 301
-    assert table.row(b'3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ') == {}
-    # valid
-    assert table.row(b'MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J') != {}
-    # text/plain
-    assert table.row(b'6VAUYENMOU2SK2OWNRPDD6WTQTECGZAD') == {}
-
-    row = table.row(b'MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J')
-    assert row[b'file:mime'] == b"application/pdf"
-    json.loads(row[b'file:cdx'].decode('utf-8'))
-
-if __name__=="__main__":
-    hb = happybase.Connection(host='')
-    with hb.connection() as conn:
-        table = conn.table('wbgrp-journal-extract-0-qa')
-        run(sys.stdin, sys.stdout, sys.stderr, table)
+
+        self.hb_table.put(key, info)
+        self.increment_counter('lines', 'success')
+
+        yield _, dict(status="success")
+
+if __name__ == '__main__':
+    MRCDXBackfillHBase.run()
 
diff --git a/backfill/tests/files/example.cdx b/backfill/tests/files/example.cdx
new file mode 100644
index 0000000..84e3271
--- /dev/null
+++ b/backfill/tests/files/example.cdx
@@ -0,0 +1,20 @@
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+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
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diff --git a/backfill/tests/test_backfill_hbase_from_cdx.py b/backfill/tests/test_backfill_hbase_from_cdx.py
new file mode 100644
index 0000000..dfed0b3
--- /dev/null
+++ b/backfill/tests/test_backfill_hbase_from_cdx.py
@@ -0,0 +1,55 @@
+
+import io
+import json
+import pytest
+import mrjob
+import happybase_mock
+from backfill_hbase_from_cdx import MRCDXBackfillHBase
+
+@pytest.fixture
+def job():
+    conn = happybase_mock.Connection()
+    conn.create_table('wbgrp-journal-extract-test', {'file': {}, 'grobid0': {}})
+    table = conn.table('wbgrp-journal-extract-test')
+
+    job = MRCDXBackfillHBase(['--no-conf', '-'], hb_table=table)
+    job.hb_table = table
+    return job
+
+#Example to read back rows...
+"""
+def basic_job_run_capturing_output(job):
+
+    job.sandbox(stdin=open('tests/files/example.cdx', 'r'))
+    results = []
+    with job.make_runner() as runner:
+        runner.run()
+        for key, value in job.parse_output(runner.cat_output()):
+            results.append(value)
+
+    print(results)
+    assert len(list(job.hb_table.scan())) == 5
+"""
+
+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'3I42H3S6NNFQ2MSVX7XZKYAYSCX5QBYJ') == {}
+    # valid
+    assert job.hb_table.row(b'MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J') != {}
+    # text/plain
+    assert job.hb_table.row(b'6VAUYENMOU2SK2OWNRPDD6WTQTECGZAD') == {}
+
+    row = job.hb_table.row(b'MPCXVWMUTRUGFP36SLPHKDLY6NGU4S3J')
+    assert row[b'file:mime'] == b"application/pdf"
+    json.loads(row[b'file:cdx'].decode('utf-8'))