extraction -> mapreduce

1 files changed, 248 insertions, 0 deletions

diff --git a/mapreduce/extraction_cdx_grobid.py b/mapreduce/extraction_cdx_grobid.py
new file mode 100755
index 0000000..27668ea
--- /dev/null
+++ b/mapreduce/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()
+