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authorMartin Czygan <martin@archive.org>2020-03-10 15:33:17 +0000
committerMartin Czygan <martin@archive.org>2020-03-10 15:33:17 +0000
commit336630e1d445fb9d233447f9af4bac94473a12bf (patch)
treeb2d4baa4ea6d3afac29b9b2760101c10d18ea30a /python/fatcat_tools/harvest/pubmed.py
parentf4cce5a765a9f80f9c5e9c907689c06dc9ebf102 (diff)
parentd18942d1ab4d394bdb275bcf9eb82d1cba814775 (diff)
downloadfatcat-336630e1d445fb9d233447f9af4bac94473a12bf.tar.gz
fatcat-336630e1d445fb9d233447f9af4bac94473a12bf.zip
Merge branch 'martin-kafka-bs4-import' into 'master'
pubmed and arxiv harvest preparations See merge request webgroup/fatcat!28
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+"""
+Pubmed harvest via FTP.
+
+Assumptions:
+
+* fixed hostname and directory structure
+* XML files are gzip compressed
+* accompanying HTML files contain correct dates
+"""
+
+import collections
+import gzip
+import io
+import os
+import re
+import shutil
+import sys
+import tempfile
+import time
+import xml.etree.ElementTree as ET
+from ftplib import FTP
+from urllib.parse import urljoin, urlparse
+
+import dateparser
+from bs4 import BeautifulSoup
+from confluent_kafka import KafkaException, Producer
+
+from .harvest_common import HarvestState
+
+
+class PubmedFTPWorker:
+ """
+ Access Pubmed FTP for daily updates.
+
+ * Server directory: ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles
+ * Docs: ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/README.txt
+
+ Daily Update Files (02/2020)
+ ----------------------------
+ Each day, NLM produces update files that include new, revised and deleted
+ citations. The first Update file to be loaded after loading the complete
+ set of 2019 MEDLINE/PubMed Baseline files is pubmed20n1016.xml.
+
+ Usually, three files per update, e.g.:
+
+ * ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed20n1016_stats.html
+ * ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed20n1016.xml.gz
+ * ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed20n1016.xml.gz.md5
+
+ Currently (02/2020) the HTML contains the date.
+
+ <html>
+ <head><title></title></head>
+ <body>
+ <h4>Filename: pubmed20n1019.xml -- Created: Wed Dec 18 14:31:09 EST 2019</h4>
+ <table cellspacing="0" cellpadding="0" border="0" width="300">
+ <tr>
+
+ """
+ def __init__(self, kafka_hosts, produce_topic, state_topic, start_date=None, end_date=None):
+ self.name = 'Pubmed'
+ self.host = 'ftp.ncbi.nlm.nih.gov'
+ self.produce_topic = produce_topic
+ self.state_topic = state_topic
+ self.kafka_config = {
+ 'bootstrap.servers': kafka_hosts,
+ 'message.max.bytes': 20000000, # ~20 MBytes; broker is ~50 MBytes
+ }
+ self.loop_sleep = 60 * 60 # how long to wait, in seconds, between date checks
+ self.state = HarvestState(start_date, end_date)
+ self.state.initialize_from_kafka(self.state_topic, self.kafka_config)
+ self.producer = self._kafka_producer()
+ self.date_file_map = None
+
+ def _kafka_producer(self):
+ def fail_fast(err, msg):
+ if err is not None:
+ print("Kafka producer delivery error: {}".format(err), file=sys.stderr)
+ print("Bailing out...", file=sys.stderr)
+ # TODO: should it be sys.exit(-1)?
+ raise KafkaException(err)
+
+ self._kafka_fail_fast = fail_fast
+
+ producer_conf = self.kafka_config.copy()
+ producer_conf.update({
+ 'delivery.report.only.error': True,
+ 'default.topic.config': {
+ 'request.required.acks': -1, # all brokers must confirm
+ },
+ })
+ return Producer(producer_conf)
+
+ def fetch_date(self, date):
+ """
+ Fetch file for a given date and feed Kafka one article per message. If
+ the fetched XML does not contain a PMID, this method will fail.
+
+ If no date file mapping is found, this will fail.
+ """
+ if self.date_file_map is None:
+ raise ValueError("cannot fetch date without date file mapping")
+
+ date_str = date.strftime('%Y-%m-%d')
+ paths = self.date_file_map.get(date_str)
+ if paths is None:
+ print("WARN: no pubmed update for this date: {} (UTC), available dates were: {}".format(date_str, self.date_file_map), file=sys.stderr)
+ return False
+
+ count = 0
+ for path in paths:
+ # Fetch and decompress file.
+ url = "ftp://{}{}".format(self.host, path)
+ filename = ftpretr(url)
+ with tempfile.NamedTemporaryFile(prefix='fatcat-ftp-tmp-', delete=False) as decomp:
+ gzf = gzip.open(filename)
+ shutil.copyfileobj(gzf, decomp)
+
+ # Here, blob is the unparsed XML; we peek into it to use PMID as
+ # message key. We need streaming, since some updates would consume
+ # GBs otherwise.
+ # WARNING: Parsing foreign XML exposes us at some
+ # https://docs.python.org/3/library/xml.html#xml-vulnerabilities
+ # here.
+ for blob in xmlstream(decomp.name, 'PubmedArticle', encoding='utf-8'):
+ soup = BeautifulSoup(blob, 'xml')
+ pmid = soup.find('PMID')
+ if pmid is None:
+ raise ValueError("no PMID found, please adjust identifier extraction")
+ count += 1
+ if count % 50 == 0:
+ print("... up to {}".format(count), file=sys.stderr)
+ self.producer.produce(self.produce_topic, blob, key=pmid.text, on_delivery=self._kafka_fail_fast)
+
+ self.producer.flush()
+ os.remove(filename)
+ os.remove(decomp.name)
+
+ return True
+
+ def run(self, continuous=False):
+ while True:
+ self.date_file_map = generate_date_file_map(host=self.host)
+ if len(self.date_file_map) == 0:
+ raise ValueError("map from dates to files should not be empty, maybe the HTML changed?")
+
+ current = self.state.next(continuous)
+ if current:
+ print("Fetching citations updated on {} (UTC)".format(current), file=sys.stderr)
+ self.fetch_date(current)
+ self.state.complete(current, kafka_topic=self.state_topic, kafka_config=self.kafka_config)
+ continue
+
+ if continuous:
+ print("Sleeping {} seconds...".format(self.loop_sleep))
+ time.sleep(self.loop_sleep)
+ else:
+ break
+ print("{} FTP ingest caught up".format(self.name))
+
+
+def generate_date_file_map(host='ftp.ncbi.nlm.nih.gov'):
+ """
+ Generate a DefaultDict[string, set] mapping dates to absolute filepaths on
+ the server (mostly we have one file, but sometimes more).
+
+ Example: {"2020-01-02": set(["/pubmed/updatefiles/pubmed20n1016.xml.gz"]), ...}
+ """
+ mapping = collections.defaultdict(set)
+ pattern = re.compile(r'Filename: ([^ ]*.xml) -- Created: ([^<]*)')
+ ftp = FTP(host)
+ ftp.login()
+ filenames = ftp.nlst('/pubmed/updatefiles')
+
+ for name in filenames:
+ if not name.endswith('.html'):
+ continue
+ sio = io.StringIO()
+ ftp.retrlines('RETR {}'.format(name), sio.write)
+ contents = sio.getvalue()
+ match = pattern.search(contents)
+ if match is None:
+ print('pattern miss in {} on: {}, may need to adjust pattern: {}'.format(name, contents, pattern), file=sys.stderr)
+ continue
+ filename, filedate = match.groups() # ('pubmed20n1017.xml', 'Tue Dec 17 15:23:32 EST 2019')
+ date = dateparser.parse(filedate)
+ fullpath = '/pubmed/updatefiles/{}.gz'.format(filename)
+ date_str = date.strftime('%Y-%m-%d')
+ mapping[date_str].add(fullpath)
+ print('added entry for {}: {}'.format(date_str, fullpath), file=sys.stderr)
+
+ print('generated date-file mapping for {} dates'.format(len(mapping)), file=sys.stderr)
+ return mapping
+
+
+def ftpretr(url):
+ """
+ Note: This might move into a generic place in the future.
+
+ Fetch (RETR) a remote file given by its URL (e.g.
+ "ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed20n1016.xml.gz") to a
+ local temporary file. Returns the name of the local, closed temporary file.
+
+ It is the reponsibility of the caller to cleanup the temporary file.
+ """
+ parsed = urlparse(url)
+ server, path = parsed.netloc, parsed.path
+ ftp = FTP(server)
+ ftp.login()
+ with tempfile.NamedTemporaryFile(prefix='fatcat-ftp-tmp-', delete=False) as f:
+ print('retrieving {} from {} to {} ...'.format(path, server, f.name), file=sys.stderr)
+ ftp.retrbinary('RETR %s' % path, f.write)
+ ftp.close()
+ return f.name
+
+
+def xmlstream(filename, tag, encoding='utf-8'):
+ """
+ Note: This might move into a generic place in the future.
+
+ Given a path to an XML file and a tag name (without namespace), stream
+ through the XML and yield elements denoted by tag as string.
+
+ for snippet in xmlstream("sample.xml", "sometag"):
+ print(len(snippet))
+
+ Known vulnerabilities: https://docs.python.org/3/library/xml.html#xml-vulnerabilities
+ """
+ def strip_ns(tag):
+ if not '}' in tag:
+ return tag
+ return tag.split('}')[1]
+
+ # https://stackoverflow.com/a/13261805, http://effbot.org/elementtree/iterparse.htm
+ context = iter(ET.iterparse(filename, events=(
+ 'start',
+ 'end',
+ )))
+ try:
+ _, root = next(context)
+ except StopIteration:
+ return
+
+ for event, elem in context:
+ if not strip_ns(elem.tag) == tag or event == 'start':
+ continue
+
+ yield ET.tostring(elem, encoding=encoding)
+ root.clear()
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