Merge branch 'martin-kafka-bs4-import' into 'master'

pubmed and arxiv harvest preparations See merge request webgroup/fatcat!28
author: Martin Czygan <martin@archive.org> 2020-03-10 15:33:17 +0000
committer: Martin Czygan <martin@archive.org> 2020-03-10 15:33:17 +0000
commit: 336630e1d445fb9d233447f9af4bac94473a12bf (patch)
tree: b2d4baa4ea6d3afac29b9b2760101c10d18ea30a /python/fatcat_tools/harvest
parent: f4cce5a765a9f80f9c5e9c907689c06dc9ebf102 (diff)
parent: d18942d1ab4d394bdb275bcf9eb82d1cba814775 (diff)
download: fatcat-336630e1d445fb9d233447f9af4bac94473a12bf.tar.gz
fatcat-336630e1d445fb9d233447f9af4bac94473a12bf.zip
3 files changed, 252 insertions, 21 deletions
diff --git a/python/fatcat_tools/harvest/__init__.py b/python/fatcat_tools/harvest/__init__.py
index 7d814696..b3757a7d 100644
--- a/python/fatcat_tools/harvest/__init__.py
+++ b/python/fatcat_tools/harvest/__init__.py
@@ -1,5 +1,6 @@
 
 from .harvest_common import HarvestState
 from .doi_registrars import HarvestCrossrefWorker, HarvestDataciteWorker
-from .oaipmh import HarvestArxivWorker, HarvestPubmedWorker,\
-    HarvestDoajArticleWorker, HarvestDoajJournalWorker
+from .oaipmh import HarvestArxivWorker, HarvestDoajArticleWorker, \
+    HarvestDoajJournalWorker
+from .pubmed import PubmedFTPWorker
diff --git a/python/fatcat_tools/harvest/oaipmh.py b/python/fatcat_tools/harvest/oaipmh.py
index 11b5fa0a..c95f3445 100644
--- a/python/fatcat_tools/harvest/oaipmh.py
+++ b/python/fatcat_tools/harvest/oaipmh.py
@@ -132,25 +132,6 @@ class HarvestArxivWorker(HarvestOaiPmhWorker):
         self.name = "arxiv"
 
 
-class HarvestPubmedWorker(HarvestOaiPmhWorker):
-    """
-    Will likely be doing MEDLINE daily batch imports for primary metadata, but
-    might also want to run a PMC importer to update fulltext and assign OA
-    licenses (when appropriate).
-
-    Pubmed refs:
-    - https://www.ncbi.nlm.nih.gov/pmc/tools/oai/
-    - https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:152494&metadataPrefix=pmc_fm
-    - https://github.com/titipata/pubmed_parser
-    """
-
-    def __init__(self, **kwargs):
-        super().__init__(**kwargs)
-        self.endpoint_url = "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi"
-        self.metadata_prefix = "pmc_fm"
-        self.name = "pubmed"
-
-
 class HarvestDoajJournalWorker(HarvestOaiPmhWorker):
     """
     WARNING: DOAJ OAI-PMH doesn't seem to respect 'from' and 'until' params
diff --git a/python/fatcat_tools/harvest/pubmed.py b/python/fatcat_tools/harvest/pubmed.py
new file mode 100644
index 00000000..3f31696e
--- /dev/null
+++ b/python/fatcat_tools/harvest/pubmed.py
@@ -0,0 +1,249 @@
+"""
+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()
author	Martin Czygan <martin@archive.org>	2020-03-10 15:33:17 +0000
committer	Martin Czygan <martin@archive.org>	2020-03-10 15:33:17 +0000
commit	336630e1d445fb9d233447f9af4bac94473a12bf (patch)
tree	b2d4baa4ea6d3afac29b9b2760101c10d18ea30a /python/fatcat_tools/harvest
parent	f4cce5a765a9f80f9c5e9c907689c06dc9ebf102 (diff)
parent	d18942d1ab4d394bdb275bcf9eb82d1cba814775 (diff)
download	fatcat-336630e1d445fb9d233447f9af4bac94473a12bf.tar.gz fatcat-336630e1d445fb9d233447f9af4bac94473a12bf.zip