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authorMartin Czygan <martin.czygan@gmail.com>2020-02-14 14:32:57 +0100
committerMartin Czygan <martin.czygan@gmail.com>2020-02-19 01:07:46 +0100
commit519b90d7f539b667e919c220a53626e7a4ac48bf (patch)
treeb7c3beed283d7dca732a8f2ab5b1dfe283bb69f3 /python/fatcat_tools
parent4cbc94cd708c1db80a232150ab2cf56dddf83e62 (diff)
downloadfatcat-519b90d7f539b667e919c220a53626e7a4ac48bf.tar.gz
fatcat-519b90d7f539b667e919c220a53626e7a4ac48bf.zip
pubmed ftp harvest and KafkaBs4XmlPusher
* add PubmedFTPWorker * utils are currently stored alongside pubmed (e.g. ftpretr, xmlstream) but may live elsewhere, as they are more generic * add KafkaBs4XmlPusher
Diffstat (limited to 'python/fatcat_tools')
-rw-r--r--python/fatcat_tools/harvest/oaipmh.py15
-rw-r--r--python/fatcat_tools/harvest/pubmed.py199
-rw-r--r--python/fatcat_tools/importers/__init__.py2
-rw-r--r--python/fatcat_tools/importers/common.py65
4 files changed, 280 insertions, 1 deletions
diff --git a/python/fatcat_tools/harvest/oaipmh.py b/python/fatcat_tools/harvest/oaipmh.py
index 11b5fa0a..8e9efea8 100644
--- a/python/fatcat_tools/harvest/oaipmh.py
+++ b/python/fatcat_tools/harvest/oaipmh.py
@@ -142,6 +142,21 @@ class HarvestPubmedWorker(HarvestOaiPmhWorker):
- 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
+
+ TODO(martin): OAI does not seem to support the format we already have an
+ importer for. Maybe we can use "Daily Update Files" --
+
+ Daily Update Files
+ ------------------
+ 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.
+ ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles
+
+ NOTES:
+
+ * OAI: https://dtd.nlm.nih.gov/archiving/2.3/xsd/archivearticle.xsd
+ * FTP: https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd
"""
def __init__(self, **kwargs):
diff --git a/python/fatcat_tools/harvest/pubmed.py b/python/fatcat_tools/harvest/pubmed.py
new file mode 100644
index 00000000..da872a10
--- /dev/null
+++ b/python/fatcat_tools/harvest/pubmed.py
@@ -0,0 +1,199 @@
+"""
+Pubmed harvest via FTP.
+"""
+
+import collections
+import io
+import re
+import sys
+import tempfile
+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 host 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
+
+ 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>
+
+ When this workers starts, it will figure out a mapping from date to XML
+ files by looking at all the HTML files.
+ """
+ def __init__(self, kafka_hosts, produce_topic, state_topic, start_date=None, end_data=None):
+ 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.date_file_map = self.generate_date_file_map()
+ if len(self.date_file_map) == 0:
+ raise ValueError('mapping from dates to files should not be empty')
+
+ def generate_date_file_map(self):
+ """
+ Generate a dictionary mapping date (strings) to filepaths. The date is
+ parsed from pubmed20n1016_stats.html, mapping to absolute path on FTP,
+ e.g. "2020-01-02": "/pubmed/updatefiles/pubmed20n1016.xml.gz".
+ """
+ mapping = collections.defaultdict(set)
+ pattern = re.compile(r'Filename: ([^ ]*.xml) -- Created: ([^<]*)')
+ ftp = FTP(self.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 on: {}, may need to adjust pattern: {}'.format(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)
+ mapping[date.format('%Y-%m-%d')].add(fullpath)
+
+ self.date_file_map = mapping
+ print('generated date-file mapping for {} dates'.format(len(mapping)), file=sys.stderr)
+
+
+ def fetch_date(self, date):
+ """
+ Fetch file for a given date and feed Kafka one article per message.
+ """
+ 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)
+ raise KafkaException(err)
+
+ 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
+ },
+ })
+ producer = Producer(producer_conf)
+
+ date_str = date.format('%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
+
+ count = 0
+ for path in paths:
+ filename = ftpretr(urljoin(self.host, path))
+ for blob in xmlstream(filename, 'PubmedArticle', encoding='utf-8'):
+ soup = BeautifulSoup(blob)
+ pmid = soup.find('PMID')
+ if pmid is None:
+ raise ValueError('no PMID found, adjust identifier extraction')
+ count += 1
+ if count % 50 == 0:
+ print("... up to {} from {}".format(count, filename))
+ producer.produce(
+ self.produce_topic,
+ blob,
+ key=pmid.text,
+ on_delivery=fail_fast)
+ producer.flush()
+
+ def run(self, continuous=False):
+ while True:
+ current = self.state.next(continuous)
+ if current:
+ print("Fetching DOIs updated on {} (UTC)".format(current))
+ 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("{} DOI ingest caught up".format(self.name))
+
+
+class ftpretr(uri):
+ """
+ Fetch (RETR) a remote file to a local temporary file.
+ """
+ parsed = urlparse(uri)
+ server, path = parsed.netloc, parsed.path
+ ftp = FTP(self.server)
+ ftp.login()
+ with tempfile.NamedTemporaryFile(prefix='fatcat-ftp-tmp-', delete=False) as f:
+ ftp.retrbinary('RETR %s' % path, f.write)
+ ftp.close()
+ return f.name
+
+
+def xmlstream(filename, tag, encoding='utf-8'):
+ """
+ Given a path to an XML file and a tag name (without namespace), stream
+ through the XML, and emit the element denoted by tag for processing as string.
+
+ for snippet in xmlstream("sample.xml", "sometag"):
+ print(len(snippet))
+ """
+ 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',
+ )))
+ _, root = next(context)
+
+ for event, elem in context:
+ if not strip_ns(elem.tag) == tag or event == 'start':
+ continue
+
+ yield ET.tostring(elem, encoding=encoding)
+ root.clear()
diff --git a/python/fatcat_tools/importers/__init__.py b/python/fatcat_tools/importers/__init__.py
index d936605f..03c7cbcc 100644
--- a/python/fatcat_tools/importers/__init__.py
+++ b/python/fatcat_tools/importers/__init__.py
@@ -12,7 +12,7 @@ To run an import you combine two classes; one each of:
"""
-from .common import EntityImporter, JsonLinePusher, LinePusher, CsvPusher, SqlitePusher, Bs4XmlFilePusher, Bs4XmlLargeFilePusher, Bs4XmlLinesPusher, Bs4XmlFileListPusher, KafkaJsonPusher, make_kafka_consumer, clean, is_cjk, LANG_MAP_MARC
+from .common import EntityImporter, JsonLinePusher, LinePusher, CsvPusher, SqlitePusher, Bs4XmlFilePusher, Bs4XmlLargeFilePusher, Bs4XmlLinesPusher, Bs4XmlFileListPusher, KafkaJsonPusher, KafkaBs4XmlPusher, make_kafka_consumer, clean, is_cjk, LANG_MAP_MARC
from .crossref import CrossrefImporter, CROSSREF_TYPE_MAP, lookup_license_slug
from .datacite import DataciteImporter
from .jalc import JalcImporter
diff --git a/python/fatcat_tools/importers/common.py b/python/fatcat_tools/importers/common.py
index 1ffbd6e7..1cb5529e 100644
--- a/python/fatcat_tools/importers/common.py
+++ b/python/fatcat_tools/importers/common.py
@@ -721,6 +721,71 @@ class Bs4XmlFileListPusher(RecordPusher):
print(counts)
return counts
+class KafkaBs4XmlPusher(RecordPusher):
+ """
+ Fetch XML for an article from Kafka, parse via Bs4.
+ """
+ def __init__(self, importer, kafka_hosts, kafka_env, topic_suffix, group, **kwargs):
+ self.importer = importer
+ self.consumer = make_kafka_consumer(
+ kafka_hosts,
+ kafka_env,
+ topic_suffix,
+ group,
+ kafka_namespace=kwargs.get('kafka_namespace', 'fatcat')
+ )
+ self.poll_interval = kwargs.get('poll_interval', 5.0)
+ self.consume_batch_size = kwargs.get('consume_batch_size', 100)
+
+ def run(self):
+ count = 0
+ last_push = datetime.datetime.now()
+ while True:
+ # Note: this is batch-oriented, because underlying importer is
+ # often batch-oriented, but this doesn't confirm that entire batch
+ # has been pushed to fatcat before commiting offset. Eg, consider
+ # case where there there is one update and thousands of creates;
+ # update would be lingering in importer, and if importer crashed
+ # never created.
+ # This is partially mitigated for the worker case by flushing any
+ # outstanding editgroups every 5 minutes, but there is still that
+ # window when editgroups might be hanging (unsubmitted).
+ batch = self.consumer.consume(
+ num_messages=self.consume_batch_size,
+ timeout=self.poll_interval)
+ print("... got {} kafka messages ({}sec poll interval)".format(
+ len(batch), self.poll_interval))
+ if not batch:
+ if datetime.datetime.now() - last_push > datetime.timedelta(minutes=5):
+ # it has been some time, so flush any current editgroup
+ self.importer.finish()
+ last_push = datetime.datetime.now()
+ #print("Flushed any partial import batch: {}".format(self.importer.counts))
+ continue
+ # first check errors on entire batch...
+ for msg in batch:
+ if msg.error():
+ raise KafkaException(msg.error())
+ # ... then process
+ for msg in batch:
+ soup = BeautifulSoup(msg.value().decode('utf-8'), "xml")
+ self.importer.push_record(soup)
+ soup.decompose()
+ count += 1
+ if count % 500 == 0:
+ print("Import counts: {}".format(self.importer.counts))
+ last_push = datetime.datetime.now()
+ for msg in batch:
+ # locally store offsets of processed messages; will be
+ # auto-commited by librdkafka from this "stored" value
+ self.consumer.store_offsets(message=msg)
+
+ # TODO: should catch UNIX signals (HUP?) to shutdown cleanly, and/or
+ # commit the current batch if it has been lingering
+ counts = self.importer.finish()
+ print(counts)
+ self.consumer.close()
+ return counts
class KafkaJsonPusher(RecordPusher):
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-22 12:52:00 +0000