diff options
Diffstat (limited to 'python/fatcat_tools/harvest')
| -rw-r--r-- | python/fatcat_tools/harvest/oaipmh.py | 15 | ||||
| -rw-r--r-- | python/fatcat_tools/harvest/pubmed.py | 199 |
2 files changed, 214 insertions, 0 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() |