diff options
Diffstat (limited to 'python')
| -rw-r--r-- | python/fatcat_tools/harvest/pubmed.py | 33 |
1 files changed, 31 insertions, 2 deletions
diff --git a/python/fatcat_tools/harvest/pubmed.py b/python/fatcat_tools/harvest/pubmed.py index d336de04..48f634d0 100644 --- a/python/fatcat_tools/harvest/pubmed.py +++ b/python/fatcat_tools/harvest/pubmed.py @@ -16,6 +16,7 @@ import os import re import shutil import socket +import subprocess import sys import tempfile import time @@ -114,7 +115,7 @@ class PubmedFTPWorker: for path in paths: # Fetch and decompress file. url = "ftp://{}{}".format(self.host, path) - filename = ftpretr(url) + filename = ftpretr(url, use_lftp=True) with tempfile.NamedTemporaryFile(prefix='fatcat-ftp-tmp-', delete=False) as decomp: try: gzf = gzip.open(filename) @@ -226,7 +227,7 @@ def generate_date_file_map(host='ftp.ncbi.nlm.nih.gov'): return mapping -def ftpretr(url, max_retries=10, retry_delay=1): +def ftpretr(url, max_retries=10, retry_delay=1, use_lftp=False): """ Note: This might move into a generic place in the future. @@ -239,6 +240,8 @@ def ftpretr(url, max_retries=10, retry_delay=1): Implements a basic retry mechanism, e.g. that became an issue in 08/2021, when we encountered EOFError while talking to the FTP server. Retry delay in seconds. """ + if use_lftp is True: + return ftpretr_lftp(url, max_retries=max_retries, retry_delay=retry_delay) parsed = urlparse(url) server, path = parsed.netloc, parsed.path for i in range(max_retries): @@ -260,6 +263,32 @@ def ftpretr(url, max_retries=10, retry_delay=1): return f.name +def ftpretr_lftp(url, max_retries=10, retry_delay=1): + """ + Same as ftpretr, but mirrors the relevant files beforehand, then picks out + the requested file. Requires a few GB spare space for the mirror. + + Mirrors everything from `path` on `host` to `sync_dir`, which will be under + the system tempdir (cf. `systemctl status systemd-tmpfiles-clean.timer`) by default. + + Workaround, since networking issues (probably internet2) limit our + bandwith; and we cannot hold a conn longer than about 90 seconds with the + python ftp lib or curl. Mitigation through a hopefully more resilient + client like lftp. + + If this does not work, check available mirrors outside nih.gov. + """ + parsed = urlparse(url) + server, path = parsed.netloc, parsed.path + with tempfile.NamedTemporaryFile(prefix='fatcat-ftp-tmp-', delete=False) as f: + print('retrieving [lftp] {} from {} to {} ...'.format(path, server, f.name), file=sys.stderr) + lftp_command = """ set net:max-retries {}; set net:reconnect-interval-base {}; pget -c {} -o {}; exit """.format(max_retries, retry_delay, path, f.name) + cmd = ["lftp", "-u", "anonymous,anonymous", "-e", lftp_command, "ftp.ncbi.nlm.nih.gov"] + result = subprocess.run(cmd) + result.check_returncode() + return f.name + + def xmlstream(filename, tag, encoding='utf-8'): """ Note: This might move into a generic place in the future. |