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authorMartin Czygan <martin.czygan@gmail.com>2021-08-30 23:23:28 +0200
committerMartin Czygan <martin.czygan@gmail.com>2021-09-08 22:02:48 +0200
commit6d9d67c9c4d1a0b208fc2056ab485a1c8d21e100 (patch)
tree323e38da3515dea702a3d244b2724348aaab61bf /python/fatcat_tools/harvest
parentfddbc81f231fb59efb9c41dc460b6486c673e94c (diff)
downloadfatcat-6d9d67c9c4d1a0b208fc2056ab485a1c8d21e100.tar.gz
fatcat-6d9d67c9c4d1a0b208fc2056ab485a1c8d21e100.zip
pubmed: add option to ftp download with lftp
lftp is a classic command line ftp client, and we hope that its retry capabilities are enough of a workaround for the current networking issue
Diffstat (limited to 'python/fatcat_tools/harvest')
-rw-r--r--python/fatcat_tools/harvest/pubmed.py33
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.