diff options
| -rw-r--r-- | python/fatcat_tools/harvest/pubmed.py | 45 |
1 files changed, 21 insertions, 24 deletions
diff --git a/python/fatcat_tools/harvest/pubmed.py b/python/fatcat_tools/harvest/pubmed.py index 48f634d0..579dd505 100644 --- a/python/fatcat_tools/harvest/pubmed.py +++ b/python/fatcat_tools/harvest/pubmed.py @@ -115,7 +115,7 @@ class PubmedFTPWorker: for path in paths: # Fetch and decompress file. url = "ftp://{}{}".format(self.host, path) - filename = ftpretr(url, use_lftp=True) + filename = ftpretr(url, proxy_hostport="159.69.240.245:15201") # TODO: proxy obsolete, when networking issue is resolved with tempfile.NamedTemporaryFile(prefix='fatcat-ftp-tmp-', delete=False) as decomp: try: gzf = gzip.open(filename) @@ -227,7 +227,7 @@ def generate_date_file_map(host='ftp.ncbi.nlm.nih.gov'): return mapping -def ftpretr(url, max_retries=10, retry_delay=1, use_lftp=False): +def ftpretr(url, max_retries=10, retry_delay=1, proxy_hostport=None): """ Note: This might move into a generic place in the future. @@ -240,8 +240,8 @@ def ftpretr(url, max_retries=10, retry_delay=1, use_lftp=False): 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) + if proxy_hostport is not None: + return ftpretr_via_http_proxy(url, proxy_hostport, max_retries=max_retries, retry_delay=retry_delay) parsed = urlparse(url) server, path = parsed.netloc, parsed.path for i in range(max_retries): @@ -263,30 +263,27 @@ def ftpretr(url, max_retries=10, retry_delay=1, use_lftp=False): return f.name -def ftpretr_lftp(url, max_retries=10, retry_delay=1): +def ftpretr_via_http_proxy(url, proxy_hostport="159.69.240.245:15201", 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. + Fetch file from FTP via external HTTP proxy, e.g. ftp.host.com:/a/b/c would + be retrievable via proxy.com/a/b/c. """ 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 + for i in range(max_retries): + try: + url = "http://{}{}".format(proxy_hostport, path) + print("retrieving file via proxy (ftpup) from {}".format(url), file=sys.stderr) + with tempfile.NamedTemporaryFile(prefix='fatcat-ftp-tmp-', delete=False) as f: + cmd = ["wget", "-c", url, "-O", f.name] + result = subprocess.run(cmd) + return f.name + except (subprocess.CalledProcessError, OSError, ValueError) as exc: + print("ftp fetch {} failed with {} ({}) ({} retries left)".format( + url, exc, type(exc), max_retries - (i + 1)), file=sys.stderr) + if i + 1 == max_retries: + raise + time.sleep(retry_delay) def xmlstream(filename, tag, encoding='utf-8'): |