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-rw-r--r--python/fatcat_tools/harvest/pubmed.py10
1 files changed, 8 insertions, 2 deletions
diff --git a/python/fatcat_tools/harvest/pubmed.py b/python/fatcat_tools/harvest/pubmed.py
index f97702c0..98bb7f00 100644
--- a/python/fatcat_tools/harvest/pubmed.py
+++ b/python/fatcat_tools/harvest/pubmed.py
@@ -20,6 +20,7 @@ import sys
import tempfile
import time
import xml.etree.ElementTree as ET
+import zlib
from urllib.parse import urlparse
import dateparser
@@ -114,8 +115,13 @@ class PubmedFTPWorker:
url = "ftp://{}{}".format(self.host, path)
filename = ftpretr(url)
with tempfile.NamedTemporaryFile(prefix='fatcat-ftp-tmp-', delete=False) as decomp:
- gzf = gzip.open(filename)
- shutil.copyfileobj(gzf, decomp)
+ try:
+ gzf = gzip.open(filename)
+ shutil.copyfileobj(gzf, decomp)
+ except zlib.error as exc:
+ print('[skip] retrieving {} failed with {} (maybe empty, missing or broken gzip)'.format(
+ url, exc), file=sys.stderr)
+ continue
# Here, blob is the unparsed XML; we peek into it to use PMID as
# message key. We need streaming, since some updates would consume