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catch sniffing exceptions in handle uploads

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Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
This commit is contained in:
Matthias Bernt
2022-01-19 14:14:54 +01:00
co-authored by Nicola Soranzo Marius van den Beek
parent 8594b13036
commit 37a2edf00a
1 changed files with 7 additions and 3 deletions
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lib/galaxy/datatypes/upload_util.py
+7 -3
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@@ -80,9 +80,13 @@ def handle_upload(
if requested_ext != 'auto':
datatype = registry.get_datatype_by_extension(requested_ext)
# Enable sniffer "validate mode" (prevents certain sniffers from disabling themselves)
if check_content and hasattr(datatype, 'sniff') and not datatype.sniff(path):
stdout = ("Warning: The file 'Type' was set to '{ext}' but the file does not appear to be of that"
" type".format(ext=requested_ext))
if check_content and hasattr(datatype, 'sniff'):
try:
is_of_datatype = datatype.sniff(path)
except Exception:
is_of_datatype = False
if not is_of_datatype:
stdout = f"Warning: The file 'Type' was set to '{requested_ext}' but the file does not appear to be of that type"
# Handle unsniffable binaries
if is_binary and ext == 'binary':