mmCIF fetch: Compressed file ended before the end-of-stream marker was reached

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-01-04)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.92 (2020-01-04)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:user

> open 6n2y

Summary of feedback from opening 6n2y fetched from pdb  
---  
note | Fetching compressed mmCIF 6n2y from
http://files.rcsb.org/download/6n2y.cif  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 600, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 345, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 44, in open  
db_models, status = _fetch_from_database(session, db_id, db_name, db_format,
name, ignore_cache, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 153, in _fetch_from_database  
ignore_cache=ignore_cache, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 434, in fetch_from_database  
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 497, in fetch  
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 383, in fetch_cb  
return fetch_shim(session, identifier, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 381, in fetch_shim  
return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 46, in fetch_from_database  
return fetcher(session, identifier, ignore_cache=ignore_cache, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 315, in fetch_mmcif  
cache, ignore_cache=ignore_cache)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 69, in fetch_file  
check_certificates=check_certificates, name=name, timeout=timeout)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 164, in retrieve_url  
read_and_uncompress(response, f, name, content_length, logger)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 194, in read_and_uncompress  
shutil.copyfileobj(uncompressed, file_out)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/shutil.py",
line 79, in copyfileobj  
buf = fsrc.read(length)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/gzip.py",
line 276, in read  
return self._buffer.read(size)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/_compression.py",
line 68, in readinto  
data = self.read(len(byte_view))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/gzip.py",
line 482, in read  
raise EOFError("Compressed file ended before the "  
EOFError: Compressed file ended before the end-of-stream marker was reached  
  
EOFError: Compressed file ended before the end-of-stream marker was reached  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/gzip.py",
line 482, in read  
raise EOFError("Compressed file ended before the "  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.3.9
OpenGL renderer: Intel(R) HD Graphics 5300
OpenGL vendor: Intel Inc.

[Tom Goddard]

Made EOFError during fetch issue an error with explanation but not generate a traceback.

This was encountered at the Stanford cryoEM workshop where the wifi network was not too reliable.