Opened 6 years ago

Closed 6 years ago

#1986 closed defect (fixed)

Problem reading CCD template: Connection reset by peer

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.5.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-13)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-04-13)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1K8W

Summary of feedback from opening 1K8W fetched from pdb  
---  
note | Fetching compressed mmCIF 1k8w from
http://files.rcsb.org/download/1k8w.cif  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 253, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2628, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 41, in open  
from_database=from_database, ignore_cache=ignore_cache, **kw))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 88, in open  
filename, format=format, name=name, ignore_cache=ignore_cache, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
return f(*args, **kw)  
File
"/Applications/ChimeraX.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.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.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 45, in fetch_from_database  
return fetcher(session, identifier, ignore_cache=ignore_cache, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 316, in fetch_mmcif  
models, status = io.open_data(session, filename, format='mmcif', name=pdb_id,
**kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 433, in open_data  
models, status = open_func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 55, in open_file  
log_info=log_info, combine_sym_atoms=combine_sym_atoms)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 73, in open_mmcif  
pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets, atomic)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 69, in <lambda>  
lambda name, session=session: _get_template(session, name))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 339, in _get_template  
return fetch_file(session, url, 'CCD %s' % name, filename, 'CCD', timeout=15)  
File
"/Applications/ChimeraX.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 142, in retrieve_url  
with urlopen(request, timeout=timeout, context=ssl_context) as response:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 222, in urlopen  
return opener.open(url, data, timeout)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 525, in open  
response = self._open(req, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 543, in _open  
'_open', req)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1345, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1320, in do_open  
r = h.getresponse()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1321, in getresponse  
response.begin()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 296, in begin  
version, status, reason = self._read_status()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 257, in _read_status  
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 589, in readinto  
return self._sock.recv_into(b)  
ConnectionResetError: [Errno 54] Connection reset by peer  
  
ConnectionResetError: [Errno 54] Connection reset by peer  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 589, in readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  

> open 1k8w

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 253, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2628, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 41, in open  
from_database=from_database, ignore_cache=ignore_cache, **kw))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 88, in open  
filename, format=format, name=name, ignore_cache=ignore_cache, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
return f(*args, **kw)  
File
"/Applications/ChimeraX.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.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 45, in fetch_from_database  
return fetcher(session, identifier, ignore_cache=ignore_cache, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 316, in fetch_mmcif  
models, status = io.open_data(session, filename, format='mmcif', name=pdb_id,
**kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 433, in open_data  
models, status = open_func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 55, in open_file  
log_info=log_info, combine_sym_atoms=combine_sym_atoms)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 73, in open_mmcif  
pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets, atomic)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 69, in <lambda>  
lambda name, session=session: _get_template(session, name))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 339, in _get_template  
return fetch_file(session, url, 'CCD %s' % name, filename, 'CCD', timeout=15)  
File
"/Applications/ChimeraX.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 142, in retrieve_url  
with urlopen(request, timeout=timeout, context=ssl_context) as response:  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 222, in urlopen  
return opener.open(url, data, timeout)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 525, in open  
response = self._open(req, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 543, in _open  
'_open', req)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1345, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1320, in do_open  
r = h.getresponse()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1321, in getresponse  
response.begin()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 296, in begin  
version, status, reason = self._read_status()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 257, in _read_status  
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 589, in readinto  
return self._sock.recv_into(b)  
socket.timeout: timed out  
  
socket.timeout: timed out  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 589, in readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.8.38
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by pett, 6 years ago

Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem reading CCD template: Connection reset by peer

comment:2 by Greg Couch, 6 years ago

Resolution: → fixed
Status: assigned → closed

Just report the failure now without a traceback.

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