id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3540 Fetch question Greg Couch Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.1.dev202007210154 (2020-07-21 01:54:46 UTC) Description Was testing negative caching of URLs that time out, but my new code in chimerax.core.fetch.fetch_file was not called. What's the status of chimerax.core.fetch? There is a lot of duplication between it and core_formats.web_fetch. And core.fetch.fetch_file is used in many places. Log: UCSF ChimeraX version: 1.1.dev202007210154 (2020-07-21) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open http://ahs.jacobsonlab.org/file.pdb Failed command: open http://ahs.jacobsonlab.org/file.pdb Traceback (most recent call last): File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\urllib\request.py"", line 1319, in do_open encode_chunked=req.has_header('Transfer-encoding')) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\http\client.py"", line 1252, in request self._send_request(method, url, body, headers, encode_chunked) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\http\client.py"", line 1298, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\http\client.py"", line 1247, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\http\client.py"", line 1026, in _send_output self.send(msg) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\http\client.py"", line 966, in send self.connect() File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\http\client.py"", line 938, in connect (self.host,self.port), self.timeout, self.source_address) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\socket.py"", line 728, in create_connection raise err File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\socket.py"", line 716, in create_connection sock.connect(sa) TimeoutError: [WinError 10060] A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 263, in execute cmd.run(cmd_text) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 95, in cmd_open return Command(session, registry=registry).run(provider_cmd_text, log=log) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 123, in provider_open (session, ident, format_name, ignore_cache), provider_kw) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 384, in collated_open return func(*func_args, **func_kw) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 63, in fetch ignore_cache=ignore_cache, **kw) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site- packages\chimerax\core_formats\web_fetch.py"", line 48, in fetch_web uncompress=uncompress) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site- packages\chimerax\core_formats\web_fetch.py"", line 127, in retrieve_url with urlopen(request, timeout=timeout, context=ssl_context) as response: File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\urllib\request.py"", line 222, in urlopen return opener.open(url, data, timeout) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\urllib\request.py"", line 525, in open response = self._open(req, data) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\urllib\request.py"", line 543, in _open '_open', req) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\urllib\request.py"", line 503, in _call_chain result = func(*args) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\urllib\request.py"", line 1347, in http_open return self.do_open(http.client.HTTPConnection, req) File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\urllib\request.py"", line 1321, in do_open raise URLError(err) urllib.error.URLError: urllib.error.URLError: File ""A:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\urllib\request.py"", line 1321, in do_open raise URLError(err) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 451.48 OpenGL renderer: GeForce GTX 970/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: MSI Model: MS-7885 OS: Microsoft Windows 10 Home (Build 18363) Memory: 34,258,157,568 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz"" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 }}} " defect closed normal Input/Output not a bug all ChimeraX