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Hi,I am new to python and your pubrunner tool. When I run some examples, I have met these problems.
D:\cancermine\pubrunner\examples\SmallTextFinder>pubrunner --test .
_____ _ _ ______ ______ _ _ __ _ __ _ _______ ______
|_____] | | |_____] |_____/ | | | \ | | \ | |______ |_____/
| |_____| |_____] | \_ |_____| | \_| | \_| |______ | \_
d:\python37\lib\site-packages\pubrunner\globalsettings.py:13: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
yamlData = yaml.load(f)
Working directory: C:\Users\詹飞/pubrunner/workspace\SmallTextFinder\test
Traceback (most recent call last):
File "d:\python37\lib\urllib\request.py", line 1317, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "d:\python37\lib\http\client.py", line 1229, in request
self._send_request(method, url, body, headers, encode_chunked)
File "d:\python37\lib\http\client.py", line 1275, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "d:\python37\lib\http\client.py", line 1224, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "d:\python37\lib\http\client.py", line 1016, in _send_output
self.send(msg)
File "d:\python37\lib\http\client.py", line 956, in send
self.connect()
File "d:\python37\lib\http\client.py", line 1384, in connect
super().connect()
File "d:\python37\lib\http\client.py", line 928, in connect
(self.host,self.port), self.timeout, self.source_address)
File "d:\python37\lib\socket.py", line 707, in create_connection
for res in getaddrinfo(host, port, 0, SOCK_STREAM):
File "d:\python37\lib\socket.py", line 748, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno 11002] getaddrinfo failed
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "d:\python37\lib\runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "d:\python37\lib\runpy.py", line 85, in _run_code
exec(code, run_globals)
File "D:\Python37\Scripts\pubrunner.exe\__main__.py", line 9, in <module>
File "d:\python37\lib\site-packages\pubrunner\command_line.py", line 66, in main
pubrunner.pubrun(args.codebase,args.test,(not args.nogetresource),forceresource_dir=args.forceresource_dir,forceresource_format=args.forceresource_format,outputdir=args.outputdir)
File "d:\python37\lib\site-packages\pubrunner\pubrun.py", line 349, in pubrun
prepareConversionAndHashingRuns(toolSettings,mode,workingDirectory)
File "d:\python37\lib\site-packages\pubrunner\pubrun.py", line 103, in prepareConversionAndHashingRuns
eutilsToFile('pmc',pmcid,filename)
File "d:\python37\lib\site-packages\pubrunner\pubrun.py", line 37, in eutilsToFile
handle = Entrez.efetch(db=db, id=id, rettype="gb", retmode="xml")
File "d:\python37\lib\site-packages\Bio\Entrez\__init__.py", line 195, in efetch
return _open(cgi, variables, post=post)
File "d:\python37\lib\site-packages\Bio\Entrez\__init__.py", line 555, in _open
handle = _urlopen(cgi)
File "d:\python37\lib\urllib\request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "d:\python37\lib\urllib\request.py", line 525, in open
response = self._open(req, data)
File "d:\python37\lib\urllib\request.py", line 543, in _open
'_open', req)
File "d:\python37\lib\urllib\request.py", line 503, in _call_chain
result = func(*args)
File "d:\python37\lib\urllib\request.py", line 1360, in https_open
context=self._context, check_hostname=self._check_hostname)
File "d:\python37\lib\urllib\request.py", line 1319, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 11002] getaddrinfo failed>
The text was updated successfully, but these errors were encountered:
Hi,I am new to python and your pubrunner tool. When I run some examples, I have met these problems.
The text was updated successfully, but these errors were encountered: