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urllib.error.URLError: <urlopen error [Errno 11002] getaddrinfo failed> #5

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Crucialer opened this issue Jul 23, 2019 · 0 comments
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@Crucialer
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Crucialer commented Jul 23, 2019

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>
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