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A framework for keeping biomedical text mining result up-to-date

License: MIT License

Python 98.47% Shell 1.16% Dockerfile 0.37%

bionlp text-mining infrastructure python snakemake pubmed pubmed-central

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wangmm88 loneknightz sannpeterson ibrahimishag kchennen monstertau

pubrunner's Issues

Unknown command pubrunner

Hi Jake,

As discussed in another thread, I am trying to run your biowordlists project to create the latest Term List. I was able to successfully install pubrunner via pip.

However, when I try to run it I get the following error -

fish: Unknown command pubrunner

FYI, I am using the fish shell, I don't think that should make a difference since I even tried to run it with bash but got the same error.

I am using Python 3.7. I thought it may be an issue of PATH so I tried to debug a bit but everything looks fine.

Ran the following command to see the installed location of pubrunner -

$ pip3 show pubrunner

Name: pubrunner
Version: 0.5.2
Summary: A framework to rerun text mining tools on the latest publications
Home-page: http://github.com/jakelever/pubrunner
Author: Jake Lever
Author-email: [email protected]
License: MIT
Location: /Users/chaitanyagupta/Library/Python/3.7/lib/python/site-packages
Requires: future, wget, six, gitpython, drmaa, bioc, snakemake, markdown2, pyfiglet, biopython, jsonlines, pymarc, ftputil, pyyaml, requests
Required-by:

I also checked my sys.path to see if it had the above location /Users/chaitanyagupta/Library/Python/3.7/lib/python/site-packages, and it is present -

$python3

Python 3.7.3 (default, Mar 27 2019, 09:23:15)
[Clang 10.0.1 (clang-1001.0.46.3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> print(sys.path)
['', '/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python37.zip', '/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7', '/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload', '/Users/chaitanyagupta/Library/Python/3.7/lib/python/site-packages', '/usr/local/lib/python3.7/site-packages']

Can you help me with this? I am not sure what I can do to get it running.

Edit: Included link to the other thread

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

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>

Error handling

The error handling needs to be improved to give more useful feedback. Below are a couple ideas

Track which slurm file to look at when there is a failure on the cluster
Deal appropriately if "IN" or "OUT" is missing in a build step

About the keyword for searching from PubMed

Thanks for your contribution!
I have one question for the PubRunner.I notice that your tool is good for downloading articles. However, when I wanna only download articles within a specific concept such as cancer, I don't know where to start. Can I ask if you have any suggeston regarding this issue?
Thank you very much. I am really appreciated your reply.

Tab requirement in YAML files

An idea to reduce YAML ambiguity: Require tabs not spaces in all the YAML files

How to run pubrunner without computer cluster?

snake make call failed. no intention to mine whole pubmed, only a subset is enough. can we run pubrunner without computer cluster?

jakelever / pubrunner Goto Github PK

pubrunner's People

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pubrunner's Issues

bioc version

Unknown command pubrunner

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

Error handling

About the keyword for searching from PubMed

Tab requirement in YAML files

How to run pubrunner without computer cluster?

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