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something wrong when installing into UBUNTU 14 LTS #24

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ppKrauss opened this issue Jan 13, 2016 · 0 comments
Open

something wrong when installing into UBUNTU 14 LTS #24

ppKrauss opened this issue Jan 13, 2016 · 0 comments

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@ppKrauss
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I am using UBUNTU 14 LTS... After sucess on using install instructions I used example1.sh that suggest oacensus run --config example-oxford-2012.yaml --reports excel with examples/example-oxford-2012.yaml. It generated an error,

oacensus run --config example-oxford-2012.yaml --reports excel

matplitlib, numpy, scipy are required for PersonalOpenness
matplitlib, numpy, scipy are required for PersonalOpenness
running pubmed scraper
.oacensus/cache/ec1df7dc810c04e3d1afdbb82e3d13a6
  calling scrape method...
  there are 311 total articles matching the search
  calling process method...
   <ArticleList: u'<Article List (311 articles): pubmed search: "Oxford University"[affiliation] AND 2012[pdat]>'>
running oag scraper
.oacensus/cache/a584348f64b47e9de802565b39119e47
  calling scrape method...
  calling process method...
  no license info returned for <Article: u'Excluded calyx following percutaneous ne...'>
  no license info returned for <Article: u'Trigeminal neuralgia-divided but not cla...'>
  no license info returned for <Article: u"British surgeons' experiences of a manda...">
  no license info returned for <Article: u'The impact of HIV-1 infection and exposu...'>
  no license info returned for <Article: u'Optimising immunogenicity with viral vec...'>
  no license info returned for <Article: u'DOK7 congenital myasthenic syndrome.'>
  no license info returned for <Article: u'Inferring diffusion in single live cells...'>
  no license info returned for <Article: u'Risk of stroke and oral anticoagulant us...'>
  no license info returned for <Article: u'Experimental evolution of adaptive pheno...'>
  no license info returned for <Article: u'Thrombocytopenia, bleeding, and use of p...'>
  no license info returned for <Article: u'Modulation of cortical excitability can ...'>
  no license info returned for <Article: u'Continuous ambulatory peritoneal dialysi...'>
  ...
  no license info returned for <Article: u'The danger of systematic bias in group-l...'>
  no license info returned for <Article: u'Nanoparticle augmented radiation treatme...'>
  no license info returned for <Article: u'Gene expression analysis of the embryoni...'>
  no license info returned for <Article: u'Mental health of displaced and refugee c...'>
  no license info returned for <Article: u'Should we allow organ donation euthanasi...'>
running doaj scraper
.oacensus/cache/0c1118ba41ec015feed7e4c9a615de1b
  calling scrape method...
  calling process method...
Traceback (most recent call last):
  File "/usr/local/bin/oacensus", line 9, in <module>
    load_entry_point('oacensus==0.0.2d', 'console_scripts', 'oacensus')()
  File "/home/peter/sandbox/oacensus/oacensus/commands.py", line 27, in run
    args.parse_and_run_command(sys.argv[1:], mod, default_command=default_cmd)
  File "/usr/local/lib/python2.7/dist-packages/modargs/args.py", line 381, in parse_and_run_command
    command_module(mod, command, options, cli_options=cli_options)
  File "/usr/local/lib/python2.7/dist-packages/modargs/args.py", line 286, in command_module
    function(**options)
  File "/home/peter/sandbox/oacensus/oacensus/commands.py", line 191, in run_command
    scraper.run()
  File "/home/peter/sandbox/oacensus/oacensus/scraper.py", line 78, in run
    return self.process()
  File "/home/peter/sandbox/oacensus/oacensus/scrapers/doaj.py", line 40, in process
    issn = row['ISSN'] or row['EISSN']
KeyError: 'ISSN'

I have python3 installed, but the run is looking for /usr/local/lib/python2.7...

Similar problems on example2.sh

oacensus run --config example-orcid.yaml --reports "personal-openness" produced,

matplitlib, numpy, scipy are required for PersonalOpenness
matplitlib, numpy, scipy are required for PersonalOpenness
removing old db file oacensus.sqlite3
running orcid scraper
.oacensus/cache/6eae9a31c606a0d8477db2ea78f40475
  calling scrape method...
  calling process method...
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/modargs/args.py", line 286, in command_module
    function(**options)
  File "/home/peter/sandbox/oacensus/oacensus/commands.py", line 191, in run_command
    scraper.run()
  File "/home/peter/sandbox/oacensus/oacensus/scraper.py", line 78, in run
    return self.process()
  File "/home/peter/sandbox/oacensus/oacensus/scrapers/orcids.py", line 44, in process
    for pub in response.publications:
  File "/usr/local/lib/python2.7/dist-packages/orcid/rest.py", line 107, in publications
    self._load_works()
  File "/usr/local/lib/python2.7/dist-packages/orcid/rest.py", line 101, in _load_works
    + '/orcid-works', headers = BASE_HEADERS)
TypeError: cannot concatenate 'str' and 'NoneType' objects
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