Joss-reviews: [PRE REVIEW]: Entrez - Call the NCBI E-utilities from Python

[whedon]

Submitting author: @jordibc (Jordi Burguet-Castell)
Repository: https://github.com/jordibc/entrez
Version: v1.0.0
Editor: Pending
Reviewer: Pending

Author instructions

Thanks for submitting your paper to JOSS @jordibc. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@jordibc if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

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Hello human, I'm @whedon. I'm here to help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #533 with the following error: 

 /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/author.rb:36:in `block in build_affiliation_string': Problem with affiliations for Jordi Burguet-Castell, perhaps the affiliations index need quoting? (RuntimeError)
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/author.rb:35:in `each'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/author.rb:35:in `build_affiliation_string'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/author.rb:11:in `initialize'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon.rb:97:in `new'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon.rb:97:in `block in parse_authors'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon.rb:95:in `each'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon.rb:95:in `parse_authors'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon.rb:76:in `initialize'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/processor.rb:26:in `new'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/lib/whedon/processor.rb:26:in `set_paper'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/bin/whedon:37:in `prepare'
    from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-8307502c3aee/bin/whedon:99:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `load'
    from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `<main>'

[jordibc]

@whedon commands

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# Compile the paper
@whedon generate pdf

[jordibc]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #533 with the following error: 

   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    15    0    15    0     0     69      0 --:--:-- --:--:-- --:--:--    69
Error reading bibliography ./paper.bib (line 1, column 9):
unexpected ","
expecting white space
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[jordibc]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #533 with the following error: 

   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100    15    0    15    0     0     83      0 --:--:-- --:--:-- --:--:--    83
Error reading bibliography ./paper.bib (line 2, column 10):
unexpected "="
expecting space or ","
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[jordibc]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

https://github.com/openjournals/joss-papers/blob/joss.00533/joss.00533/10.21105.joss.00533.pdf

[jordibc]

Good, I'm fine with the current status. Please let me know if there is anything I need to do from my side.

[arfon]

Hi @jordibc - many thanks for your submission to JOSS. Unfortunately this submission isn't acceptable to JOSS. As documented in our submission criteria we don't allow minor packages such as thin API clients which this looks to be.

[jordibc]

Hi @arfon , you are absolutely right, it escaped me. Thanks for pointing it out (and for your work on JOSS and the feedback!).