Recology

R/etc.

cites - citation stuff from the command line

    API crossref
 Source: .Rmd/.md

I’ve been learning Ruby, and decided to scratch an itch: getting citations for papers to put in a bibtex file or my Zotero library. This usually requires two parts: 1) searching for an article with keywords, and then 2) getting the citation once the paper is found. Since I am lazy, I would prefer to do this from the command line instead of opening up a browser. Thus => cites. (Note, I’m sure someone has created something better - the point is I’m learnin’ me some Ruby)

cites does two things:

Each of the two above tasks are functions that you can use within Ruby, and are available from the command line/terminal so that you don’t have to spin up Ruby. During a typical writing workflow (in which you are using bibtex formatted references) one can want a citation for their paper, and instead of opening up a browser and using Google Scholar or Web of Science, etc., you can quickly search in your terminal by doing e.g., thor cite:search 'keywords that will help find the paper, including author, year, etc.'. Which if matches will give you a DOI. Then you can do thor cite:getcite DOI/string | pbcopy and you get the bibtex reference in your clipboard. Then just paste into your bibtex file or references manager. See more examples below.

First, we need to install dependencies

gem install httparty bibtex-ruby launchy
sudo gem install thor

Then clone the repo down. The Makefile in the repo builds the gem, and installs the Thor module so you have access to it from anywhere. If you don’t want the Thor commands, just do make install and just the gem will be installed.

git clone git@github.com:sckott/cites.git
cd cites
make



From the command line: Thor

I decided to use Thor to make functions within cites available on the cli. Thor is cool. For example, you can list the commands available like

thor list
cite
-----
thor cite:getcite        # Get a citation from a DOI
thor cite:launch paper   # Open a paper from a given DOI in your default browser
thor cite:search STRING  # Get a DOI from a search string

Get help for a particular method

thor help cite:getcite
Usage:
  thor cite:getcite

Options:
  [--format=FORMAT]
                     # Default: text
  [--style=STYLE]
                     # Default: apa
  [--locale=LOCALE]
                     # Default: en-US

Get a citation from a DOI

This is what’s associated with cites from the cli using Thor.

Other commands are available, just type thor on the cli, and press enter.

Search for a paper

From the CLI

thor cite:search 'Piwowar sharing data increases citation PLOS'
{"match"=>true, "doi"=>"10.1371/journal.pone.0000308", "text"=>"Piwowar sharing data increases citation PLOS"}

And you can do many searches, separated with commas, like

thor cite:search 'Piwowar sharing data increases citation PLOS,boettiger Modeling stabilizing selection'

Search within Ruby

require 'cites'
Cites.search('Piwowar sharing data increases citation PLOS')
=> [{"match"=>true,
  "doi"=>"10.1371/journal.pone.0000308",
  "text"=>"Piwowar sharing data increases citation PLOS"}]



Get a reference from a DOI

From the CLI, default output is text format, apa style, locale en-US

thor cite:getcite '10.1186/1471-2105-14-16'
Boyle, B., Hopkins, N., Lu, Z., Raygoza Garay, J. A., Mozzherin, D., Rees, T., Matasci, N., et al. (2013). The taxonomic name resolution service: an online tool for automated standardization of plant names. BMC Bioinformatics, 14(1), 16. Springer (Biomed Central Ltd.). doi:10.1186/1471-2105-14-16

Because we’re using thor you can pass in options to the call on the cli, like here choose ris for the format

thor cite:getcite '10.1371/journal.pone.0000308' --format=ris
TY  - JOUR
T2  - PLoS ONE
AU  - Piwowar, Heather A.
AU  - Day, Roger S.
AU  - Fridsma, Douglas B.
SN  - 1932-6203
TI  - Sharing Detailed Research Data Is Associated with Increased Citation Rate
SP  - e308
VL  - 2
PB  - Public Library of Science
DO  - 10.1371/journal.pone.0000308
PY  - 2007
UR  - http://dx.doi.org/10.1371/journal.pone.0000308
ER  -

And here bibtex for the format

thor cite:getcite '10.1371/journal.pone.0000308' --format=bibtex
@article{Piwowar_Day_Fridsma_2007,
  title = {Sharing Detailed Research Data Is Associated with Increased Citation Rate},
  volume = {2},
  url = {http://dx.doi.org/10.1371/journal.pone.0000308},
  doi = {10.1371/journal.pone.0000308},
  number = {3},
  journal = {PLoS ONE},
  publisher = {Public Library of Science},
  author = {Piwowar, Heather A. and Day, Roger S. and Fridsma, Douglas B.},
  editor = {Ioannidis, JohnEditor},
  year = {2007},
  month = {mar},
  pages = {e308}
}

Two more options, style and locale are only available with text format, like

thor cite:getcite '10.1371/journal.pone.0000308' --format=text --style=mla --locale=fr-FR
Piwowar, Heather A., Roger S. Day, et Douglas B. Fridsma. « Sharing Detailed Research Data Is Associated with Increased Citation Rate ». éd par. John Ioannidis. PLoS ONE 2.3 (2007): e308.

Within Ruby

require 'cites'
Cites.doi2cit('10.1371/journal.pone.0000308')
=> ["Piwowar, H. A., Day, R. S., & Fridsma, D. B. (2007). Sharing Detailed Research Data Is Associated with Increased Citation Rate. (J. Ioannidis, Ed.)PLoS ONE, 2(3), e308. Public Library of Science. doi:10.1371/journal.pone.0000308"]



Open paper in browser

Uses Macrodocs. The default, using Macrodocs, only works for open access (#OA) articles. You can set the option oa to be false.

thor cite:launch '10.1371/journal.pone.0000308'

It’s super simple, it just concatenates your DOI onto http://macrodocs.org/?doi= to give in this case http://macrodocs.org/?doi=10.1371/journal.pone.0000308 for what you will get from that command.

When you don’t have an open access article, set the oa option flag to false, like --oa=false

thor cite:launch '10.1111/1365-2745.12157' --oa=false

Setting --oa=false simply concatenates your doi onto http://dx.doi.org/, which then attempts to resolve to likely the publishers page for the article.

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