Getting paper references with papis

Today I would like to talk about how I normally download references of papers using the tool Papis. I will be writing in the future more posts about this tool and about how it makes my life easier.

Usually when I am researching a topic and I read a paper about it, I want to check out some references cited in the paper. However, I find it very tiresome to copy the reference or the link (if any is available in the pdf), paste it in the browser and download it with papis. I mean, this is still ok, and sometimes I do exactly this. But most of the times, I can do better, and I want to tell you exactly how.

To see how this works we are going to work with the following landmark paper:

@article{Theory.of.SuperBardee1957,
  author = {Bardeen, J. and Cooper, L. N. and Schrieffer, J. R.},
  doi = {10.1103/PhysRev.108.1175},
  issue = {5},
  journal = {Physical Review},
  pages = {1175--1204},
  title = {Theory of Superconductivity},
  url = {http://link.aps.org/article/10.1103/PhysRev.108.1175},
  volume = {108},
  year = {1957},
}

Right now when papis adds a paper through the doi importer, i.e., when you do something like

papis add --from doi 10.1103/PhysRev.108.1175

or simply

papis add 10.1103/PhysRev.108.1175

you get information similar to the following in the info.yaml file

abbrev_journal_title: Phys. Rev.
author: Bardeen, J. and Cooper, L. N. and Schrieffer, J. R.
author_list:
- given_name: J.
  surname: Bardeen
- given_name: L. N.
  surname: Cooper
- given_name: J. R.
  surname: Schrieffer
citations:
- doi: 10.1007/BF01504252
- doi: 10.1098/rspa.1935.0048
- doi: 10.1016/S0031-8914(35)90097-0
- doi: 10.1103/PhysRev.74.562
- doi: 10.1098/rspa.1953.0040
- doi: 10.1103/PhysRev.97.1724
- doi: 10.1007/BFb0109284
- doi: 10.1007/BF01322787
- doi: 10.1103/PhysRev.78.477
- doi: 10.1103/PhysRev.78.487
- doi: 10.1103/PhysRev.79.845
- doi: 10.1103/PhysRev.79.167.3
- doi: 10.1103/PhysRev.80.567
- doi: 10.1103/PhysRev.81.829
- doi: 10.1103/RevModPhys.23.261
- doi: 10.1098/rspa.1952.0212
- doi: 10.1103/PhysRev.99.1140
- doi: 10.1103/PhysRev.106.162
- doi: 10.1103/PhysRev.100.1215
- doi: 10.1103/PhysRev.102.656
- doi: 10.1103/PhysRev.102.662
- doi: 10.1103/PhysRev.104.844
- doi: 10.1002/prop.19530010302
- doi: 10.1103/PhysRev.107.354
- doi: 10.1103/PhysRev.100.481
- doi: 10.1103/PhysRev.100.502
- doi: 10.1103/PhysRev.104.1189
- doi: 10.1103/PhysRev.101.1431
- doi: 10.1103/PhysRev.107.901
- doi: 10.1007/BF02856068
- doi: 10.1098/rspa.1948.0123
- doi: 10.1103/PhysRev.106.208
doc_url: http://harvest.aps.org/v2/journals/articles/10.1103/PhysRev.108.1175/fulltext
doi: 10.1103/PhysRev.108.1175
files:
- Theory-of-Superconductivity-Bardeen-J.-and-Cooper-L.-N.-and-Schrieffer-J.-R..pdf
first_page: '1175'
full_journal_title: Physical Review
issue: '5'
journal: Physical Review
last_page: '1204'
pages: 1175--1204
ref: Theory.of.SuperBardee1957
title: Theory of Superconductivity
url: http://link.aps.org/article/10.1103/PhysRev.108.1175
volume: '108'
year: '1957'

Take a look at the citations section, we get a list of most doi strings referenced in the paper.

Papis has a command called explore which offers much functionality. One of the subcommands of explore is called citations, so that you can explore the citations in the citations field of your info file. Since explore commands are quite long, I normally define a bash function or an alias to use them. In this case I define the following function in my ~/.bashrc file

citget() {
  query=$1
  shift
  papis explore citations -s "$query" pick cmd "papis add --from doi {doc[doi]} $@"
}

If this seems like a magic incantation to you, let us break it down. The help message of the citations command reads like

papis explore citations -h

Usage: papis explore citations [OPTIONS] [QUERY]

  Query the citations of a paper

  Example:

  Go through the citations of a paper and export it in a yaml file

      papis explore citations 'einstein' export --format yaml einstein.yaml

Options:
  --doc-folder PATH            Apply action to a document path
  -h, --help                   Show this message and exit.
  -s, --save                   Store the citations in the document's folder
                               for later use

  --rmfile                     Remove the stored citations file
  -m, --max-citations INTEGER  Number of citations to be retrieved

The flag -s means that the citations downloaded should be stored in a citations.yaml file in the document’s folder. Whichever citation we then choose, we will pass it to the cmd command, which accepts a string that will be run in the shell. In this case, we select a cited document and apply the papis add --from doi {doc[doi]} format, which replaces the {doc[doi]} part in the format string by the doi of the selected document.

Here you can see it in action, it first checks if a citation doi is already in the library, in which case the information is already there. If the doi of the citation is not in our library, then the infomation gets downloaded via crossref.

And this is pretty much it!

For comments check out the Reddit post.