https://github.com/billbrod/literature

Files to import literature from Mendeley into org mode and keep updated

https://github.com/billbrod/literature

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Files to import literature from Mendeley into org mode and keep updated

README.org

* Requirements
** System
   
   All these can be done through apt-get
   
   - poppler-data
   - poppler-utils
   - git

** Emacs

   * bibtex-utils
   * org-ref
   * helm-bibtex
   * biblio

* Set-up

  To use, download and place on your load path. Only ~literature.el~
  is required, ~literature-config.el~ adds it to the load path and
  require literature, as well as defining some hooks, key shortcuts,
  and variables. Those are all optional and you can use as you see
  fit.

  Before use, make sure to set the ~literature-paper-directory~,
  ~literature-master-bib~, and ~literature-master-org~ variables. To
  make sure the different libraries talk to each other correctly, you
  should also set:
  - ~bibtex-completion-bibliography~
  - ~bibtex-completion-library-path~
  - ~bibtex-completion-notes-extension~
  - ~reftex-default-bibliography~
  - ~org-ref-bibliography-notes~
  - ~org-ref-default-bibliography~
  - ~org-ref-pdf-directory~

  See ~literature-config.el~ for an example of how they should be set.

  It's also recommended you set the various ~bibtex-autokey-*~
  variables so that the key generated by ~bibtex-autokey~ (as used in
  ~org-ref-clean-bibtex-entry~) is one you like. Again, an example is
  found in ~literature-config.el~

  To get ~literature-add-file~ as an option in helm-find-files, add
  the line ~alias literature-add-file literature-add-file $1~ to your
  eshell aliases file (eg, ~.emacs.d/eshell/alias~).  Then, using
  helm-find-files (not necessarily bound to ~C-x C-f~! Check that it
  is), typing ~M-!~ and selecting ~literature-add-file~ will run it on
  the highlighted file (you can mark multiple files and then
  ~literature-add-file~ will be run on them one after the other).
  
  For now, there's an issue with ~bibtex-utils~, where the version
  that exists on ~el-get~ starts with a bunch of uncommented text,
  which can lead to a ~Symbol is void: A~ error. If this happens, find
  the version of ~bibtex-utils.el~ that is being loaded, comment out
  the text at the beginning (and the closing brackets at the end),
  delete the compiled version (~bibtex-utils.elc~) and try again.

* Android set-up
  
  This set-up can be made to work on Android, but it takes a tiny
  amount of work. I use [[https://play.google.com/store/apps/details?id=me.bares.refmaster&hl=en][RefMaster]], but I think this would work with
  [[https://play.google.com/store/apps/details?id=com.cgogolin.library&hl=en][Library]] as well. The links need to be relative and formatted to work
  with JabRef (which they are), but you also need to have all the
  files on your local device. If you use Dropbox, they aren't all
  downloaded, so you need to use something like [[https://play.google.com/store/apps/details?id=com.ttxapps.dropsync&hl=en][Dropsync]], which links
  a local folder on your device to one of your Dropbox folders. This
  will take up a fair amount of space, depending on how many files you
  have, but if you have a wifi-only tablet and so don't have
  consistent network access, you probably want all the files on your
  device anyway, so you can read anywhere. 

  Then simply load in your literature.bib file, and you should be good
  to go!
  
* Acknowledgments

  I spent a lot of time reading around on the internet before deciding
  how best to do this. As for as I could find, no one had specifically
  moved from Mendeley to using org mode for reference management, so I
  used a lot of things piece-meal.

  Obviously, for the emacs setup, I use [[https://emacs-helm.github.io/helm/][helm]] and [[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] directly,
  both of which are wonderful packages. I also use [[https://github.com/politza/pdf-tools][pdf-tools]] for
  editing pdfs in emacs, which is a great package as well.

  I first came across the idea of using org-mode and emacs as
  reference management in a blog post [[https://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/][here]], which has been linked to
  several times by people doing related projects. The main inspiration
  for my organization is a post by [[http://blog.nguyenvq.com/blog/2011/07/24/research-paper-management-or-library-with-emacs/][Vinh Nguyen]]. For getting
  annotations out of pdfs in Python, I based my code on [[http://coda.caseykuhlman.com/entries/2014/pdf-extract.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%253A+caseykuhlman%252Fcoda+%2528The+Legal+Coda%2529][two]] [[http://socialdatablog.com/extract-pdf-annotations.html][posts]], and
  the get_annotations() function comes almost directly from the second
  of those. Using python to extract Mendeley notes and metadata
  information came from [[http://www.danielhnyk.cz/blog/view/export-pdf-annotations-mendeley-csv-or-txt][here]], and an idea for the structure for how to
  export Mendeley information came from the R code found [[https://github.com/rdiaz02/Adios_Mendeley][here]], though
  the information I took differs from both of them. For obtaining
  bibtex entries from a doi, I used code from [[https://github.com/jgilchrist/pybib][pybib]] (specifically,
  pybib/utils.py); I was unable to do what I wanted (get bibtex
  information from inside a python function) with the installed
  version of pybib, so I just copied the relevant parts of code.

  

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