# Citation management in Org mode

For a long time, I was using Emacs to manage academic resources and produce nice LaTeX pdf files. It was a little bit of trouble getting it going, and it was a pain to use it with attendings since they prefer to work off of word. I ended up uninstalling all the plugins I need to use with it, which I now regret. So this blog post will serve as a log while I try to reinstall the modules and get it all running again.

## Org-Ref

Org-Ref is a supposedly obselete package available on the Melpa database. It provides a lot of the machinery that lets Org play nicely with bibtex files and citations.

It looks like a lot of my old config stuck around. I had to add a few lines to my init code:

;; Initialize Org-Ref for citations
(require 'org-ref)

(setq reftex-default-bibliography '("~/org/bibliography/references.bib"))

;; see org-ref for use of these variables
(setq org-ref-bibliography-notes "~/org/bibliography/notes.org"
org-ref-default-bibliography '("~/org/bibliography/references.bib")
org-ref-pdf-directory "~/org/bibliography/bibtex-pdfs/")

(setq bibtex-completion-bibliography "~/org/bibliography/references.bib"
bibtex-completion-library-path "~/org/bibliography/bibtex-pdfs"
bibtex-completion-notes-path "~/org/bibliography/helm-bibtex-notes")

;; open pdf with system pdf viewer (works on mac)
(setq bibtex-completion-pdf-open-function
(lambda (fpath)
(start-process "open" "*open*" "open" fpath)))


## LaTeX Specifics

Along the way, I had to install MacTEX to handle emacs org tex output. I had one small dependency issue, listed below for reference.

==> Pouring ghostscript--9.23_1.high_sierra.bottle.tar.gz
Error: The brew link step did not complete successfully
The formula built, but is not symlinked into /usr/local
Target /usr/local/bin/dvipdf
already exists. You may want to remove it:
rm '/usr/local/bin/dvipdf'

To force the link and overwrite all conflicting files:

To list all files that would be deleted:


I’m also finding pdflatex already installed. I think there might be a problem with telling emacs which shell scripts to use. There’s a package called exec-path-from-shell that helps with this. You have to initialize it once it’s installed with the command (exec-path-from-shell-initialize).

I had to add a bit of code to my Init in order to get Org to process bibliographies with Bibtex:

(setq org-latex-pdf-process
'("pdflatex -interaction nonstopmode -output-directory %o %f"
"bibtex %b"
"pdflatex -interaction nonstopmode -output-directory %o %f"
"pdflatex -interaction nonstopmode -output-directory %o %f"))


## Use

Citations are placed in the file ~/org/bibliography/references.bib. Citations are indexed automatically from this file and can be added to other org files with the key combination C-c ]. The LaTeX header I’m using is as follows:

#+LaTeX_HEADER: \usepackage{mathptmx}

Make sure to add \printbibliography at the end of the file. Exports with LaTeX should now work!
To add new entries to the bibliography by DOI, use the command doi-utils-add-bibtex-entry-from-doi. For now, I’ve linked this command with the key combo C-c d. So just type in that combo, hit enter, and there you go. Supposedly there is a mode that can find and download pdf files of the articles you link to, but I haven’t found a way to make that work yet.