Zoterto is an excellent reference and citation manager. It runs within Firefox, making it very easy to record sources that you encounter on the web (and in this age of publication databases almost everything is on the web). There are plugins for LibreOffice and for Word which can then format those citations to meet your paper's requirements. Zotero's Firefox application can also output for other systems, such as Wikipedia and LaTeX. You can keep your references in the Zotero cloud, which is a huge help if you use different computers at home and work or school.

The competing product is EndNote. Frankly, EndNote belongs to a previous era of researcher methods. If you use Windows, Word and Internet Explorer and have a spare $100 then you might wish to consider it. For me there's a host of showstoppers, such as not running on Linux and not being able to bookmark a reference from my phone when it is mentioned in a seminar.

Anyway, this article isn't a Zotero versus EndNote smackdown, there's plenty of those on the web. This article is to show a how to configure Zotero's full text indexing for the RaspberryPi and other Debian machines.

Installing Zotero

There are two parts to install: a plugin for Firefox, and extensions for Word or LibreOffice. (OpenOffice works too, but to be frank again, LibreOffice is the mainstream project of that application these days.)

Zotero keeps its database as part of your Firefox profile. Now if you're about to embark on a multi-year research project you may one day have trouble with Firefox and someone will suggest clearing your Firefox profile, and Firefox once again works fine. But then you wonder, "where are my years of carefully-collected references?" And then you cry before carefully trying to re-sync.

So the first task in serious use of Zotero on Linux is to move that database out of Firefox. After installing Zotero on Firefox press the "Z" button, press the Gear icon, select "Preferences" from the dropbox menu. On the resulting panel select "Advanced" and "Files and folders". Press the radio button "Data directory location -- custom" and enter a directory name.

I'd suggest using a directory named "/home/vk5tu/.zotero" or "/home/vk5tu/zotero" (amended for your own userid, of course). The standalone client uses a directory named "/home/vk5tu/.zotero" but there are advantages to not keeping years of precious data in some hidden directory.

After making the change quit from Firefox. Now move the directory in the Firefox profile to whereever you told Zotero to look:

$ cd
$ mv .mozilla/firefox/*.default/zotero .zotero

Full text indexing of PDF files

Zotero can create a full-text index of PDF files. You want that. The directions for configuring the tools are simple.

Too simple. Because downloading a statically-linked binary from the internet which is then run over PDFs from a huge range of sources is not the best of ideas.

The page does have instructions for manual configuration but the page lacks a worked example. Let's do that here.

Manual configuration of PDF full indexing utilities on Debian

Install the pdftotext and pdfinfo programs:

    $ sudo apt-get install poppler-utils

Find the kernel and architecture:

$ uname --kernel-name --machine
Linux armv7l

In the Zotero data directory create a symbolic link to the installed programs. The printed kernel-name and machine is part of the link's name:

$ cd ~/.zotero
$ ln -s $(which pdftotext) pdftotext-$(uname -s)-$(uname -m)
$ ln -s $(which pdfinfo) pdfinfo-$(uname -s)-$(uname -m)

Install a small helper script to alter pdftotext paramaters:

$ cd ~/.zotero
$ wget -O redirect.sh https://raw.githubusercontent.com/zotero/zotero/4.0/resource/redirect.sh
$ chmod a+x redirect.sh

Create some files named *.version containing the version numbers of the utilities. The version number appears in the third field of the first line on stderr:

$ cd ~/.zotero
$ pdftotext -v 2>&1 | head -1 | cut -d ' ' -f3 > pdftotext-$(uname -s)-$(uname -m).version
$ pdfinfo -v 2>&1 | head -1 | cut -d ' ' -f3 > pdfinfo-$(uname -s)-$(uname -m).version

Start Firefox and Zotero's gear icon, "Preferences", "Search" should report something like:

PDF indexing
  pdftotext version 0.26.5 is installed
  pdfinfo version 0.26.5 is installed

Do not press "check for update". The usual maintenance of the operating system will keep those utilities up to date.


Glen Turner

July 2017

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