Pu(b)mex

Nowadays, it’s not a big issue, with all Mendeley and other tools, however...

I don’t want to put any PDF file collected on the way into my library, because then it gets super big (and then it’s hard to sync it for example with Dropbox). So now I can keep these PDF files into pdf-icebox and re-name them niecely automatically:

$ ls
Hnisz.Sharp.Phase.Separation.Model.Transcriptional.Control.Cell.2017.pdf
Sharp.Hockfield.Convergence.The.future.health.Science.2017.pdf

Usage:

    $ pubmex.py -a -f sharp2017.pdf -r
    Sharp.Hockfield.Convergence.The.future.health.Science.2017.pdf
    mv  sharp2017.pdf --> ./Sharp.Hockfield.Convergence.The.future.health.Science.2017.pdf

    $ pubmex.py -a -f Query.Konarska.pdf -r
    the title is ...  Smith.Konarska."Nought.may.endure.but.mutability".spliceosome.dynamics.regulation.splicing.MolCell.2008.pdf
    mv  Query.Konarska.pdf --> Smith.Konarska."Nought.may.endure.but.mutability".spliceosome.dynamics.regulation.splicing.MolCell.2008.pdf

.. and we get a file:

Smith.Konarska."Nought.may.endure.but.mutability".spliceosome.dynamics.regulation.splicing.MolCell.2008.pdf

DESCRIPTION

pubmex.py is a script to get a fancy paper title based on given DOI or PMID.

Format of the title:

a first author . a last author - (title("dotted") or your customed title) . PMID . journal . year . pdf
e.g.
  Kelley.Scott.The.evolution.biology.shift.towards.engineering.prediction-generating.tools.away.traditional.research.practice.EMBORep.2008.pdf

Using xclip pubmex.py automatically copy the title to the clipboard. Just type Ctrl+V or paste it somewhere else.

DEPENDENCIES

biopython (http://biopython.org/wiki/Biopython)
pdftotext (http://linux.die.net/man/1/pdftotext)
xclip (http://sourceforge.net/projects/xclip/) (not required)

INSTALLATION

Python 3 is required.

git clone https://github.com/mmagnus/pubmex
pip install -e pubmex

Ubuntu (Debian-based system)

apt-get install xclip python-biopython pdftotext

.. clone & run it :-) Set PATHs to pubmex.py

MAC OSX

sudo port install poppler #pdftotext
sudo port install py-pip # 
sudo pip install biopython # or sudo port install biopython # (but it did't work for me)

.. clone & run it :-) Set PATHs to pubmex.py

WINDOWS (NOT TESTED!!!!!!!)

Install:

Python http://www.python.org/ftp/python/2.6.4/python-2.6.4.msi
Biopython http://biopython.org/DIST/biopython-1.53.win32-py2.6.exe
GTK+ http://sourceforge.net/projects/gtk-win/ direct link http://downloads.sourceforge.net/project/gtk-win/GTK%2B%20Runtime%20Environment/GTK%2B%202.16/gtk2-runtime-2.16.6-2010-02-24-ash.exe?use_mirror=garr
pyGTK http://ftp.gnome.org/pub/GNOME/binaries/win32/pygtk/2.16/pygtk-2.16.0+glade.win32-py2.6.exe
and pdftotext if you want to use -a

.. and it might work. I don't know (I don't care ;-))

EXAMPLES

Visit https://github.com/m4rx9/pubmex/wiki

Run a script with examples:

./examples-test.sh

BUGS

pubmex.py might have still problem if it has to parse title of authors with characters like ółą and so on.

COPYRIGHT AND LICENCE

This program is free software; you can redistribute it and/or modify it under the same terms as GLP

AUTHOR INFORMATION

Marcin Magnus, m.magnus@o2.pl

ACKNOWLEDGEMENTS

@todo

HISTORY

version 0.3

osx installation

version 0.2

small changes

lclem / pubmex