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
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.
- biopython (http://biopython.org/wiki/Biopython)
- pdftotext (http://linux.die.net/man/1/pdftotext)
- xclip (http://sourceforge.net/projects/xclip/) (not required)
Python 3 is required.
git clone https://github.com/mmagnus/pubmex
pip install -e pubmex
apt-get install xclip python-biopython pdftotext
.. clone & run it :-) Set PATHs to pubmex.py
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
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 ;-))
Visit https://github.com/m4rx9/pubmex/wiki
Run a script with examples:
./examples-test.sh
pubmex.py
might have still problem if it has to parse title of authors with characters like ółą and so on.
pubmex.py is Copyright (C) 2010-2015 Marcin Magnus. All rights reserved.
This program is free software; you can redistribute it and/or modify it under the same terms as GLP
Marcin Magnus, m.magnus@o2.pl
@todo
version 0.3
- osx installation
version 0.2
- small changes