JabRef 3.7 on debian, to fix medline fetches since ncbi went https

Introduction

As of the weekend of 5th November 2016, old versions of JabRef are no longer able to fetch medline due to https being enforced on US government web servers.

JabRef 3.7 development version is fixed.

To install JabRef we first need to install Java 8.

Install java 8

These instructions are from https://satishchilukuri.com/blog/entry/installing-java-8-and-tomcat-8-on-debian-wheezy

1. Download JRE Server JRE (Java SE Runtime Environment) 8u112 from http://www.oracle.com/technetwork/java/javase/downloads/server-jre8-downloads-2133154.html
2. Change to root and extract the .tar.gz in /opt
3. In /opt do ln -s jdk1.8.0_25 java8
4. Add the path to the profile by adding the following line somewhere, I would save it as java8.sh in /etc/profile.d but you could put it in your user's .profile file

   PATH="/opt/java8/bin:$PATH 
   

Re-login

Download the new JabRef

Get the development version from https://builds.jabref.org/master/ (see http://www.jabref.org/ if you want to check the parent page)

Run the new Jabref

java -jar JabRef-3.7-dev--snapshot--2016-11-04--master--949ca17.jar

Make the new JabRef the default program

I have not been able to make this work yet!

The following are notes in draft only!

Copy the JabRef jar file to /usr/share/jabref
You will see that /usr/share/java/jabref.jar links to ../jabref/JabRef-2.7b.jar

This old link can be backed up or deleted, or if you want to overwrite it the use ln with the --force option

ln -sf /usr/share/jabref/JabRef-3.7-dev--snapshot--2016-11-04--master--949ca17.jar /usr/share/java/jabref.jar 

Come out of root

exit

Check it with

jabref