First sketch of a contentmine dockerfile

README.md

Contentmine Docker CLI App

An attempt to make it easier to use Contentmine tools, by simplifying the install...

Based on some cribs from Distributing Command Line Tools with Docker

• create a contentmine directory: eg mkdir -p contentmine
• download the Dockerfile into it
• from a Docker CLI, cd in to the directory; create an image using eg docker build -t psychemedia/contentmine .
• download the contentmine script and make it executable: chmod u+x contentmine
• create a folder on host in the contentmine folder to act as a shared folder with the contentmine container: eg mkdir -p cm
• run commands
  • ./contentmine getpapers -q aardvark -o /contentmine/aardvark -x
  • ./contentmine norma --project /contentmine/aardvark -i fulltext.xml -o scholarly.html --transform nlm2html
  • ./contentmine cmine /contentmine/aardvark

Contentmine Home: Contentmine

contentmine

#!/bin/bash
## contentmine - a wrapper script for runnining contentmine packages
#/via Distributing Command Line Tools with Docker https://spin.atomicobject.com/2015/11/30/command-line-tools-docker/
#Make this file executable: chmod u+x contentmine

docker run --rm --volume "${PWD}/cm":/contentmine --tty --interactive psychemedia/contentmine "$@"

Dockerfile

FROM node:4.3.2

##Based on
MAINTAINER Tony Hirst


RUN apt-get clean -y && apt-get -y update && apt-get -y upgrade && \
  apt-get -y update && apt-get install -y wget ant unzip openjdk-7-jdk  && \
 	apt-get clean -y
 	
RUN wget --no-check-certificate https://github.com/ContentMine/norma/releases/download/v0.2.26/norma_0.1.SNAPSHOT_all.deb

RUN wget --no-check-certificate https://github.com/ContentMine/ami/releases/download/v0.2.24/ami2_0.1.SNAPSHOT_all.deb

RUN dpkg -i norma_0.1.SNAPSHOT_all.deb
RUN dpkg -i ami2_0.1.SNAPSHOT_all.deb

RUN npm install --global getpapers


RUN mkdir /contentmine
VOLUME /contentmine

RUN cd /contentmine

#The intuition behind this is: 'can we avoid setup hassles by distributing contentmine commandline app via a container?'

#docker build -t psychemedia/contentmine .
#Then maybe something like:
#mkdir -p cm
#docker run  --volume "${PWD}/cm":/contentmine  --interactive psychemedia/contentmine  getpapers -q aardvark -o /contentmine/aardvark -x
#docker run  --volume "${PWD}/cm":/contentmine  --interactive psychemedia/contentmine  norma --project /contentmine/aardvark -i fulltext.xml -o scholarly.html --transform nlm2html
#docker run  --volume "${PWD}/cm":/contentmine  --interactive psychemedia/contentmine cmine /contentmine/aardvark
#
##Following https://spin.atomicobject.com/2015/11/30/command-line-tools-docker/ how about:
#Create the following script as contentmine; chmod u+x contentmine
#--
##!/bin/bash
## contentmine - a wrapper script for runnining contentmine packages
#docker run --volume "${PWD}/cm":/contentmine --tty --interactive psychemedia/contentmine "$@"
#--
#Then run eg: ./contentmine  getpapers -q aardvark -o /contentmine/aardvark2 -x
  

Thanks Tony, this will be very useful. Some people are having minor difficulties in installing the native CLI versions and this will help to get them off the ground.