Public Repository

Last pushed: a year ago
Short Description
Image containing contentmine applications.
Full Description

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


Original build

  • 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
#!/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 "${PWD}/cm":/contentmine --tty --interactive psychemedia/contentmine "$@"
  • 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

Dockerfile avalable here.


For an early example of some IPython magic to call functions with this container from a Jupyter notebook container, see Steps Towards Some Docker IPython Magic – Draft Magic to Call a Contentmine Container from a Jupyter Notebook Container.

Docker Pull Command
Owner
psychemedia

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