regtm / contentmine_dockerized

Dockerfile for contentmine

Contentmine Dockerized

Dockerfile to build a contentmine container including getpapers, norma and ami.

Find the contentmine project here.

Installation

Install from docker hub with:

docker pull regtm/contentmine

Build locally with:

docker build -t regtm/contentmine .

Usage

The contentmine script can simply be used this way (dont forget to make it executable chmod +x ./contentmine):

./contentmine $TOOL $PARAMETERS

Example

1. Fetch papers from PubMed:

   ./contentmine getpapers --query querystring --xml --limit 100 -o ./data

   A description of the query string format can be found at the europepmc documentation: https://europepmc.org/Help#mostofsearch

2. Convert fulltext XML files to "scholarly" html:

   ./contentmine norma -q ./ -i fulltext.xml -p scholarly.html --transform nlm2html

Manual Usage

Initially the data folder has to be created on the host and made readable for all to avoid permission issues inside the container:

mkdir -p data
chmod -R a+rw data

The container can be used via terminal/comandline. Replace $TOOL with the tool from contentmine that you want to use:

docker run --rm --volume "${PWD}/data":/data --tty --interactive regtm/contentmine $TOOL