Edit the Dockerfile to use a jar and multi stage build.

[vemonet]

Edit the Dockerfile to use a jar and multi stage build.

Description

• rewriting the Dockerfile to build the standalone jar in a maven container before running it in a openjdk slim container
  • First packaging the jar using the cli-standalone profile in a maven container
  • then copying it to a lightweight and clean image to run it
  • use absolute path to run the jar in the Docker entrypoint

Motivation and Context

It allows to avoid issue when the docker runtime is using a different workdir by default (which cause the mvn java:exec to fail)
Allows to run it using:

• Kubernetes / OpenShift
• CWL workflows

Issue: #98

How Has This Been Tested?

Tested on Ubuntu 18.04. Part of a workflow containing other components:

• On Kubernetes
  • Install kubectl and Argo on local machine (following this tutorial: https://maastrichtu-ids.github.io/dsri-documentation/docs/guide-local-install#install-kubectl )
  • Run aksw/rdfunit in a Kubernetes pod
    It can be done reusing this pod definition: https://github.com/MaastrichtU-IDS/d2s-argo-workflows/blob/cd8b1432940595e6ff52b7efaa339f5d653aa609/tests/test-devnull-pod.yaml
  • Connect to it to run bin/rdfunit
  • Kubernetes version:

**Client Version:** version.Info{Major:"1", Minor:"11+", GitVersion:"v1.11.0+d4cacc0", GitCommit:"d4cacc0", GitTreeState:"clean", BuildDate:"2018-10-10T16:38:01Z", GoVersion:"go1.10.3", Compiler:"gc", Platform:"linux/amd64"}
**Server Version:** version.Info{Major:"1", Minor:"17", GitVersion:"v1.17.0", GitCommit:"70132b0f130acc0bed193d9ba59dd186f0e634cf", GitTreeState:"clean", BuildDate:"2019-12-07T21:12:17Z", GoVersion:"go1.13.4", Compiler:"gc", Platform:"linux/amd64"}

• On CWL
  The 2 first commands are to create the workspace directories (on Ubuntu). The last command is to run the workflow from the root of the GitHub repository https://github.com/MaastrichtU-IDS/d2s-cwl-workflows (after cloning it)

mkdir -p /data/dqa-workspace/output/tmp-outdir
sudo chown -R ${USER}:${USER} /data/dqa-workspace

git clone https://github.com/MaastrichtU-IDS/d2s-cwl-workflows
cd d2s-cwl-workflows

cwl-runner \
  --outdir /data/dqa-workspace/output \
  --tmp-outdir-prefix=/data/dqa-workspace/output/tmp-outdir/ \
  --tmpdir-prefix=/data/dqa-workspace/output/tmp-outdir/tmp- \
  workflows/workflow-dqa.cwl \
  support/config-cwl-dqa.yml

Screenshots (if appropriate):

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have added tests to cover my changes.
• All new and existing tests passed.

[coveralls]

Coverage remained the same at 54.365% when pulling b38d524 on vemonet:develop into c8ae88a on AKSW:master.

[jimkont]

Looks very good 👍 we could also shorten the workdir to something like /app as you suggested

[jimkont]

Thank you for your contribution @vemonet