Fortress test-case for 5S-TES - document steps specific to test case (not 5S-TES setup steps)

[OliverWoolland]

Carri documented setting up their container with 5S-TES here: https://github.com/UoMResearchIT/RTP-396-nwcybercomm/issues/59

Read through, repeat the process using a development instance (on own laptop?) and note here the steps specific to FORTRESS. Note that some steps - dind etc - might need updating to reflect changes to the stack since these docs were written.

[AnnieZQH]

Steps:

• Switch to fortress branch
  • The branch has five-safes-tes.patch applied with some modifications
    • Updated org name in git clone
    • Checkout tags/${FUNNEL_VERSION} instead of the development branch
    • Updated FUNNEL_VERSION to v0.11.12 to fix issues caused by v0.11.8 using the old org name `ohsu-comp-bio
• Start the containers manually (docker compose up ...) and follow steps 2 and 3 in the quickstart guide
  • Funnel prerequisite and step 1 is not relevant as we are using dockerised funnel
• Create PAT with read:packages permission and log in to GHCR

  docker login ghcr.io -u <username>
  

• Build tes_nw_wrapper image

  docker pull ghcr.io/uomresearchit/rtp-396-nwcybercomm/fortress:main
  docker build -t tes_nw_wrapper . -f tes_nw_wrapper.dockerfile
  

  tes_nw_wrapper.dockerfile:

  FROM ghcr.io/uomresearchit/rtp-396-nwcybercomm/fortress:main
  
  ENTRYPOINT []
  CMD ["/opt/venv/bin/python", "/app/NWCyberComm/nw_wrapper.py", "--scripts-path", "/app/NWCyberComm"]
  

• Copy the image into the dind container

  docker save tes_nw_wrapper:latest -o /tmp/tes_nw_wrapper.tar && cat /tmp/tes_nw_wrapper.tar | docker exec -i demostack-dind-1 docker -H tcp://localhost:2375 load 2>&1 && rm /tmp/tes_nw_wrapper.tar
  

• Follow quickstart guide steps 4-6 using the following test submission JSON

Test submission JSON

{
  "state": 0,
  "name": "NW Wrapper",
  "inputs": [],
  "outputs": [
    {
      "name": "Std",
      "description": "Std results",
      "url": "s3://",
      "path": "/outputs",
      "type": "DIRECTORY"
    }
  ],
  "executors": [
    {
      "image": "tes_nw_wrapper:latest",
      "command": ["/opt/venv/bin/python", "/app/NWCyberComm/nw_wrapper.py", "--scripts-path", "/app/NWCyberComm", "-h"],
      "stdout": "/outputs/nw_wrapper_out.txt",
      "stderr": "/outputs/nw_wrapper_err.txt"
    }
  ],
  "volumes": null,
  "tags": {
    "project": "Testing",
    "tres": "DEMO"
  },
  "logs": null,
  "creation_time": null
}

[ianhinder]

Need to create a PR for merging the changes in the attached branch.