Build SSDF as Application Package

[jjacob7734]

Build updated SSDF Jupyter notebook (see tickets ...) as OGC-compliant application package. You can use the Unity App Generator (https://github.com/unity-sds/unity-app-generator) tool to build the Docker image and workflow CWL files. That tool can also register the docker image into a registry (Docker Hub, etc) and the CWL artifacts into Dockstore. For assistance, reach out to the U-ADS team led by @mcduffie.

Acceptance Criteria

• [ ] Docker image built and registered into registry
• [ ] CWL artifacts built and registered into Dockstore

[jjacob7734]

How to prepare environment for Unity App Generator:

• Ensure you have Python >= 3.9

  pip install ./app-pack-generator pip install ./unity-app-generator

• Above provides executable called build_ogc_app

How to build Application Package:

• Login to Docker Hub

  docker login

• Built app package
  • Change directory to the source code with your notebook

    build_ogc_app init .

  • Above creates hidden directory: .unity_app_gen

    build_ogc_app build_docker build_ogc_app push_docker DOCKER-USER build_ogc_app build_cwl

  • Above populates the hidden .unity_app_gen directory with the CWL files.

    build_ogc_app push_app_registry --api_url API-URL/api --token TOKEN

  • In the above the api_url and token are in the Dockstore onboarding setup and saved in ~/.dockstore/config as described in the Unity Dockstore section above.
• Test workflow following the directions under the "Launch" tab at API-URL/my-workflows/dockstore.org/DOCKSTORE-USER/SSDF_Unity_python3

[jjacob7734]

Status:

• @zx128 is learning how the Unity App Generator works.
• Reviewed process with @jjacob7734 as in the comment above.

[jjacob7734]

Status:

• @jjacob7734 and @zx128 had vacation weeks so moving this into the 24.3.3 sprint.
• @zx128 is working on installing environment/dependencies and building SSDF into OGC application package.
• Following the Unity application example to do this.
• Expect to get a process step container built this week.

[jjacob7734]

Status:

• Built process step Docker image with the Unity Application Generator tool
• Built CWL with the Unity Application Generator tool
• Pushed Docker image to Docker Hub with the Unity Application Generator tool
• Working on getting Dockstore set up and will push the CWL to Dockstore and then try running it on U-SPS.

[jjacob7734]

Unity Dockstore URL (currently used by all venues) : http://awslbdockstorestack-lb-1429770210.us-west-2.elb.amazonaws.com:9998/