buildspec-infant.yml

# see https://docs.aws.amazon.com/codebuild/latest/userguide/build-spec-ref.html
version: 0.2

env:
  shell: bash
  # https://stackoverflow.com/questions/58216549/how-to-retrieve-secret-manager-data-in-buildspec-yaml
  parameter-store:
    DOCKERHUB_PASS_PARAM: /dockerhub-access-token-for-pwighton
    FS_LICENSE_PARAM: /freesurfer-ci-license
            
phases:
  install:
    on-failure: ABORT
    commands:
      - export DOCKERHUB_PASS=$DOCKERHUB_PASS_PARAM
      - export FS_LICENSE=$FS_LICENSE_PARAM
      - docker login --username pwighton --password $DOCKERHUB_PASS
      # even though we use `pwighton/neurodocker:latest` to create the Dockerfile for now
      # (until https://github.com/pwighton/neurodocker/tree/20210226-fs-source is merged; but that is
      # based off of, and waiting on https://github.com/ReproNim/neurodocker/pull/378, then we can 
      # switch to `repronim/neurodocker:latest`)
      # we need still need neurodocker outside of docker for `neurodocker minify`
      - pip install neurodocker
  build:
    on-failure: ABORT
    commands:
      - ND="docker run pwighton/neurodocker:latest" FS_LICENSE_BASE64=$FS_LICENSE make fs-infant-dev
      # Docker push now while debugging buildspec
      - docker push pwighton/fs-infant-dev:latest
      #!! TO save time when debugging the test/minify (comment out `make fs-infant-dev` and `docker push` above
      #!!- docker pull pwighton/fs-infant-dev:latest
  # Minify this beast of a container    
  post_build:
    on-failure: ABORT
    commands:
      # Setup test/minify env
      - aws configure set region 'us-east-2'
      - export FS_DATAIN=/tmp/run/fs-datain
      - export FS_SUB=/tmp/run/fs-sub
      - export FS_INFANT_MODEL=/tmp/run/fs-infant-model
      - export SUB=sub-CC00656XX13-ses-217601
      - export SUB_S3_IN=s3://fs-infant/test/smoke/sub-CC00656XX13_ses-217601_desc-restore_space-T2w_T1w.nii.gz
      - export FS_INFANT_MODEL_S3_IN=s3://fs-infant/model/dev/
      - mkdir -p ${FS_DATAIN}
      - mkdir -p ${FS_SUB}
      - mkdir -p ${FS_INFANT_MODEL}
      - rm -rf ${FS_SUB}/${SUB}
      - mkdir -p ${FS_SUB}/${SUB}
      - aws s3 cp ${SUB_S3_IN} ${FS_SUB}/${SUB}/mprage.nii.gz
      - aws s3 cp --recursive --include '*' ${FS_INFANT_MODEL_S3_IN} ${FS_INFANT_MODEL}/
      ### END Setup test/minify env
      # the test command (without minify)
      # pw 2021/05/20: not sure why I have to specificy the entrypoint explicitly... wont work without it tho
      #- docker run --rm --entrypoint /bin/infant-container-entrypoint.bash -e SUBJECTS_DIR=/ext/fs-subjects -v ${FS_SUB}:/ext/fs-subjects -v ${FS_INFANT_MODEL}:/opt/fs-infant-model pwighton/fs-infant-dev:latest infant_recon_all --s sub-CC00656XX13-ses-217601 --age 0
      # the minify commands
      - cmd1="/bin/infant-container-entrypoint.bash"
      - cmd2="infant_recon_all --s sub-CC00656XX13-ses-217601 --age 0"
      # prep for minify
      - docker run --security-opt seccomp:unconfined --rm -it -d --name container-to-min --entrypoint /bin/bash -e SUBJECTS_DIR=/ext/fs-subjects -v ${FS_SUB}:/ext/fs-subjects -v ${FS_INFANT_MODEL}:/opt/fs-infant-model pwighton/fs-infant-dev:latest
      - sleep 1
      # minify
      - yes | neurodocker-minify --container container-to-min --dirs-to-prune /opt --commands "$cmd1" "$cmd2" 
      # export minified container
      - docker export container-to-min | docker import - pwighton/fs-infant-dev:min
      # push containers, if all went well
      - docker push pwighton/fs-infant-dev:latest
      - docker push pwighton/fs-infant-dev:min