test_latest.yml

---
name: test latest image

on:
  schedule:
  - cron: 0 0 1 * *
  workflow_dispatch:

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

defaults:
  run:
    shell: bash -l {0}

jobs:

  test_dataset_without_session:

    runs-on: ubuntu-latest

    steps:
    - name: Install dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y tree

    - name: Clone repo
      uses: actions/checkout@v3

    - name: pull docker image
      run: docker pull bids/freesurfer:latest

    - name: add license
      run: |
        mkdir -p ~/license
        echo "cHJpbnRmICJEeWxhbi5OaWVsc29uQGdtYWlsLmNvbVxuMzcwNjNcbiAqQ1lrZWhQYUNvRDlNXG4gRlM2N1BTWmRFV2lqb1xuIiA+IH4vbGljZW5zZS9saWNlbnNlLnR4dA==" | base64 -d | sh

    - name: print version
      run: |
        docker run -t --rm --read-only \
            bids/freesurfer:latest --version
        docker run -t --rm --read-only \
            bids/freesurfer:latest --help

    - name: get data
      run: |
        wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh
        bash get_data_from_osf.sh ds114_test1
        bash get_data_from_osf.sh ds114_test1_freesurfer_precomp_v6.0.0

    - name: prepare output dir
      run: |
        mkdir -p ${HOME}/outputs1

    - name: dataset with no session - participant 01
      run: |
        docker run -t --rm --read-only \
          -v ${HOME}/data/ds114_test1:/bids_dataset \
          -v ${HOME}/outputs1:/outputs \
          -v ${HOME}/license/license.txt:/license.txt \
          --tmpfs /tmp \
          --tmpfs /var/tmp \
            bids/freesurfer:latest \
              /bids_dataset /outputs participant \
                --participant_label 01 \
                --license_file=/license.txt --stages autorecon1

        cat ${HOME}/outputs1/sub-01/scripts/recon-all.done

    - name: check output
      run: tree ${HOME}/outputs1

    - name: dataset with no session - group
      run: |
        docker run -t --rm --read-only \
        -v ${HOME}/data/ds114_test1:/bids_dataset \
        -v ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0:/outputs \
        -v ${HOME}/license/license.txt:/license.txt \
        --tmpfs /tmp \
        --tmpfs /var/tmp \
          bids/freesurfer \
            /bids_dataset \
            /outputs \
            group2 \
              --license_file=/license.txt

        mkdir -p ${HOME}/outputs1_group/
        sudo mv ${HOME}/data/ds114_test1_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs1_group/
        cat ${HOME}/outputs1_group/00_group2_stats_tables/lh.aparc.thickness.tsv
        cat ${HOME}/outputs1_group/00_group2_stats_tables/euler.tsv

  test_dataset_with_session:

    runs-on: ubuntu-latest

    steps:
    - name: Install dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y tree

    - name: Clone repo
      uses: actions/checkout@v3

    - name: pull docker image
      run: docker pull bids/freesurfer:latest

    - name: add license
      run: |
        mkdir -p ~/license
        echo "cHJpbnRmICJEeWxhbi5OaWVsc29uQGdtYWlsLmNvbVxuMzcwNjNcbiAqQ1lrZWhQYUNvRDlNXG4gRlM2N1BTWmRFV2lqb1xuIiA+IH4vbGljZW5zZS9saWNlbnNlLnR4dA==" | base64 -d | sh

    - name: print version
      run: |
        docker run -t --rm --read-only \
            bids/freesurfer:latest --version
        docker run -t --rm --read-only \
            bids/freesurfer:latest --help

    - name: get data
      run: |
        wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh
        bash get_data_from_osf.sh ds114_test2
        bash get_data_from_osf.sh ds114_test2_freesurfer_precomp_v6.0.0

    - name: prepare output dir
      run: |
        mkdir -p ${HOME}/outputs2

    - name: dataset with session - participant 01
      run: |
        docker run -t --rm --read-only \
          -v ${HOME}/data/ds114_test2:/bids_dataset \
          -v ${HOME}/outputs2:/outputs \
          -v ${HOME}/license/license.txt:/license.txt \
          --tmpfs /tmp \
          --tmpfs /var/tmp \
            bids/freesurfer:latest \
              /bids_dataset /outputs participant \
                --participant_label 01 \
                --license_file=/license.txt \
                --stages autorecon1 \
                --steps cross-sectional \
                --session_label test

        cat ${HOME}/outputs2/sub-01_ses-test/scripts/recon-all.done

    - name: check output
      run: tree ${HOME}/outputs2

    - name: dataset with session - group
      run: |
        docker run -t --rm --read-only \
        -v ${HOME}/data/ds114_test2:/bids_dataset \
        -v ${HOME}/data/ds114_test2_freesurfer_precomp_v6.0.0:/outputs \
        -v ${HOME}/license/license.txt:/license.txt \
        --tmpfs /tmp \
        --tmpfs /var/tmp \
          bids/freesurfer \
            /bids_dataset \
            /outputs \
            group2 \
            --license_file=/license.txt

        mkdir -p ${HOME}/outputs2_group/
        sudo mv ${HOME}/data/ds114_test2_freesurfer_precomp_v6.0.0/00_group* ${HOME}/outputs2_group/
        cat ${HOME}/outputs2_group/00_group2_stats_tables/lh.aparc.thickness.tsv
        cat ${HOME}/outputs2_group/00_group2_stats_tables/euler.tsv