stages:
    - check
    - test
    - test_docker
    - cache_docker
    - test_singularity
    - cache_singularity

variables:
    GIT_STRATEGY: clone


# Execute this script for everybody. YAML anchor.
.all-script-before: &all-script-before
  - pwd
  - env
  - ls -laht
  - whoami


### All base jobs.

# Astrocyte jobs, assumed to need to run on the cluster where they have access to the module lists.
.astrocyte:
  before_script:
    - *all-script-before
    - module load astrocyte/0.4.0
  tags:
    - cluster_node

.docker:
  before_script:
    - *all-script-before
    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY

### Setup scripts

before_script:
  - *all-script-before

# This performs validation of the astrocyte_pkg.yml file
astrocyte_check:
  extends: .astrocyte
  stage: check
  script:
  - astrocyte_cli check "$CI_PROJECT_DIR"
  
nextflow_test_docker:
  stage: test
  script:
  - module load nextflow/20.01.0 
  - module load singularity/3.5.3 
  - cd $CI_PROJECT_DIR/workflow
  - nextflow  -C $CI_PROJECT_DIR/workflow/configs/biohpc_docker.config  run main.nf -with-trace -with-timeline -resume --verbose -bg
  artifacts:
    paths:
    - $CI_PROJECT_DIR/workflow/.nextflow.log
  tags:
    - cluster_node

nextflow_test_singularity:
  stage: test
  script:
  - module load nextflow/20.01.0 
  - module load singularity/3.5.3 
  - cd $CI_PROJECT_DIR/workflow
  - nextflow  -C $CI_PROJECT_DIR/workflow/configs/biohpc_singularity.config  run main.nf -with-trace -with-timeline -resume --verbose -bg
  artifacts:
    paths:
    - $CI_PROJECT_DIR/workflow/.nextflow.log
  tags:
    - cluster_node


# This runs the workflow with test data and does a simple
# check for the expected output file
astrocyte_test:
  extends: .astrocyte
  stage: test
  script:
  - astrocyte_cli run "$CI_PROJECT_DIR" --option=q
  - test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
  artifacts:
    paths:
    - $CI_PROJECT_DIR/workflow/.nextflow.log  

# This runs the workflow, opting to use Docker containers.
docker_astrocyte_test:
  stage: test_docker
  variables: 
    config_path : "workflow/configs/"
    config_filename : "biohpc_docker.config"
  script:
  - sed -i "s|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27${config_filename}\x27|" astrocyte_pkg.yml
  - echo "Run astrocyte using dockerhub/docker.io registry pulls"
  - nextflow -C ./${config_path}/${config_filename} config -flat
  - astrocyte_cli run "$CI_PROJECT_DIR" --option=q
  - test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
  tags:
    - cluster_node

cache_docker_image:
  stage: cache_docker
  script:
  - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY
  - echo "Pull Docker image from the docker.io registry, re-tag, and push to our GitLab"
  - docker
  - echo "Need to know what the docker image is ahead of time"
 
singularity_astrocyte_test:
  stage: test_singularity
  script:
  # Note the biohpc_singularity.config replacement.
  - sed -i 's|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27biohpc_singularity.config\x27|' astrocyte_pkg.yml
  - echo "Run astrocyte using singularity with dockerhub/docker.io registry pulls"
  - astrocyte_cli run "$CI_PROJECT_DIR" --option=q
  - test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"

cache_singularity_image:
  stage: cache_singularity
  script:
  - echo "Pull from our gitlab OCI registry using singularity and save as SIF on the cluster"

# This verifies we can install the shiny vizapp dependencies
# and start the vizapp running.
astrocyte_shiny:
  stage: test
  script:
  - astrocyte_cli shiny-prepare "$CI_PROJECT_DIR"
  - 'timeout 10 astrocyte_cli shiny "$CI_PROJECT_DIR" &'
  - 'SHINY_PID=$!'
  - sleep 5
  - unset http_proxy
  - unset all_proxy
  - wget "http://127.0.0.1:8123"