.gitlab-ci.yml

# Change pip's cache directory to be inside the project directory since we can
# only cache local items.
variables:
  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
  PACKAGES_DIR: "$CI_PROJECT_DIR/packages/"
  CI_PYTHON_PATH: "NOT_SET"
  FULL_FAT_RUN_DATE:
    value: "default"
    options:
      - "default"
      - "today"
      - "yesterday"
      - "custom"
    description: "Full-fat tests will pull data from the deployment environment. For robustness, the default option is a
    pre-selected date we know works. Select \"today\" or \"yesterday\" to test with recent live data. If \"custom\" is 
    selected, manually enter the key value pair using the format in this example: CUSTOM_RUN_DATE 20230115"

  CUSTOM_RUN_DATE: "NOT_SET"

# Pip's cache doesn't store the python packages
# https://pip.pypa.io/en/stable/reference/pip_install/#caching
#
# If you want to also cache the installed packages, you have to install
# them in a virtualenv and cache it as well.
cache:
  paths:
    - .cache/pip
    - venv/

stages:
  - half-fat
  - full-fat

.half_fat_before_script:
  before_script:
      - python3 -V  # Print out python version for debugging
      - echo $PACKAGES_DIR
      - mkdir $PACKAGES_DIR
      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-source-generation.git" $PACKAGES_DIR/source_gen
      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_plotting.git" $PACKAGES_DIR/plotting
      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/flagdir.git" $PACKAGES_DIR/flagdir
      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-epimodel.git" $PACKAGES_DIR/epimodel
      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-advisory-builder.git" $PACKAGES_DIR/advisory_builder
      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_environmental_suitability_v2.git" $PACKAGES_DIR/environmental_suitability
      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-postprocessing.git" $PACKAGES_DIR/post_processing
      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_met_data_extraction.git" $PACKAGES_DIR/met_extractor_v2
      - ls $PACKAGES_DIR
      - source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
      - pip install coverage

#.full_fat_before_script:
#  before_script:
#      - source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
#      - pip install coverage
#      - pwd
#      - CODE_DIR="/storage/app/EWS_prod/code/"
#      - flagdir=$CODE_DIR/flagdir
#      - epimodel=$CODE_DIR/epimodel
#      - advisory=$CODE_DIR/advisory_builder
#      - met_processing=$CODE_DIR/met_extractor_v2/met_data_extraction
#      - met_processor=$CODE_DIR/environmental_suitability/environmental_suitability
#      - plotting=$CODE_DIR/plotting/plotting
#      - post_processing=$CODE_DIR/post_processing/ews_postprocessing
#      - source_gen=$CODE_DIR/source_gen
#      - coordinator=$CODE_DIR/coordinator/coordinator
#      - coordinator_tests=$CODE_DIR/coordinator/tests
#      - export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing:$coordinator:$coordinator_tests
#
#      - echo $PYTHONPATH
#      - CI_PYTHON_PATH=$PYTHONPATH

half_fat_tests:
  when: manual
  stage: half-fat
  extends: .half_fat_before_script
  image: lb584/ews_coordinator:latest

  script:
    - export PYTHONPATH="$CI_PYTHON_PATH"
    - echo $FULL_FAT_RUN_DATE
#    - echo $PYTHONPATH
    - cd $CI_PROJECT_DIR/tests/unit/coordinator/
    - python3 -m coverage run -m unittest *
    - python -m coverage report
    - python -m coverage html -d $CI_PROJECT_DIR/coverage
    - cd $CI_PROJECT_DIR/tests/integration/partial/
    - python3 -m coverage run -m unittest test_advisory.py
    - python3 -m coverage run -m unittest test_deposition.py
    - python3 -m coverage run -m unittest test_env_suit.py
    - python3 -m coverage run -m unittest test_survey.py
    - python3 -m coverage report
    - python3 -m coverage html -d $CI_PROJECT_DIR/coverage
    - ls
  artifacts:
    paths:
      - $CI_PROJECT_DIR/coverage
    expire_in: 30 days

half_fat_epi_tests:
  when: manual
  stage: half-fat
  extends: .half_fat_before_script
  image: lb584/ews_coordinator:latest

  script:
    - cd $CI_PROJECT_DIR/tests/integration/partial/
    - python3 -m coverage run -m unittest test_epi.py
    - python3 -m coverage report
    - python3 -m coverage html -d $CI_PROJECT_DIR/coverage
    - ls
  artifacts:
    paths:
      - $CI_PROJECT_DIR/coverage
    expire_in: 30 days

full_fat_tests:
  when: manual
  stage: full-fat
  extends: .half_fat_before_script
  image: lb584/ews_coordinator:latest
  tags: ["ewas-production"]
  script:
    - >
      echo $FULL_FAT_RUN_DATE
    
      echo $CUSTOM_RUN_DATE

      echo "this is a manual job"
    
      cd $CI_PROJECT_DIR/tests/integration/full/

      ls
      
      #rm /storage/app/EWS_prod/regions/EastAfrica/workspace/DEPOSITION_20230126/STATUS_*
    
      python3 full_test_deposition.py 
      --config /storage/app/EWS_prod/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json
      --outdir /storage/app/EWS_prod/regions/EastAfrica/workspace/
      --email_cred /storage/app/EWS_prod/envs/credentials/Cred_gmail.json
      --run_date_type $FULL_FAT_RUN_DATE
      --custom_run_date $CUSTOM_RUN_DATE