.gitlab-ci.yml

variables:
  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
  PACKAGES_DIR: "$CI_PROJECT_DIR/packages/"
#  OUTPUT_DIR: "$CI_PROJECT_DIR/outputs/"
  OUTPUT_DIR: "/storage/app/EWS_prod/regions/EastAfrica/workspace/"
  TEST_WORKSPACE_DIR: "/storage/app/EWS_prod/regions/EastAfrica/test_workspace/"
  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"

  FULL_FAT_COPY_OUTPUT:
    value: "false"
    options:
      - "true"
      - "false"
    description: "Select \"true\" to make a copy of the full-fat integration test output. Outputs will be copied to the
    production machine at /storage/app/EWS_prod/regions/EastAfrica/test_workspace"

cache:
  paths:
    - .cache/pip
    - venv/

stages:
  - half-fat
  - full-fat

.half_fat_before_script:
  before_script:

      - echo "packages dir - " $PACKAGES_DIR
      - echo "full-fat run date - " $FULL_FAT_RUN_DATE
      - echo "custom full-fat run date - " $CUSTOM_RUN_DATE
      - echo "pythonpath - " $PYTHONPATH

      - python3 -V  # Print out python version for debugging
      - pip install coverage
      - mkdir $PACKAGES_DIR
      - mkdir $OUTPUT_DIR
      - git clone "https://nouser:$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" $PACKAGES_DIR/met_extractor_v2
      - flagdir=$PACKAGES_DIR/flagdir
      - epimodel=$PACKAGES_DIR/epimodel
      - advisory=$PACKAGES_DIR/advisory_builder
      - met_processing=$PACKAGES_DIR/met_extractor_v2/met_data_extraction
      - met_processor=$PACKAGES_DIR/environmental_suitability/environmental_suitability
      - plotting=$PACKAGES_DIR/plotting/plotting
      - post_processing=$PACKAGES_DIR/post_processing/ews_postprocessing
      - source_gen=$PACKAGES_DIR/source_gen
      - coordinator=$CI_PROJECT_DIR/coordinator
      - coordinator_tests=$CI_PROJECT_DIR/tests
      - export PYTHONPATH=$PYTHONPATH:$coordinator:$coordinator_tests

      - ls $PACKAGES_DIR
      - source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/

#.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: 10 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: 10 days

full_fat_depo:
  when: manual
  stage: full-fat
  extends: .half_fat_before_script
  image: lb584/ews_coordinator:latest
  tags: ["ewas-production"]
  script:
    - >
      cd $CI_PROJECT_DIR/tests/integration/full/

      python3 full_test_deposition.py 
      --config /storage/app/EWS_prod/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json
      --outdir $OUTPUT_DIR
      --email_cred /storage/app/EWS_prod/envs/credentials/Cred_gmail.json
      --run_date_type $FULL_FAT_RUN_DATE
      --custom_run_date $CUSTOM_RUN_DATE

      if [[ "$FULL_FAT_COPY_OUTPUT" == "true" ]];
      then
      date=$(date '+%Y-%m-%d-%H%M');
      mkdir ${TEST_WORKSPACE_DIR}/integration/full/${date};
      cp -rv $OUTPUT_DIR/* ${TEST_WORKSPACE_DIR}/integration/full/${date};
      fi
      
  artifacts:
    paths:
      - $OUTPUT_DIR/*/log.txt
    expire_in: 10 days