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.gitlab-ci.yml 9.47 KiB 

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/"
  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

.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 "output dir - " $OUTPUT_DIR

      - source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
      - pip install coverage
      - python3 -V  # Print out python version for debugging
      - mkdir $PACKAGES_DIR
      - mkdir -p $OUTPUT_DIR
      - git clone "https://nouser:$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:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing:$coordinator:$coordinator_tests
      - echo "pythonpath - " $PYTHONPATH

      - ls $PACKAGES_DIR

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

  script:
    - cd $CI_PROJECT_DIR/tests/integration/partial/
    - python3 -m coverage run run_test_suite.py $CI_PROJECT_DIR/test_reports
    - 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:
    when: always
    paths:
      - $CI_PROJECT_DIR/coverage
      - $CI_PROJECT_DIR/test_reports
    reports:
      junit: report.xml
    expire_in: 10 days

half_fat_epi_tests:
  when: manual
  stage: half-fat
  extends: .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
      - $CI_PROJECT_DIR/test_reports
    expire_in: 10 days

full_fat_depo:
  when: manual
  stage: full-fat
  extends: .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
      --test_report_dir $CI_PROJECT_DIR/test_reports
      --run_date_type $FULL_FAT_RUN_DATE
      --custom_run_date $CUSTOM_RUN_DATE

  after_script:
    - >
      if [[ "$FULL_FAT_COPY_OUTPUT" == "true" ]];
      then
      date=$(date '+%Y-%m-%d-%H%M');
      mkdir ${TEST_WORKSPACE_DIR}/integration/full/${date};
      cp -r $OUTPUT_DIR/* ${TEST_WORKSPACE_DIR}/integration/full/${date};
      fi

  artifacts:
    paths:
      - $CI_PROJECT_DIR/coverage
      - $CI_PROJECT_DIR/test_reports
    expire_in: 10 days

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

      python3 full_test_env_suit.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

  after_script:
    - >
      if [[ "$FULL_FAT_COPY_OUTPUT" == "true" ]];
      then
      date=$(date '+%Y-%m-%d-%H%M');
      mkdir ${TEST_WORKSPACE_DIR}/integration/full/${date};
      cp -r $OUTPUT_DIR/* ${TEST_WORKSPACE_DIR}/integration/full/${date};
      fi

  artifacts:
    when: on_failure
    paths:
      - $OUTPUT_DIR/*/log.txt
      - $OUTPUT_DIR/*.txt
    expire_in: 10 days

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

      python3 full_test_survey.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

  after_script:
    - >
      if [[ "$FULL_FAT_COPY_OUTPUT" == "true" ]];
      then
      date=$(date '+%Y-%m-%d-%H%M');
      mkdir ${TEST_WORKSPACE_DIR}/integration/full/${date};
      cp -r $OUTPUT_DIR/* ${TEST_WORKSPACE_DIR}/integration/full/${date};
      fi

  artifacts:
    when: on_failure
    paths:
      - $OUTPUT_DIR/*/log.txt
      - $OUTPUT_DIR/*.txt
    expire_in: 10 days

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

      python3 full_test_advisory.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

  after_script:
    - >
      if [[ "$FULL_FAT_COPY_OUTPUT" == "true" ]];
      then
      date=$(date '+%Y-%m-%d-%H%M');
      mkdir ${TEST_WORKSPACE_DIR}/integration/full/${date};
      cp -r $OUTPUT_DIR/* ${TEST_WORKSPACE_DIR}/integration/full/${date};
      fi

  artifacts:
    when: on_failure
    paths:
      - $OUTPUT_DIR/*/log.txt
      - $OUTPUT_DIR/*.txt
    expire_in: 10 days

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

      python3 full_test_epi.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

  after_script:
    - >
      if [[ "$FULL_FAT_COPY_OUTPUT" == "true" ]];
      then
      date=$(date '+%Y-%m-%d-%H%M');
      mkdir ${TEST_WORKSPACE_DIR}/integration/full/${date};
      cp -r $OUTPUT_DIR/* ${TEST_WORKSPACE_DIR}/integration/full/${date};
      fi

  artifacts:
    when: on_failure
    paths:
      - $OUTPUT_DIR/*/log.txt
      - $OUTPUT_DIR/*.txt
    expire_in: 10 days