diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 6e9f1048c38e9fde4bdd9d4b09a3867bf512d31a..9fb81097448cb4585a02219b221f71978353f7db 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -37,9 +37,14 @@ stages: .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 - - echo $PACKAGES_DIR - 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" $PACKAGES_DIR/source_gen @@ -61,7 +66,6 @@ stages: - coordinator=$CI_PROJECT_DIR/coordinator - coordinator_tests=$CI_PROJECT_DIR/tests - export PYTHONPATH=$PYTHONPATH:$coordinator:$coordinator_tests - - echo $PYTHONPATH - ls $PACKAGES_DIR - source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/ @@ -131,7 +135,7 @@ half_fat_epi_tests: - $CI_PROJECT_DIR/coverage expire_in: 10 days -full_fat_tests: +full_fat_depo: when: manual stage: full-fat extends: .half_fat_before_script @@ -139,35 +143,8 @@ full_fat_tests: tags: ["ewas-production"] script: - > - - echo $FULL_FAT_RUN_DATE - - echo $CUSTOM_RUN_DATE - - #echo $PYTHONPATH - - #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_* - - #mkdir -p $OUTPUT_DIR/deposition_123445 - - #touch $OUTPUT_DIR/deposition_123445/log.txt - - #echo "stuff" > $OUTPUT_DIR/deposition_123445/log.txt - - #mkdir $OUTPUT_DIR/survey_123445 - - #touch $OUTPUT_DIR/survey_123445/log.txt - - #echo "stuff2" > $OUTPUT_DIR/survey_123445/log.txt - - #echo $TEST_WORKSPACE_DIR - python3 full_test_deposition.py --config /storage/app/EWS_prod/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json --outdir $OUTPUT_DIR diff --git a/configs/docker/run/runDockerEWS.sh b/configs/docker/run/runDockerEWS.sh index 3fd000dd5583571d20eb68d01dd9031b6eba0598..9e7612251e622d3949bcd1c75557ca7fa2cfc7fa 100755 --- a/configs/docker/run/runDockerEWS.sh +++ b/configs/docker/run/runDockerEWS.sh @@ -1,7 +1,7 @@ #!/bin/bash set -e -#upload='--noupload' # default +upload='--noupload' # default rundate=$(date '+%Y%m%d') # default today SHORT=p:,c:,s:,h diff --git a/tests/integration/full/full_test_deposition.py b/tests/integration/full/full_test_deposition.py index 626ddda4c4a12a702334f0003a076618bd7232d4..8f06e5ad6a31265c8e82790d59545a990062f32a 100644 --- a/tests/integration/full/full_test_deposition.py +++ b/tests/integration/full/full_test_deposition.py @@ -10,7 +10,7 @@ from integration.partial.integration_test_utils import IntegrationTestUtils class TestFullDeposition(unittest.TestCase): TEST_OUT_PATH: str = "not_set" - TEST_START_DATE: str = '20230126' + TEST_START_DATE: str = 'NOT_SET' TEST_JOB_DIR: str = "DEPOSITION_" + TEST_START_DATE