trying to get full integrations test working via runner

.gitlab-ci.yml

@@ -52,26 +52,26 @@ stages:
       - CI_PYTHON_PATH=$PYTHONPATH
       - ls ../
 
-.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
+#.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
@@ -122,10 +122,11 @@ manual_job:
   image: lb584/ews_coordinator:latest
   tags: ["ewas-production"]
   script:
-    - cd /storage/app/EWS_prod/code/coordinator/tests/integration/full/
+    - export PYTHONPATH="$CI_PYTHON_PATH"
     - echo $PYTHONPATH
     - echo "this is a manual jobb"
+    - cd $CI_PROJECT_DIR/tests/integration/full/
     - ls
-    - rm /storage/app/EWS_prod/regions/EastAfrica/workspace/DEPOSITION_20230126/STATUS_*
+#    - 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