adding run tests shell script

.gitlab-ci.yml

@@ -36,21 +36,21 @@ stages:
       - source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
       - pip install coverage
       - pwd
-      - 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:$coordinator_tests
+#      - flagdir=$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 $PYTHONPATH
-      - CI_PYTHON_PATH=$PYTHONPATH
-      - ls ../
+#      - CI_PYTHON_PATH=$PYTHONPATH
+#      - ls ../
 
 #.full_fat_before_script:
 #  before_script:
@@ -116,15 +116,15 @@ half_fat_epi_tests:
       - $CI_PROJECT_DIR/coverage
     expire_in: 30 days
 
-manual_job:
+full_fat_tests:
   stage: full-fat
   extends: .half_fat_before_script
   image: lb584/ews_coordinator:latest
   tags: ["ewas-production"]
   script:
-    - export PYTHONPATH="$CI_PYTHON_PATH"
+#    - export PYTHONPATH="$CI_PYTHON_PATH"
     - echo $PYTHONPATH
-    - echo "this is a manual jobb"
+    - 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_*

configs/docker/build/Dockerfile

@@ -39,4 +39,21 @@ ARG GID=1008
 RUN groupadd -g $GID $GNAME
 RUN useradd -m -u $UID -g $GID -o -s /bin/bash $UNAME
 USER ewsmanager
+
+#get the pythonpath ready to point at the pipeline code, which will get mounted at runtime
+ENV CODE_DIR="/storage/app/EWS_prod/code/"
+ENV flagdir=$CODE_DIR/flagdir
+ENV epimodel=$CODE_DIR/epimodel
+ENV advisory=$CODE_DIR/advisory_builder
+ENV met_processing=$CODE_DIR/met_extractor_v2/met_data_extraction
+ENV met_processor=$CODE_DIR/environmental_suitability/environmental_suitability
+ENV plotting=$CODE_DIR/plotting/plotting
+ENV post_processing=$CODE_DIR/post_processing/ews_postprocessing
+ENV source_gen=$CODE_DIR/source_gen
+ENV coordinator=$CODE_DIR/coordinator/coordinator
+ENV coordinator_tests=$CODE_DIR/coordinator/tests
+ENV PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing:$coordinator:$coordinator_tests
+
+RUN echo $PYTHONPATH
+
 WORKDIR /home/ewsmanager