modifying docker launch script to pass through optional args from command line

configs/docker/run/runDockerEWS.sh

 #!/bin/bash
 set -e
 
+upload=''
+islive=''
+clearup=''
 component='not_set'
 config='/storage/app/EWS_prod/regions/EastAfrica/resources/coordinator/configs/config_EastAfrica_fc_live.json' # default
 rundate=$(date '+%Y%m%d') # default today
-optionalArgs=""
 
 
 SHORT=p:c:s:h
@@ -29,15 +31,15 @@ do
       shift 2
       ;;
     --noupload )
-      optionalArgs="$optionalArgs --noupload"
+      upload="--noupload"
       shift 2;
       ;;
     --islive )
-      optionalArgs="$optionalArgs --islive"
+      islive="--islive"
       shift 2;
       ;;
     --clearup )
-      optionalArgs="$optionalArgs --clearup"
+      clearup="--clearup"
       shift 2;
       ;;
     -h | --help)
@@ -58,7 +60,7 @@ done
 
 function run_coordinator() {
     printf "component: %s\nconfig: %s\nrundate: %s\n" "$component" "$config" "$rundate"
-    printf "optional args:\n%s\n" "$optionalArgs"
+    printf "optional args:\n%s\n" "$upload $islive $clearup"
     docker container ls;
     docker exec \
     ews_runner \
@@ -66,7 +68,9 @@ function run_coordinator() {
     -p "$component" \
     -c "$config" \
     -s "$rundate" \
-    "$optionalArgs"
+    $upload \
+    $islive \
+    $clearup
 }
 
 run_coordinator

tests/integration/full/run_tests.sh

@@ -4,7 +4,8 @@
 
 source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
 
-PACKAGES_DIR="../../../../" # assumes run from the tests/integration/partial dir
+# assumes run from the tests/integration/full dir, and that all necessary packages are checked out alongside
+PACKAGES_DIR="../../../../"
 
 flagdir=$PACKAGES_DIR/flagdir
 epimodel=$PACKAGES_DIR/epimodel

tests/integration/partial/run_test_suite.sh

@@ -4,7 +4,8 @@
 
 source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
 
-PACKAGES_DIR="../../../../" # assumes run from the tests/integration/partial dir
+# assumes run from the tests/integration/partial dir, and that all necessary packages are checked out alongside
+PACKAGES_DIR="../../../../"
 
 flagdir=$PACKAGES_DIR/flagdir
 epimodel=$PACKAGES_DIR/epimodel
@@ -22,8 +23,3 @@ export PYTHONPATH=$PYTHONPATH:$flagdir:$epimodel:$advisory:$met_processing:$met_
 echo $PYTHONPATH
 
 python3 -m coverage run run_test_suite.py
-#python3 -m unittest test_advisory.py
-#python3 -m unittest test_deposition.py
-#python3 -m unittest test_env_suit.py
-#python3 -m unittest test_epi.py
-#python3 -m unittest test_survey.py