Amended testing scripts, param.bash envs and how run_proc is called. #66

Author: Hatim Chahout

tests/run_test_setup.bash

@@ -23,18 +23,35 @@ function setup_test_env() {
   echo "export MSKPATH=$TMP_DIR/MESH_MASK_DIR" >> "param.bash"
   echo "export CDFPATH=$TMP_DIR/CDFTOOLS_DIR/bin" >> "param.bash"
   echo "export NMLPATH=$TMP_DIR/nam_cdf_names" >> "param.bash"
+  echo "export EXEPATH=$TMP_DIR" >> "param.bash"
+  echo "export SCRPATH=$TMP_DIR/SCRIPT" >> "param.bash"
+  echo "export DATPATH=$TMP_DIR/DATA" >> "param.bash"
   echo "export OBSPATH=$TMP_DIR/OBS_PATH_DIR" >> "param.bash"
+  echo "export OBS_MESH=\${OBSPATH}/obs_mesh.nc" >> "param.bash"
+  echo "export OBS_ABS_SAL=\${OBSPATH}/obs_abs_sal.nc" >> "param.bash"
+  echo "export OBS_CON_TEM=\${OBSPATH}/obs_con_tem.nc" >> "param.bash"
+  # echo "export runOBS=1" >> "param.bash"
+
+  echo "Contents of param.bash:"
+  cat param.bash
+
+  # Source the param.bash file to set environment variables
+  source "param.bash"
 
   # Create the necessary directories and files
-  mkdir -p "$TMP_DIR/CDFTOOLS_DIR/bin"
-  mkdir -p "$TMP_DIR/MESH_MASK_DIR"
-  mkdir -p "$TMP_DIR/OBS_PATH_DIR"
-  touch "$TMP_DIR/CDFTOOLS_DIR/bin/cdf_tool"
-  touch "$TMP_DIR/MESH_MASK_DIR/mesh_mask.nc"
-  touch "$TMP_DIR/MESH_MASK_DIR/bathy.nc"
-  touch "$TMP_DIR/nam_cdf_names"
-  touch "$TMP_DIR/OBS_PATH_DIR/obs_abs_sal.nc"
-  touch "$TMP_DIR/OBS_PATH_DIR/obs_con_tem.nc"
+  mkdir -p "$MSKPATH"
+  mkdir -p "$CDFPATH"
+  mkdir -p "$SCRPATH"
+  mkdir -p "$DATPATH"
+  mkdir -p "$OBSPATH"
+
+  touch "$NMLPATH"
+  touch "$CDFPATH/cdf_tool"
+  touch "$MSKPATH/mesh_mask.nc"
+  touch "$MSKPATH/bathy.nc"
+  touch "$OBS_MESH"
+  touch "$OBS_ABS_SAL"
+  touch "$OBS_CON_TEM"
 }
 
 # Function to clean up the temporary environment after a test

tests/test_valid_run.bash

@@ -11,8 +11,9 @@ setup_test_env
 
 echo "Changing to temporary directory..."
 cd "$TMP_DIR"
+
 echo "Running the process with valid parameters..."
-bash ./run_proc.bash -B $MSKPATH/bathy.nc -C 1 $MSKPATH/mesh_mask.nc 2020 2020 1m RUNID_TEST > output.txt 2>&1
+source ./run_proc.bash -B bathy.nc -C 1 mesh_mask.nc 2020 2020 1m RUNID_TEST > output.txt 2>&1
 
 if ! grep -q "MOCK SBATCH: --output=.*mk_msks.out /.*/mk_msks.bash" output.txt; then
   echo "Test failed: Expected 'mk_msks.bash' job was not submitted."