Generalization

Changes:

• Adapted plugin to work with CMORized data retrieved from the databrowser
• Input parameters now retrieved from JSON file
• Added regional selection and changed selection of time covering dates
• Adapted test data, production and functional tests
• Added additional logs/output
• Refactored some code to follow DRY and for better readability

@k202187 Could you please have a look?

src/pet/calculate_pet.sh

@@ -47,6 +47,9 @@ START_YEAR=$(cut -c 1-4 <<< ${START_DATE})		# start year
 END_YEAR=$(cut -c 1-4 <<< ${END_DATE})			# end year
 REGION=$(jq '.region' $1 | sed 's/\"//g')		# region (W,E,S,N)
 
+### DEBUG MODE
+DEBUG=$(jq '.debug' $1 | sed 's/\"//g')
+
 ### CONSTANTS ###
 MAXPP=30
 
@@ -67,7 +70,8 @@ echo 'System Parameters:'
 echo '------------------'
 echo 'CACHE_DIR: '${TMP_DIR}
 echo 'OUTPUT_DIR: '${OUTPUT_DIR}
-echo 'ALTITUDE FILE:'${ALTI_FILE}
+echo 'ALTITUDE FILE: '${ALTI_FILE}
+echo 'DEBUG: '${DEBUG}
 
 echo ''
 echo 'Input Parameters:'
@@ -110,38 +114,37 @@ echo ''
 echo '### Starting checks'
 echo '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
 ### CHECKING IF LIST OG DATA FILES CONTAINS ALL VARAIBLES NEEDED
-echo 'Checking availability of all necessary variables...'
+log_debug 'Checking availability of all necessary variables...'
 
 VARIABLES=$(jq '.files | keys | .[]' $1)
 for VAR in ${VARIABLES[@]}; do
 	if [ $(jq ".files.$VAR | length " $1) > 0 ]; then
-		echo ${VAR//\"}'...OK'
+		log_debug "${VAR//\"}...OK"
 	else
-		echo 'ERROR: No data for '${VAR}' available!'
-	        echo 'Please select a dataset containg all necessary varaiables ('${VARIABLES}')!'
+		log_error 'ERROR: No data for '${VAR}' available!'
+	  log_error 'Please select a dataset containg all necessary varaiables ('${VARIABLES}')!'
 		exit 1
 	fi
 done
 echo ''
 
 ### PREPARING DATA (MERGING FILES; SELECTION TIME PERIOD) ###
-echo 'Preparing files for checks...'
+log_debug 'Preparing files for checks...'
 for VAR in ${VARIABLES[@]}; do
 
   # requirement: allfiles for a specific variable are located within one directory
   VAR_FILES=$(jq ".files.${VAR//\"}[]" $1 | sed 's/\"//g' | grep '.nc')
   TMP_FILE=${TMP_DIR}'/'${VAR//\"}'_'${START_YEAR}'-'${END_YEAR}'.nc'
-  echo '---'${VAR//\"}'---'
 
   # merge files and select time period
-  echo 'Selecting time period...'
+  log_debug 'Selecting time period...'
   TIME_FILE=${TMP_DIR}'/'${VAR//\"}'_timeperiod.nc'
   if [ ! ${START_DATE} == null ] && [ ! ${END_DATE} == null ]; then
       cdo seldate,${START_DATE}'T00:00:00',${END_DATE}'T00:00:00' -mergetime ${VAR_FILES} ${TIME_FILE}
   fi
 
   if [ ! -f ${TIME_FILE} ]; then
-      echo 'Error selecting time and creating: '${TIME_FILE}
+      log_error 'Error selecting time and creating: '${TIME_FILE}
       exit 1
   else
       mv ${TIME_FILE} ${TMP_FILE}
@@ -151,11 +154,11 @@ for VAR in ${VARIABLES[@]}; do
   if [ ! ${REGION} == null ]; then
       REGION_FILE=${TMP_DIR}'/'${VAR//\"}'_region.nc'
 
-      echo 'Selecting region...'
+      log_debug 'Selecting region...'
       cdo -sellonlatbox,${REGION} ${TMP_FILE} ${REGION_FILE}
 
       if [ ! -f ${REGION_FILE} ]; then
-          echo 'Error selecting region and creating: '${REGION_FILE}
+          log_error "Error selecting region and creating: ${REGION_FILE}"
           exit 1
       else
           mv ${REGION_FILE} ${TMP_FILE}
@@ -166,23 +169,23 @@ done
 
 
 ### CHECKING VARIABLE NAME; HEIGHT AND UNIT
-echo 'Checking variable names, heights and units...'
+log_debug 'Checking variable names, heights and units...'
 for VAR in ${VARIABLES[@]}; do
   VAR_FILE_NAME=${TMP_DIR}'/'${VAR//\"}'_'${START_YEAR}'-'${END_YEAR}'.nc'
 
   X_SIZE=$(get_x_size ${VAR_FILE_NAME})
   Y_SIZE=$(get_y_size ${VAR_FILE_NAME})
-  echo 'Grid info: '${X_SIZE}'x'${Y_SIZE}
+  log_debug "Grid info: ${X_SIZE}x${Y_SIZE}"
 
   # grepping unit from attribute table of data file, check and convert if needed
   VAR_UNIT=$(cdo partab ${VAR_FILE_NAME} | grep "units" | grep -o -P '(?<=").*(?=")')
   VAR_NAME=$(cdo codetab ${VAR_FILE_NAME} | awk '{print $2;}')  ### Error if there are multiple variables -> needs to be tested
   VAR_HEIGHT=$(get_height ${VAR_FILE_NAME})
 
-  echo "${VAR} [${VAR_UNIT}], HEIGHT: ${VAR_HEIGHT}M"
+  log_debug "${VAR} [${VAR_UNIT}], HEIGHT: ${VAR_HEIGHT}M"
 
   if [ ! ${VAR_NAME} == ${VAR//\"} ]; then
-    echo "ERROR: Variable name in data (${VAR_NAME}) doesn't match variable name in data file name (${VAR})"
+    log_error "ERROR: Variable name in data (${VAR_NAME}) doesn't match variable name in data file name (${VAR})"
   fi
 
   # converting units if neccessary
@@ -202,7 +205,7 @@ case "${ALTITUDE_UNIT}" in
         cdo -setmissval,nan -select,name=${ALTITUDE_NAME} ${ALTI_FILE} ${TMP_ALT_FILE}
         ;;
       *)
-        echo "ERROR: Altitude unit must be 'm'"
+        log_error "ERROR: Altitude unit must be 'm'"
         exit 1
         ;;
 esac
@@ -272,7 +275,7 @@ for ((YEAR=$START_YEAR;YEAR<END_YEAR+1;YEAR+=1)); do
     MYEXP_FILE=$(dirname "$0")/helper/myexpr
     cdo exprf,${MYEXP_FILE} ${INPUT_FILE} ${TMP_DIR_YEAR}'/res_'${YEAR}'.nc'
     if [ ! -f ${TMP_DIR_YEAR}'/res_'${YEAR}'.nc' ]; then
-        echo 'Error create: '${TMP_DIR_YEAR}'/res_'${YEAR}'.nc'
+        log_error 'Error create: '${TMP_DIR_YEAR}'/res_'${YEAR}'.nc'
         exit 1
     fi
     ### to-do replace in myexpr: _var_tmax=TMAX_2M; with global variable names ???