#!/bin/bash      

# This^^ command sets bash, in the '/bin' directory, as the default shell for executing commands in this file. Check bash location with: $ which bash                                                                                                                                                                             

. /YOUR-PATH-TO-TOOL/qc-env/bin/activate

# Schema definitions:
ROUND='ISIMIP2b'
DATATYPE='OutputData'
SECTOR=‘water_global’

# Define working directories:
UNCHECKED_DIR=/YOUR-PATH/TO/DOWNLOADED-FILES
CHECKED_DIR=/YOUR-PATH/TO/PROCESSED-FILES
LOG_DIR=/YOUR-PATH/TO/LOG-FILES
echo $UNCHECKED_DIR
echo $CHECKED_DIR
echo $LOG_DIR

# Uncomment to only show the working directories:                                                                                                                            
#exit                                                                                                                                                                                          

# Create working directories if needed:
[ ! -d $CHECKED_DIR ] && mkdir -p $CHECKED_DIR
[ ! -d $LOG_DIR ] && mkdir -p $LOG_DIR

# Additional definitions for options
CHECKONE=check_time_dimension # check_variable                                                                                              
PROTOCOL_LOC=/YOUR-PATH/qc-env/isimip-protocol-2
VARNAME=csoil

# Command line:
isimip-qc $ROUND/$DATATYPE/$SECTOR/  \
    -f \
    --include $VARNAME \
    --log-level=INFO \
    --log-path=$LOG_DIR \
    --unchecked-path=$UNCHECKED_DIR \
    --checked-path=$CHECKED_DIR \

# Other options:
#   --check $CHECKONE                                                                                                                                                                         
#   --protocol-location=$PROTOCOL_LOC \                                                                                                                                                       
#   --skip-time-span-check \
#   --fix --move # --copy                                                                                                                                                                   
#   --fix --fix-datamodel=cdo —copy
#   --minmax

# NOTE: the ‘—fix-datamodel=cdo’ option also fixes warnings on data model found using NCCOPY or CDO (this can be slow).                                       

# NOTE: I store this script as an executable ‘*.sh’ file (-rwxr-xr-x) at ‘/YOUR-PATH-TO-TOOL/qc-env/’