preprocess.sh

#!/bin/bash
  
#########################################################################
### THIS IS A TEMPLATE FILE. SUBSTITUTE #PATH# WITH THE MODEL EXECUTABLE.
#########################################################################

# arg 1 CANDLE_DATA_DIR
# arg 2 CANDLE_CONFIG

### Path and Name to your CANDLEized model's main Python script###

# e.g. CANDLE_MODEL=graphdrp_preprocess.py
CANDLE_MODEL_SCRIPT=dualgcn_preprocess_improve.py

# Set env if CANDLE_MODEL is not in same directory as this script
IMPROVE_MODEL_DIR=${IMPROVE_MODEL_DIR:-$( dirname -- "$0" )}

# Combine path and name and check if executable exists
CANDLE_MODEL=${IMPROVE_MODEL_DIR}/${CANDLE_MODEL_SCRIPT}
if [ ! -f ${CANDLE_MODEL} ] ; then
	echo No such file ${CANDLE_MODEL}
	exit 404
fi



if [ $# -lt 2 ] ; then
        echo "Illegal number of parameters"
        echo "CANDLE_DATA_DIR PARAMS are required"
        exit -1
fi



if [ $# -eq 2 ] ; then
      
        CANDLE_DATA_DIR=$1 ; shift
        
	# if $2 is a file, then set candle_config
	if [ -f $CANDLE_DATA_DIR/$1 ] ; then
 		CONFIG_FILE=$1 ; shift
        	CMD="python ${CANDLE_MODEL} --config_file ${CONFIG_FILE}"
	else
 		CMD="python ${CANDLE_MODEL} $@"
                echo CMD=\"$CMD\"
        fi

elif [ $# -ge 3 ] ; then 

        CANDLE_DATA_DIR=$1 ; shift

        # if $2 is a file, then set candle_config
        if [ -f $CANDLE_DATA_DIR/$1 ] ; then
		echo "$1 is a file"
                CANDLE_CONFIG=$1 ; shift
                CMD="python ${CANDLE_MODEL} --config_file $CANDLE_CONFIG $@"
                echo "CMD = $CMD $@"

        # else passthrough $@
        else
		echo "$1 is not a file"
                CMD="python ${CANDLE_MODEL} $@"
                echo "CMD = $CMD"

        fi
fi

# Display runtime arguments
echo "using CANDLE_DATA_DIR ${CANDLE_DATA_DIR}"
echo "using CANDLE_CONFIG ${CANDLE_CONFIG}"
echo "running command ${CMD}"

# Set up environmental variables and execute model
# source /opt/conda/bin/activate /usr/local/conda_envs/Paccmann_MCA

IMPROVE_DATA_DIR=${CANDLE_DATA_DIR} CANDLE_DATA_DIR=${CANDLE_DATA_DIR} $CMD