Merge pull request #8 from JDACS4C-IMPROVE/6-missing-preprocesssh

Added interface script for preprocessing

Author: adpartin

preprocess.sh

@@ -0,0 +1,72 @@
+#!/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=IGTD_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 ${CMD}"
+
+# Set up environmental variables and execute model
+# source /opt/conda/bin/activate /usr/local/conda_envs/Paccmann_MCA
+CANDLE_DATA_DIR=${CANDLE_DATA_DIR} $CMD
+