#!/bin/bash

# Title:        inSiliCow-run.sh
# Address:	main/run
# Description:  Launch simulations
# Authors:      Olivier MARTIN ( https://orcid.org/0000-0001-7375-2850 )
#               Pierre Blavy
# Contact:      olivier.martin-mosar@inrae.fr
# Date:         2025
# Usage: inSiliCow-run.sh example_xx  [out]
#        example_xx is a folder in examples/
#        out is the output folder, default ./out

clear

#--------------------------------------
#--- Colors for display in terminal ---
#--------------------------------------

# Set Bold High Intensity colors 
R='\033[1;91m'	# Red
B='\033[1;94m'	# Blue
NC='\033[0m' 	# No Color

#Set BIP sound
BIP='\007'

# --- Opening message ---
echo -e ${B}"\n> Launching inSiliCow"${NC}

# -----------------------
# --- Input arguments ---
# -----------------------
#$1 is an example folder that exists in examples
#$2 is the output folder, must exists, default "./out"

if [ "$#" -le 0 ]; then
  echo -e ${B}"\n>> Missing argument"
  echo -e ">> Usage:"${NC}" inSilicow-run example_00 [out]"
  echo -e ${B}"\n>> Aborted\n"${NC}
  exit 1
fi

INPUT_DIR=$(realpath "examples/$1"  ) 
OUTPUT_DIR=$(realpath ${2:-"./out"})
mkdir -p $OUTPUT_DIR


FARMER_LOG=$(realpath "examples/farmer-log.txt"  ) 
SCRIPTS_DIR=$(realpath ./)
SCILAB=$(ls -drt $HOME/* | grep scilab- | tail -1)"/bin/scilab-cli"
INSILICOW=$(realpath ./../insilicow-linux)

CURRENT=`pwd`

# --------------------------
# --- Check things ---------
# --------------------------

#Input does'nt exists => return
if [ ! -d "$INPUT_DIR" ]; then
  echo -e ${BIP}${R}"\n>> Input directory $INPUT_DIR does not exist\n";
  echo -e ">> Aborted\n";
  exit 1;
fi

#Output does'nt exists => return
#if [ ! -d "$OUTPUT_DIR" ]; then
#  echo -e ${BIP}${R}"\n>> Output directory $OUTPUT_DIR does not exist\n";
#  echo -e ">> Aborted\n";
#  exit 1;
#fi

#inSiliCow binary does'nt exists => return
if [ ! -e "$INSILICOW" ]; then
  echo -e ${BIP}${R}"\n>> inSiliCow binary $INSILICOW does not exist\n";
  echo -e ">> Aborted\n";
  exit 1;
fi

# -----------------------
# --- Output ------------
# -----------------------

#Get current date to name output folder 
d=`date "+%Y%m%d_%H%M%S_%N"`
OUT_JOB="$OUTPUT_DIR/job-$d"
ZIP_FILE=$(realpath "$OUTPUT_DIR/simulations-$d.zip" ) 

# ------------------------------
# --- Print input and output ---
# ------------------------------

echo -e ${B}"\n>> Pathways:"
echo -e "     Input:\t$INPUT_DIR";
echo -e "    Output:\t$OUT_JOB";
echo -e "    Scilab:\t$SCILAB";
echo -e " inSiliCow:\t$INSILICOW\n"${NC};


# ---------------------------------
# --- Make output folders ---------
# ---------------------------------
mkdir -p "$OUT_JOB/in";
mkdir -p "$OUT_JOB/out";

# -------------------------------------
# --- check if scilab is responding ---
# -------------------------------------

#check-scilab.sci xxx creates a file called "xxx/scilab_is_ok"
rm -f "$OUTPUT_DIR/scilab_is_ok"

#"$SCILAB" -f "$SCRIPTS_DIR/check-scilab.sci" -nwni -quit -args "$OUTPUT_DIR";

#if [ ! -f "$OUTPUT_DIR/scilab_is_ok" ]; then
#  echo -e ${BIP}${R}"\n>> Scilab is not responding\n";
#  echo -e ">> Aborted\n";
#  exit 0;
#fi

rm "$OUTPUT_DIR/scilab_is_ok"

# --------------------------
# --- Run the jobs ---------
# --------------------------

# --- Track time ---
SECONDS=0;

#Format elapsed time
FormatSeconds () { 
  seconds="$1"
  date -ud @${seconds} +"$(( seconds/3600/24 ))d %Hh %Mm %Ss" \
    | sed -r 's/\b0([0-9])/\1/g; s/\b0(s|m|h|d)//g; s/ +/ /g; s/^ +//; s/ +$//; s/^$/0s/'
}

#copy input to $OUT_JOB/in
cp -r "$INPUT_DIR/"* "$OUT_JOB/in/"
cp "$FARMER_LOG" "$OUT_JOB/in/"

echo -e ${B}"\n>> Starting job $d\n"${NC}

# --------------
# --- explan ---
# --------------

#Create file explan-config.txt with right paths 
cat > "$OUT_JOB/in/explan-config.txt" << EOF
explan{
	IN_CPU          = 4  #number of parallel jobs
	IN_EXPLAN       = $OUT_JOB/in/explan.txt
	OUT_FOLDER      = $OUT_JOB/out/
	IN_FOLDER	= $OUT_JOB/in/
	IN_EXE   	= $INSILICOW
	SCRIPT_FOLDER	= $SCRIPTS_DIR
	OUT_FOLDER	= $OUT_JOB/sim
	IN_SCILAB       = $SCILAB
}
EOF


# Execute R script to launch simulations  
echo -e ${B}"\n>> Starting simulation\n"${NC}
Rscript "$SCRIPTS_DIR/explan2.R" "$OUT_JOB/in/explan-config.txt"


# ZIP

#uncomment the block below to zip output 

#rm -f "$ZIP_FILE"
#echo -e ${B}"\n>> Compress simulation to $ZIP_FILE \n"${NC}
#cd "$OUT_JOB" && \
#zip -rq9 "$ZIP_FILE" ./  -x out/sim_*/log_herd.txt && \
#cd "$CURRENT"  && \
#rm -rf "$OUT_JOB" 


# -----------------------------------
# --- display final message ---------
# -----------------------------------

echo -e ${B}"\n>> Job "$d" done in $(FormatSeconds $SECONDS)${NC}\n"