arcade.sh

#!/bin/bash

case ${SIMULATION_TYPE} in
    AWS)
        # Set input and output file paths
        INPUT_FILE_PATH="${BATCH_WORKING_URL}inputs/"
        OUTPUT_FILE_PATH="${BATCH_WORKING_URL}outputs/"
        INIT_FILE_PATH="${BATCH_WORKING_URL}inits/"

        # Get copy of the input file
        INPUT_FILE_NAME="${FILE_SET_NAME}_${AWS_BATCH_JOB_ARRAY_INDEX:-0}.xml"
        aws s3 cp $INPUT_FILE_PATH$INPUT_FILE_NAME input/input.xml

        # Get copies of .CELL initialization files (if they exist)
        INIT_CELL_FILES=$(aws s3 sync ${INIT_FILE_PATH} init/ --exclude="*" --include="*.CELLS.json" --dryrun)
        if test -n "$INIT_CELL_FILES"; then
            LOAD_CELLS=true
            aws s3 cp $INIT_FILE_PATH init/ --recursive --exclude="*" --include="*.CELLS.json"
        fi

        # Get copies of .LOCATION initialization files (if they exist)
        INIT_LOCATION_FILES=$(aws s3 sync ${INIT_FILE_PATH} init/ --exclude="*" --include="*.LOCATIONS.json" --dryrun)
        if test -n "$INIT_LOCATION_FILES"; then
            LOAD_LOCATIONS=true
            aws s3 cp $INIT_FILE_PATH init/ --recursive --exclude="*" --include="*.LOCATIONS.json"
        fi
    ;;
    LOCAL)
        # Set input, output, and init file paths
        INPUT_FILE_PATH="/mnt/inputs/"
        OUTPUT_FILE_PATH="/mnt/outputs/"
        INIT_FILE_PATH="/mnt/inits/"

        # Get copy of the input file
        INPUT_FILE_NAME="${FILE_SET_NAME}_${JOB_ARRAY_INDEX}.xml"
        cp $INPUT_FILE_PATH$INPUT_FILE_NAME input/input.xml

        # Get copies of .CELL initialization files (if they exist)
        INIT_CELL_FILES=$(find ${INIT_FILE_PATH} -name '*.CELLS.json' -print -quit)
        if test -n "$INIT_CELL_FILES"; then
            LOAD_CELLS=true
            cp ${INIT_FILE_PATH}*.CELLS.json init/
        fi

        # Get copies of .LOCATION initialization files (if they exist)
        INIT_LOCATION_FILES=$(find ${INIT_FILE_PATH} -name '*.LOCATIONS.json' -print -quit)
        if test -n "$INIT_LOCATION_FILES"; then
            LOAD_LOCATIONS=true
            cp ${INIT_FILE_PATH}*.LOCATIONS.json init/
        fi
    ;;
esac

# Set load command flags.
LOAD_COMMAND=""
if [ "$LOAD_CELLS" = true ] || [ "$LOAD_LOCATIONS" = true ]; then
    LOAD_COMMAND+="--loadpath init/${FILE_SET_NAME}_[#]"
fi
if [ "$LOAD_CELLS" = true ]; then
    LOAD_COMMAND+=" --cells"
fi
if [ "$LOAD_LOCATIONS" = true ]; then
    LOAD_COMMAND+=" --locations"
fi

# Run the jar
java -jar arcade.jar potts input/input.xml output/ $LOAD_COMMAND
EXIT_CODE=$?

# Save output files
if [ $EXIT_CODE -eq 0 ]
then
    cd output/

    FILE_REGEX='([A-Za-z0-9\_]+_[0-9]{4})_([0-9]{6})\.([A-Za-z]+)\.json'

    PREFIXES=()
    SUFFIXES=()

    for f in *.json; do
        if [[ $f =~ $FILE_REGEX ]]; then
            PREFIXES+=(${BASH_REMATCH[1]})
            SUFFIXES+=(${BASH_REMATCH[3]})
        fi
    done

    UNIQUE_PREFIXES=($(printf "%s\n" "${PREFIXES[@]}" | sort -u | tr '\n' ' '))
    UNIQUE_SUFFIXES=($(printf "%s\n" "${SUFFIXES[@]}" | sort -u | tr '\n' ' '))

    for prefix in "${UNIQUE_PREFIXES[@]}"; do
        for suffix in "${UNIQUE_SUFFIXES[@]}"; do
            echo $prefix $suffix
            mkdir $prefix.$suffix
            mv $prefix*.$suffix.json $prefix.$suffix
            cd $prefix.$suffix
            COPYFILE_DISABLE=1 tar cJf ../$prefix.$suffix.tar.xz *.json
            cd ..
        done
    done

    case ${SIMULATION_TYPE} in
        AWS)
            aws s3 cp . $OUTPUT_FILE_PATH --recursive --exclude "*" --include "*.tar.xz"
            aws s3 cp . $OUTPUT_FILE_PATH --recursive --exclude "*" --include "*.json" --exclude "*/*"
        ;;
        LOCAL)
            mkdir -p $OUTPUT_FILE_PATH
            cp *.tar.xz $OUTPUT_FILE_PATH
            cp *.json $OUTPUT_FILE_PATH
        ;;
    esac
fi