run

#!/bin/bash
#
#	template based on:  https://github.com/scitran-apps/fsl-bet/blob/master/run
#
#

CONTAINER="[histoQC]"
echo -e "$CONTAINER  Initiated"



###############################################################################
## Built to flywheel-v0 spec.
FLYWHEEL_BASE=/flywheel/v0
OUTPUT_DIR=$FLYWHEEL_BASE/output_temp
input_im_DIR=$FLYWHEEL_BASE/input/input_image
config_DIR=$FLYWHEEL_BASE/input/config
MANIFEST=$FLYWHEEL_BASE/manifest.json
CONFIG_FILE=$FLYWHEEL_BASE/config.json


###############################################################################
## Configure the ENV
export USER=Flywheel

###############################################################################
## Execute the main processes
function jsonValue() {
KEY=$1
num=$2
awk -F"[,:}]" '{for(i=1;i<=NF;i++){if($i~/'$KEY'\042/){print $(i+1)}}}' | tr -d '"' | sed -n ${num}p
}

## get all user configurations
# if [[ -f $CONFIG_FILE ]]; then
#   echo "$CONTAINER  $CONFIG_FILE found. Loading config..."

#   config_fn="$(cat $CONFIG_FILE | jsonValue config_file)"

# else
#   echo "$CONTAINER  $CONFIG_FILE not found. Using default QC pipeline (v2.1)"
#   config_fn=v2.1

# fi


## Find the input files
input_im_file=$(find $input_im_DIR/* -maxdepth 0 -type f -name "*.svs*")
echo "$input_im_file"
file=$(basename "${input_im_file}")
echo "$file"

user_config_file=$(find $config_DIR/* -maxdepth 0 -type f -name "*.ini*")
echo "$user_config_file"
echo "config-file =" $(basename "${user_config_file}")

## If necessary input files are found, run the thing
if [[ -f $input_im_file ]] ; then

  HistoQC_dir=$FLYWHEEL_BASE/HistoQC   # path to install (in Docker container)

  echo "$CONTAINER  Running HistoQC"
  if [[ -f $user_config_file ]]; then
    python3 -m histoqc -c ${user_config_file} -n 3 "${input_im_file}" -o ${OUTPUT_DIR}
  else
    python3 -m histoqc -c v2.1 -n 3 "${input_im_file}" -o ${OUTPUT_DIR}
  fi   

  # move output directories to temp for Flywheel container
  for d in output_temp/* ; do
    if [[ -d ${d} ]] ; then
        echo ${d} 
        mv ${d}/* ./output_temp
        rm -r ${d}
    fi
  done

  # check for results file to check the status
  if test -f /flywheel/v0/output_temp/results.tsv; then
    echo "File exists."

    # create new acq and move all the output along with the file metadata to slide file
    export bashvar=$file
    export output=$OUTPUT_DIR
    my_value=$(python3 create_acq.py)
    echo $my_value
    exit 0

  else
    echo $STATUS
    exit 1
  fi 

################# Finish up #################
  STATUS=$?
else
  echo "$CONTAINER  Input files not found!"
  exit 1
fi

# Check exit status
if [[ $STATUS == 0 ]]
  then
    echo -e "$CONTAINER  Done!"

  else
    echo "$CONTAINER  command returned a non-zero exit code = [$STATUS]."
    exit 1
fi