run

#!/bin/bash
FLYWHEEL_BASE=/flywheel/v0
MANIFEST_FILE=$FLYWHEEL_BASE/manifest.json
CONFIG_FILE=$FLYWHEEL_BASE/config.json
ANALYSIS_ID=$(jq -r '.destination.id' $CONFIG_FILE)
GEAR_INPUT_DIR=$FLYWHEEL_BASE/input
GEAR_OUTPUT_DIR=$FLYWHEEL_BASE/output
ANTS_OUTPUT_DIR=$GEAR_OUTPUT_DIR/"$ANALYSIS_ID"
#WORKING_DIR=$GEAR_OUTPUT_DIR/"$ANALYSIS_ID"_work
BIDS_DIR=$GEAR_INPUT_DIR/bids_dataset
CONTAINER='[flywheel/antsct]'
EXE_SCRIPT=$GEAR_OUTPUT_DIR/antsct_run.sh

# CRITICAL: re-create the environment
cat ${FLYWHEEL_BASE}/docker-env.sh
# shellcheck source=/flywheel/v0/docker-env.sh
source ${FLYWHEEL_BASE}/docker-env.sh

function error_exit()
{
	echo "$@" 1>&2
	exit 1
}
function parse_config {
  # Parse the config file
  if [[ -f $CONFIG_FILE ]]; then
    echo "$(cat $CONFIG_FILE | jq -r '.config.'"$1")"
  else
    CONFIG_FILE=$MANIFEST_FILE
    echo "$(cat $MANIFEST_FILE | jq -r '.config.'"$1"'.default')"
  fi
}

# determine the input format
inputFormat='bids' #default to BIDS
isManualInput=$(jq '.inputs.t1_anatomy' "$CONFIG_FILE")
if [[ ! $isManualInput = null ]]; then
  inputFormat='manual'
else
  inputFormat='bids'
fi

# Download BIDS and write command
# Do the download no matter the input format because BIDS dataset needed to determine the prefix
if [[ ! -d ${BIDS_DIR} ]]; then
  timeout 30m /usr/local/miniconda/bin/python /flywheel/v0/prepare_run.py
fi

if [[ ! -f $EXE_SCRIPT ]]; then
  echo "$CONTAINER Unable to create ANTsCT run environment! Exiting"
  error_exit 1
fi

bash -x ${FLYWHEEL_BASE}/output/antsct_run.sh

ANTS_EXITSTATUS=$?

if [[ $ANTS_EXITSTATUS == 0 ]]; then

  # parse the run script to get the file-root (aka prefix)
  fileRoot=$(cat ${FLYWHEEL_BASE}/output/antsct_run.sh | grep -o -P '(?<=file-root ).*(?=_ --denoise)')
  subjectName=$(echo "$fileRoot" | cut -d '_' -f 1)
  sessionName=$(echo "$fileRoot" | cut -d '_' -f 2)

  LOOSE_DIR=$GEAR_OUTPUT_DIR/loose
  mkdir $LOOSE_DIR

  if [[ $inputFormat = 'bids' ]]; then

      # make a BIDS derivatives folder and zip
      BIDS_OUTPUT_DIR="$GEAR_OUTPUT_DIR/ants-ct"
      mkdir -p "$BIDS_OUTPUT_DIR"

      # arrange derivatives
      bash ${FLYWHEEL_BASE}/BIDsDerivative.sh "$GEAR_OUTPUT_DIR" "$BIDS_OUTPUT_DIR" "$fileRoot" #$subjectName" "$sessionName"
      # zip folder (cd there is easier)
      pushd "$GEAR_OUTPUT_DIR"
    #  zip -r "${GEAR_OUTPUT_DIR}/antsct_${ANALYSIS_ID}_bids.zip" ants-ct
      zip -r "${GEAR_OUTPUT_DIR}/antsct_${subjectName}_${sessionName}_bids.zip" ants-ct
      popd

      mv $(find "$BIDS_OUTPUT_DIR" -type f | grep csv) "$LOOSE_DIR"
      mv $(find "$BIDS_OUTPUT_DIR" -type f | grep png) "$LOOSE_DIR"
      mv $(find "$BIDS_OUTPUT_DIR" -type f | grep desc-thickness) "$LOOSE_DIR"
      rm -rf "$BIDS_OUTPUT_DIR"
  elif [[ $inputFormat = 'manual' ]]; then
      # move everything in outputs folder to a single directory and zip
      LEGACY_OUTPUT_DIR="$GEAR_OUTPUT_DIR/antsct_${ANALYSIS_ID}"
      mkdir -p "$LEGACY_OUTPUT_DIR"
      find "$GEAR_OUTPUT_DIR" -type f -maxdepth 1 | grep -v antsct | while read line
      do
        mv $line $LEGACY_OUTPUT_DIR/
      done
      # zip folder (cd there is easier)
      pushd "$LEGACY_OUTPUT_DIR"
      #zip -r "${GEAR_OUTPUT_DIR}/antsct_${ANALYSIS_ID}.zip" ./*
      zip -r "${GEAR_OUTPUT_DIR}/antsct_${subjectName}_${subjectName}.zip" ./*
      popd

      mv $(find "$LEGACY_OUTPUT_DIR" -type f | grep csv) "$LOOSE_DIR"
      mv $(find "$LEGACY_OUTPUT_DIR" -type f | grep png) "$LOOSE_DIR"
      mv $(find "$LEGACY_OUTPUT_DIR" -type f | grep CorticalThickness) "$LOOSE_DIR"
      rm -rf "$LEGACY_OUTPUT_DIR"
  else
    error_exit "Unable to determine input format..."
  fi
  rm $(find "$GEAR_OUTPUT_DIR" -maxdepth 1 -type f | grep -v antsct | grep -v loose) || echo "No loose files in output folder."
  mv $LOOSE_DIR/* $GEAR_OUTPUT_DIR
  rmdir $LOOSE_DIR
fi

# Clean up
rm -rf "$ANTS_OUTPUT_DIR"
echo -e "Wrote: $(ls -lh $GEAR_OUTPUT_DIR)"
exit $ANTS_EXITSTATUS