run

#! /bin/bash
#
# Run dtiError Gear
# Built to flywheel-v0 spec.
#
LOG_FILE=/flywheel/v0/output/dtiErrorLog.log

(
  CONTAINER="[scitran/dti-error]"
  echo -e "$CONTAINER  Initiated"

  # Configure the ENV
  export LD_LIBRARY_PATH=/opt/mcr/v90/runtime/glnxa64:/opt/mcr/v90/bin/glnxa64:/opt/mcr/v90/sys/os/glnxa64:$LD_LIBRARY_PATH
  export XAPPLRESDIR=/opt/mcr/v90/X11/app-defaults

  # Set DISPLAY for xvfb
  export DISPLAY=:1.0

  # Define the start Xvfb function
  start_xvfb() {
    Xvfb :1 -screen 0 1920x1200x24+32 &> /dev/null &
  }

  # Configure paths
  FLYWHEEL_BASE=/flywheel/v0
  OUTPUT_DIR=$FLYWHEEL_BASE/output
  INPUT_DIR=$FLYWHEEL_BASE/input
  ZIP_DIR=$INPUT_DIR/dtiInit_Archive # Must match input from the manifest
  WORK_DIR=$INPUT_DIR/work
  CONFIG_FILE=${FLYWHEEL_BASE}/config.json

  # Ensure there is an output directory
  if [[ ! -d "$OUTPUT_DIR" ]]
  then
    echo "$CONTAINER  $OUTPUT_DIR not found!"
    exit 1
  fi

  # Make the directories
  mkdir ${WORK_DIR}

  # Move files into work directory and do the work
  ZIP_FILE=$(find ${ZIP_DIR} -type f -name "*.zip" | head -1)
  unzip ${ZIP_FILE} -d ${WORK_DIR}

  # Find the input directory from extracted archive
  DTIE_INPUT_DIR=$(find ${WORK_DIR} -maxdepth 1 -type d -name "dti*" | head -1)

  # Parse Config File
  if [[ -f $CONFIG_FILE ]]; then
    # Parse config from config.json
    echo "Loading configuration from ${CONFIG_FILE}"
    error_type=$(cat $CONFIG_FILE | jq -r '.config.error_type')
    ncoords=$(cat $CONFIG_FILE | jq -r '.config.ncoords')
    wm_prob=$(cat $CONFIG_FILE | jq -r '.config.wm_prob')
  else
    # Parse defaults from the manifest.json
    CONFIG_FILE=$FLYWHEEL_BASE/manifest.json
    echo "Loading defaults from ${CONFIG_FILE}"
    error_type=$(cat $CONFIG_FILE | jq -r '.config.error_type.default')
    ncoords=$(cat $CONFIG_FILE | jq -r '.config.ncoords.default')
    wm_prob=$(cat $CONFIG_FILE | jq -r '.config.wm_prob.default')
  fi

  # Start Xvfb and pass the input arguments to AFQ execute the algorithm
  start_xvfb && time /usr/local/bin/dtiError ${DTIE_INPUT_DIR} ${OUTPUT_DIR} ${error_type} ${ncoords} ${wm_prob}

  # # Check status code and die
  # if [[ $? !== 0 ]]; then
  #   exit 1
  # fi

  # Xvfb occasionally hangs -- make sure that it dies
  kill -9 %1

  # Get a list of the files in the output directory
  outputs=$(find $OUTPUT_DIR/* -maxdepth 0 -type f -name "*.png")

  # If outputs exist go home happy
  if [[ -z $outputs ]]
  then
    echo "$CONTAINER  FAILED: No results found in output directory... Exiting"
    exit 1
  else
    # Set permissions for outputs (prevent root only r/w)
    chmod -R 777 $OUTPUT_DIR

    # End
    echo -e "$CONTAINER  Wrote: `ls ${OUTPUT_DIR}`"
    echo -e "$CONTAINER  Done!"
  fi

  exit 0
)  2>&1 | tee $LOG_FILE