pfp.sh

#!/usr/bin/env bash
# This is designed to be run from within a directory that contains the following files:
# annotations.r
# spek.json
# performance.csv
# templates.json
# causal_pathways.json

COL_WIDTH=30
COL_WIDTH=30
LOG_FILE="${PFP_LOG_FILE:=vignette.log}"
KNOWLEDGE_BASE_DIR="${PFP_KNOWLEDGE_BASE_DIR:=.}"
DATA_DIR="${PFP_DATA_DIR:=.}"
OUTPUT_DIR="${PFP_OUTPUT_DIR:=outputs}"

# CHeck for data and knowledge base overrides
PARAMS=()
while (("$#")); do
  case "$1" in
  -k | --knowledge)
    KNOWLEDGE_BASE_DIR="${2}"
    shift 2
    ;;
  -d | --data)
    PFP_DATA_DIR="${2}"
    shift 2
    ;;
  -f | --file)
    PFP_DATA_FILE="${2}"
    shift 2
    ;;
  -o | --output)
    OUTPUT_DIR="${2}"
    shift 2
    ;;
  -l | --log)
    LOG_FILE="${2}"
    shift 2
    ;;
  -x | --debug)
    DEBUG_MODE="TRUE"
    shift 1
    ;;
  --) # end argument parsing
    shift
    break
    ;;
  -* | --*=) # unsupported flags
    echo "Aborting: Unsupported flag $1" >&2
    exit 1
    ;;
  *) # preserve positional arguments
    PARAMS+=("${1}")
    shift
    ;;
  esac
done

# Define
# Check for dependencies

command -v Rscript 1>/dev/null 2>&1 ||
  {
    echo >&2 "Rscript required but it's not installed.  Aborting."
    exit 1
  }

command -v ruby 1>/dev/null 2>&1 ||
  {
    echo >&2 "ruby required but it's not installed.  Aborting."
    exit 1
  }

command -v jq 1>/dev/null 2>&1 ||
  {
    echo >&2 "jq required but it's not installed.  Aborting."
    exit 1
  }

# Create ${OUTPUT_DIR} directory
mkdir -p ${OUTPUT_DIR}

# Create log file, or append
if [[ -z ${LOG_FILE} ]]; then
  date >${LOG_FILE}
else
  date | tee -a ${LOG_FILE}
fi

# Run bitstomach on performance data, spek, and annotations
total_time_start=$(date +%s)

printf "Running BitStomach -------------------------------\n" | tee -a ${LOG_FILE}
start=$(date +%s)
if [[ -z ${PFP_DATA_FILE} ]]; then
  $DISPLAY_LAB_HOME/bit-stomach/bin/bitstomach.sh \
    -s ${KNOWLEDGE_BASE_DIR}/spek.json \
    -d ${PFP_DATA_DIR}/performance.csv \
    -a ${KNOWLEDGE_BASE_DIR}/annotations.r \
    2>>${LOG_FILE} | jq . \
    >${OUTPUT_DIR}/spek_bs.json
else
  $DISPLAY_LAB_HOME/bit-stomach/bin/bitstomach.sh \
    -s ${KNOWLEDGE_BASE_DIR}/spek.json \
    -d ${PFP_DATA_DIR}/${PFP_DATA_FILE} \
    -a ${KNOWLEDGE_BASE_DIR}/annotations.r \
    2>>${LOG_FILE} | jq . \
    >${OUTPUT_DIR}/spek_bs.json
fi
end=$(date +%s)
runtime=$(echo "$end - $start" | bc -l)
printf "execution time: ${runtime} seconds\n" | tee -a ${LOG_FILE}
printf "exit status: %d\n" "${?}" | tee -a ${LOG_FILE}

# Run candidate smasher on spek (spek_bs.json) and templates
printf "Running Candidate Smasher ------------------------\n" | tee -a ${LOG_FILE}

start=$(date +%s)
$DISPLAY_LAB_HOME/candidate-smasher/bin/cansmash \
  --path=${OUTPUT_DIR}/spek_bs.json \
  --md-source=${KNOWLEDGE_BASE_DIR}/templates.json \
  2>>${LOG_FILE} | jq . \
  >${OUTPUT_DIR}/spek_cs.json
end=$(date +%s)
runtime=$(echo "$end - $start" | bc -l)
printf "execution time: ${runtime} seconds\n" | tee -a ${LOG_FILE}
printf "exit status: %d\n" "${?}" | tee -a ${LOG_FILE}

# Run think pudding on spek (spek_cs.json) and causal pathways
printf "Running Think Pudding ----------------------------\n" | tee -a ${LOG_FILE}

start=$(date +%s)
$DISPLAY_LAB_HOME/think-pudding/bin/thinkpudding.sh \
  -s ${OUTPUT_DIR}/spek_cs.json \
  -p ${KNOWLEDGE_BASE_DIR}/causal_pathways.json \
  2>>${LOG_FILE} \
  >${OUTPUT_DIR}/spek_tp.json
end=$(date +%s)
runtime=$(echo "$end - $start" | bc -l)
printf "execution time: ${runtime} seconds\n" | tee -a ${LOG_FILE}
printf "exit status: %d\n" "${?}" | tee -a ${LOG_FILE}

## Run presteemer on spek (spek_tp.json)
printf "Running Presteemer -------------------------------\n" | tee -a ${LOG_FILE}

start=$(date +%s)
$DISPLAY_LAB_HOME/esteemer/bin/presteemer.sh \
  -s ${OUTPUT_DIR}/spek_tp.json \
  2>>${LOG_FILE} \
  >${OUTPUT_DIR}/spek_pe.ttl
end=$(date +%s)
runtime=$(echo "$end - $start" | bc -l)
printf "execution time: ${runtime} seconds\n" | tee -a ${LOG_FILE}
printf "exit status: %d\n" "${?}" | tee -a ${LOG_FILE}

# Run esteemer on spek (spek_pe.json)
printf "Running Esteemer ---------------------------------\n" | tee -a ${LOG_FILE}

start=$(date +%s)
$DISPLAY_LAB_HOME/esteemer/bin/esteemer.sh \
  -s ${OUTPUT_DIR}/spek_pe.ttl \
  -p ${KNOWLEDGE_BASE_DIR}/causal_pathways.json \
  2>>${LOG_FILE} \
  >${OUTPUT_DIR}/spek_es.json
end=$(date +%s)
runtime=$(echo "$end - $start" | bc -l)
printf "execution time: ${runtime} seconds\n" | tee -a ${LOG_FILE}
printf "exit status: %d\n" "${?}" | tee -a ${LOG_FILE}

total_time_end=$(date +%s)
total_runtime=$(echo "$total_time_end - $total_time_start" | bc -l)
printf "total pipeline execution time: ${total_runtime} seconds\n" | tee -a ${LOG_FILE}

# Run cleanup if debug is not enabled
if [[ -z ${DEBUG_MODE} ]]; then
  printf "Running Cleanup ------------------------\n" | tee -a ${LOG_FILE}
  $DISPLAY_LAB_HOME/vert-ramp-affirmation/scripts/cleanup.sh | tee -a ${LOG_FILE}
  printf "exit status: %d\n" "${?}" | tee -a ${LOG_FILE}
fi

printf "Log written to ${LOG_FILE}\n"