#!/usr/bin/env bash
# Copyright 2024 Bryan C. Roessler
# This is currently a code scratchpad for organizing the Hartman Lab Server workflow
# It contains a mixture of code/pseudocode and shouldn't be run until this message is removed
# Allow indirect functions
# shellcheck disable=SC2317
#
# shdoc info
# @name HartmanLabWorkflow
# @brief One script to rule them all (see: xkcd #927)
# @description Executes the Hartman Lab image analysis workflow
# @arg $1 string A project name
#
shopt -s extglob

# @section Libraries
# @description Change these variables to use different libraries
JAVA="${JAVA:-java}"
PYTHON="${PYTHON:-python3}"
PERL="${PERL:-perl}"

# @section Help
# @description Print a helpful message
print_help() {
  echo "Running: ${FUNCNAME[0]}"

  cat <<-EOF
		USAGE:
			script-run-workflow [[OPTION] [VALUE]]...

			Some options (--project, --module) can be passed multiple times for batch operations.

		OPTIONS:
			--project, -p PROJECT
				PROJECT should follow the pattern ${PROJECT_PREFIX}_UNIQUE_PROJECT_NAME
			--include, -i MODULE
				See MODULES section below for list of available modules
				If no --module is specified, all modules are run
			--exclude, -x MODULE
				See MODULES section below for list of available modules
			--yes, -y, --auto
				Always answer yes to questions (non-interactive mode)
			--debug, -d
				Print extra debugging info
			--help, -h
				Print this help message and exit

		MODULES:
			${ALL_MODULES[*]}

		DEPENDENCIES:
			binaries (system): graphviz pandoc pdftk-java gd-devel
			perl (cpan): File::Map ExtUtils::PkgConfig GD GO::TermFinder
			R (default): BiocManager ontologyIndex ggrepel tidyverse sos openxlsx ggplot2 plyr extrafont gridExtra gplots stringr plotly ggthemes pandoc rmarkdown
			R (BiocManager):

		EXAMPLES:
			script-run-workflow --module ${ALL_MODULES[0]} --module ${ALL_MODULES[1]}
			script-run-workflow --project ${PROJECT_PREFIX}_MY_PROJECT --module ${ALL_MODULES[0]} --module ${ALL_MODULES[1]}
			script-run-workflow --project ${PROJECT_PREFIX}_MY_PROJECT --module ${ALL_MODULES[1]} --module ${ALL_MODULES[2]} --yes
	EOF
}


# @section User Input
# @description Creates array and switches from user input
parse_input() {
  echo "Running: ${FUNCNAME[0]}" "$@"

  long_opts="project:,include:,exclude:,yes,auto,debug,help"
  #long_opts+="restorefile:,betapass:,"
  short_opts="+p:i:x:yhd"

  if input=$(getopt -o $short_opts -l $long_opts -- "$@"); then
    eval set -- "$input"
    while true; do
      case $1 in
        --project|-p)
          shift
          declare -ga PROJECT_NAMES+=("$1")
          ;;
        --include|-i)
          shift
          declare -ga MODULES+=("$1")
          ;;
        --exclude|-x)
          shift
          declare -ga EXCLUDE_MODULES+=("$1")
          ;;
        --yes|-y|--auto)
          declare -g YES=1
          ;;
        --debug|-d)
          declare -g DEBUG=1
          ;;
        --help|-h)
          print_help; exit 0
          ;;
        --)
          shift
          break
          ;;
      esac
      shift
    done
  else
    err "Incorrect options provided"; exit 1
  fi
}


# @section Initialize a new job in the scans directory
# @description Create a new ExpJobs project
# TODO Copy over source image directories from robot - are these alse named by the ExpJobs name?
init_job() {
  echo "Running: ${FUNCNAME[0]}"

  if [[ -d $SCAN_DIR ]]; then
    ask "$SCAN_DIR already exists, re-initialize?" || return 0
  else
    ask "Initialize a new project at $SCAN_DIR?" || return 1
    mkdir -p "$SCAN_DIR"
  fi

  [[ -d $SCAN_DIR/MasterPlateFiles ]] || mkdir -p "$SCAN_DIR/MasterPlateFiles"

  DRUG_MEDIA_FILE="$SCAN_DIR/MasterPlateFiles/DrugMedia_$PROJECT_NAME.xls"
  MASTER_PLATE_FILE="$SCAN_DIR/MasterPlateFiles/MasterPlate_$PROJECT_NAME.xls"

  # TODO Where are the actual templates?
  for f in $DRUG_MEDIA_FILE $MASTER_PLATE_FILE; do
    touch "$f"
  done

}


# @section EASY
# @description Start an EASY analysis
# The QHTCPImageFolders and ‘MasterPlateFiles’ folder are the inputs for image analysis with EASY software. 
# EASY will automatically generate a ‘Results’ directory (within the ExpJobs/‘ExperimentJob’ folder) w/ timestamp and an optional short description provided by the user (Fig.2). 
# The ‘Results’ directory is created and entered, using the “File >> New Experiment” dropdown in EASY. 
# Multiple ‘Results’ files may be created (and uniquely named) within an ‘ExperimentJob’ folder.
easy() {
  echo "Running: ${FUNCNAME[0]}"
  EASY="/mnt/data/EASY/EasyDev2024/BU/EASY240430AppExported/EstartConsole.m"

  pushd "$SCAN_DIR" || return 1 

  # Launch graphical matlab if the user wants
  ask "Start EASY in MATLAB? This requires a GUI." && matlab -nosplash -r "$EASY"

  # glob EASY output and make sure it exists
  shopt -s nullglob
  EASY_RESULTS_DIRS=( Results* )
  shopt -u nullglob
  [[ ${#EASY_RESULTS_DIRS} -ge 1 ]] || (echo "Missing EASY output"; exit 1)

  declare -a EASY_OUT_ARRAY
  for EASY_RESULTS_DIR in "${EASY_RESULTS_DIRS[@]}"; do
    [[ -d $EASY_RESULTS_DIR ]] && echo "Found EASY Results directory: $EASY_RESULTS_DIR"
    EASY_PRINT_RESULTS_DIR="$EASY_RESULTS_DIR/PrintResults"
    [[ -d $EASY_PRINT_RESULTS_DIR ]] && echo "Found EASY PrintResults directory: $EASY_PRINT_RESULTS_DIR"
    EASY_PRINT_RESULTS_FILES=(
      "$EASY_PRINT_RESULTS_DIR/!!"* 
      "$EASY_PRINT_RESULTS_DIR"/NoGrowth_*.txt
      "$EASY_PRINT_RESULTS_DIR"/GrowthOnly_*.txt
    )
    EASY_OUT_ARRAY+=("$EASY_RESULTS_DIR" "$EASY_PRINT_RESULTS_DIR" "${EASY_PRINT_RESULTS_FILES[@]}")
  done

  echo "EASY OUTPUT ARRAY: " "${EASY_OUT_ARRAY[@]}"
}

# @section EZView
ezview() {
  echo "Running: ${FUNCNAME[0]}"
  EZVIEW_DIR="/mnt/data/EZVIEW"
  echo "$EZVIEW_DIR"
}


# @section StudiesQHTCP
# @ description This section is derived from the earliest work of Jinyu Guo.  As such it uses Perl scripts. Without porting these two Perl scripts into a new intergrated R script or Python script, one is contrained to use the rather crude copy-paste and and shell script inherient in the original procedures. These two Perl scripts are analyze_v2.pl and terms2tsv_v4.pl which were written in 2003 by Gavin Sherlock for the SGD gene ontology system and require perl installations of such files.  These also require that the gene_ontology_edit.obo, SGD_features.tab files used in the ../Code also be included here. Without rewriting the code, one must compromise directory convenience.  

# @description Main loop for qhtcp modules (rewrite of REMcMaster3.sh)
qhtcp() {
  echo "Running: ${FUNCNAME[0]}"
  TEMPLATE_DIR="$SCRIPT_DIR/templates/qhtcp"
  QHTCP_DIR="/mnt/data/StudiesQHTCP/$PROJECT_NAME"
  
  while [[ -d $QHTCP_DIR ]]; do
    echo "A project already exists at $QHTCP_DIR"
    ask "Safely update $QHTCP_DIR from the $TEMPLATE_DIR template?" && break
    if ask "Back up $QHTCP_DIR to $QHTCP_DIR.bk and start fresh?"; then
      mv "$QHTCP_DIR" "$QHTCP_DIR.bk" || (echo "Backup unsuccessful, exiting"; exit 1)
    fi
  done

  # Copy template to QHTCP project directory
  if rsync --archive --update "$TEMPLATE_DIR"/ "$QHTCP_DIR"; then
    echo "New project created at $QHTCP_DIR"
  fi

  # Enter REMc directory to run the scripts there
  pushd "$QHTCP_DIR/REMc" || return 1

  r_join_interact &&
  java_jingyu_extract &&
  r_add_shift_values &&
  r_heat_maps_zscores &&
  r_heat_maps_homology &&
  py_gtf &&
  r_compile_gtf

  popd || return 1
}


# @description JoinInteractExps3dev.R creates REMcRdy_lm_only.csv and Shift_only.csv
r_join_interact() {
  echo "Running: ${FUNCNAME[0]}"
  echo "Rscript JoinInteractExps3dev.R"
  Rscript JoinInteractExps3dev.R
  out_file="REMcRdy_lm_only.csv"
  out_file2="Shift_only.csv"
  for f in "$out_file" "$out_file2"; do
    [[ -f $f ]] || (echo "$f does not exist"; return 1)
  done
}


# @description Jingyu's REMc java utility using file input file REMcRdy_lm_only.csv 
# and output REMcRdy_lm_only.csv-finalTable.csv
java_jingyu_extract() {
  echo "Running: ${FUNCNAME[0]}"
  classpath="jingyuJava_1_7_extractLib.jar"
  out_file="REMcRdy_lm_only.csv-finalTable.csv"

  # backup REMcRdy_lm_only.csv-finalTable.csv
  [[ -f $out_file ]] && mv "$out_file" "$out_file.bk"

  java_cmd=(
    "$JAVA" -Xms512m -Xmx2048m -Dfile.encoding=UTF-8 -classpath "$classpath" ExecMain
    "REMcRdy_lm_only.csv"
    "GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab"
    "ORF_List_Without_DAmPs.txt" 1 true true
  )

  echo "${java_cmd[@]}"
  "${java_cmd[@]}"
  [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
}


# @description Add shift values back to REMcRdy_lm_only.csv-finalTable.csv
# and output "REMcWithShift.csv" for use with the REMc heat maps
r_add_shift_values() {
  echo "Running: ${FUNCNAME[0]}"
  out_file="REMcHeatmaps/REMcWithShift.csv"
  echo "Rscript AddShiftVals2.R"
  Rscript AddShiftVals2.R
  rm -f "REMcHeatmaps/"*.pdf
  [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
}


# @description Execute REMcHeatmaps_zscores.R
r_heat_maps_zscores() {
  echo "Running: ${FUNCNAME[0]}"
  out_file="REMcHeatmaps/compiledREMcHeatmaps.pdf"
  echo "Rscript REMcHeatmaps_zscores.R"
  Rscript REMcHeatmaps_zscores.R
  pdfs=(REMcHeatmaps/*.pdf)
  echo "pdftk ${pdfs[*]} output $out_file"
  pdftk "${pdfs[@]}" output "$out_file"
  [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
}


# @description Execute REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R
r_heat_maps_homology() {
  echo "Running: ${FUNCNAME[0]}"
  work_dir="REMcHeatmapsWithHomology"
  source_file="REMcHeatmaps/REMcWithShift.csv"
  target_file="$work_dir/REMcWithShift.csv"
  out_file="$work_dir/Homology/compiledREMcHomologyHeatmaps.pdf"
  echo "rsync --archive $source_file $target_file"
  rsync --archive "$source_file" "$target_file"

  # Clean old output
  rm "$work_dir/Homology/"*.{pdf,csv}

  pushd "$work_dir" || return 1
  Rscript \
    REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R \
    REMcWithShift.csv \
    Homology \
    17_0503_DAmPs_Only.txt \
    Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv
  popd || return 1

  pdfs=("$work_dir"/Homology/*.pdf)
  pdftk "${pdfs[@]}" output "$out_file"

  [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
}


# @description Perform GTF
py_gtf() {
  echo "Running: ${FUNCNAME[0]}"
  process_dir="GTF/Process"
  function_dir="GTF/Function"
  component_dir="GTF/Component"
  in_file="REMcRdy_lm_only.csv-finalTable.csv"
  out_file="$process_dir/REMcRdy_lm_only/1-0-0-finaltable.csv"
  echo "$PYTHON DconJG2.py $in_file $process_dir/"
  "$PYTHON" DconJG2.py "$in_file" "$process_dir/"
  [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
  unset out_file
  rsync -a "$process_dir/REMcRdy_lm_only" GTF/Function/
  rsync -a "$process_dir/REMcRdy_lm_only" GTF/Component/

  # @description Not sure what to name this
  # @arg $1 string directory name
  _process() {
    echo "Running: ${FUNCNAME[0]}" "$@"
    pushd "$1" || return 1

    shopt -s nullglob
    set2=(REMcRdy_lm_only/*.txt)
    shopt -u nullglob

    for s in "${set2[@]}"; do
      echo "$PERL analyze_v2.pl -an gene_association.sgd -as P -o gene_ontology_edit.obo -b $set1 $s"
      echo "TODO: analyze_v2.pl should be translated"
      "$PERL" analyze_v2.pl -an gene_association.sgd -as P -o gene_ontology_edit.obo -b "$set1" "$s"
      echo "$PERL terms2tsv_v4.pl $s.terms > $s.tsv"
      echo "TODO: terms2tsv_v4.pl should be translated"
		  "$PERL" terms2tsv_v4.pl "$s.terms" > "$s.tsv"
    done

    # Concat the process ontology outputs from the /REMcReady_lm_only folder
    echo "$PYTHON Concatenate_GTF_results.py REMcRdy_lm_only/ $out_file"
    echo "TODO: Concatenate_GTF_results.py should be translated to bash"
    "$PYTHON" Concatenate_GTF_results.py REMcRdy_lm_only/ "$out_file"

    [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
    popd || return 1
  }

  # Perform operations in each directory
  for d in "$process_dir" "$function_dir" "$component_dir"; do 
    set1="ORF_List_Without_DAmPs.txt"
    out_file="${d##*/}Results.txt" # Use the dirname to create each Results filename
    _process "$d" & # parallelize
  done

}

# @description Compile GTF in R
r_compile_gtf() {
  echo "Running: ${FUNCNAME[0]}"
  echo "Rscript CompileGTF.R"
  Rscript CompileGTF.R
}


# @description Installs dependencies for the workflow
install_dependencies() {
  echo "Running: ${FUNCNAME[0]}"

  # Install system-wide dependencies
  echo "Installing system dependencies"
  case "$(uname -s)" in
    Linux*|CYGWIN*|MINGW*)
      ask "Detected Linux platform, continue?" || return 1
      echo "You may be prompted for your sudo password to install system packages"
      if hash dnf &>/dev/null; then
        sudo dnf install graphviz pandoc pdftk-java gd-devel
      elif hash apt &>/dev/null; then
        sudo apt install graphviz pandoc pdftk-java libgd-dev
      fi
      ;;
    Darwin*)
      ask "Detected Mac platform, continue?" || return 1
      export HOMEBREW_BREW_GIT_REMOTE="https://github.com/Homebrew/brew"
      curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh|bash
      brew install graphiz
      brew install gd
      brew install pdftk-java
      brew install pandoc 
      cpan File::Map ExtUtils::PkgConfig GD GO::TermFinder
      ;;
    *)          
      echo "Your system could not be detected, please install dependencies manually"
      ;;
  esac
  
  # Install perl CPAN modules
  echo "Installing perl CPAN modules"
  echo "cpan File::Map ExtUtils::PkgConfig GD GO::TermFinder"
  cpan File::Map ExtUtils::PkgConfig GD GO::TermFinder

  # Install R packages
  echo "Installing R packages"
  Rscript -e 'install.packages(c(\
    "BiocManager", \
    "ontologyIndex" \
    "ggrepel" \
    "tidyverse" \
    "sos" \
    "openxlsx" \
    "ggplot2" \
    "plyr" \
    "extrafont" \
    "gridExtra" \
    "gplots" \
    "stringr" \
    "plotly" \
    "ggthemes" \
    "pandoc" \
    "rmarkdown" \
    ), dep=TRUE, repos="https://cloud.r-project.org")'
  Rscript -e 'BiocManager::install("org.Sc.sgd.db")'
}


# @internal
ask() {
    declare response
    (( YES )) && return 0
    read -r -p "$* [y/N]: " response
    [[ ${response,,} =~ ^(yes|y)$ ]]
}
# @internal
err() { echo "Error: $*" >&2; }
# @internal
ask_pn() { 
  declare -g PROJECT_NAME
  read -r -p "Enter a full project name (ex. ${PROJECT_PREFIX}_PROJECT_NAME): " PROJECT_NAME
}
# @internal
debug() { (( DEBUG )) && echo "Debug: $*"; }


# @description The main loop of script-run-workflow
# May eventually need to add git ops
# Passes on arguments
# Most variables in main() are user configurable or can be overriden by env
main() {
  echo "Running: ${FUNCNAME[0]}" "$@"
  
  # Where are we located?
  SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )

  # Set the automatic project directory prefix
  PROJECT_PREFIX="$(whoami)_$(date +%y_%m_%d)"

  # When adding a module, it also should be added to this list
  ALL_MODULES=(
    install_dependencies
    init_job
    easy
    ezview
    qhtcp
  )
  
  declare -a PROJECT_NAMES=() # this array will hold all of the projects to run
  [[ $# -eq 1 ]] && PROJECT_NAMES+=("$1") # easy way to run on single dir
  [[ $# -ge 2 ]] && parse_input "$@" # parse arguments with getopt

  # Prompt user for the PROJECT_NAME if we still don't have one
  if [[ ${#PROJECT_NAMES[@]} -eq 0 ]]; then # still allows for environment overrides
    ask_pn
    PROJECT_NAMES+=("$PROJECT_NAME")
  fi

  # Sanitize PROJECT_NAMES
  # This regex should match PROJECT_PREFIX
  san() { [[ $1 =~ .+_[0-9][0-9]_[0-9][0-9]_[0-9][0-9]_.+ ]]; }
  for i in "${!PROJECT_NAMES[@]}"; do
    if ! san "${PROJECT_NAME[i]}"; then
      echo "Project name ${PROJECT_NAME[$i]} is invalid"
      echo "Enter a replacement"
      ask_pn
      san "$PROJECT_NAME" || (echo "RTFM"; return 1)
      PROJECT_NAME[i]="$PROJECT_NAME"
    fi
  done

  SCANS_DIR="${SCANS_DIR:-"/mnt/data/ExpJobs"}" # TODO propose changing this to something else

  # If we don't catch with getopt or env, run all
  [[ ${#MODULES[@]} -eq 0 ]] && MODULES=("${ALL_MODULES[@]}")

  # Exclude modules overrides include
  arr=()
  for m in "${MODULES[@]}"; do
    [[ " ${EXCLUDE_MODULES[*]} " =~ [[:space:]]${m}[[:space:]] ]] || arr+=("$m")
  done
  MODULES=("${arr[@]}")
  unset arr
    
  # Sanitize MODULES
  for i in "${!MODULES[@]}"; do
    if ! [[ " ${ALL_MODULES[*]} " =~ [[:space:]]${MODULES[i]}[[:space:]] ]]; then
      echo "Module $m not in the module list"
      echo "Available modules: ${ALL_MODULES[*]}"
      read -r -p "Enter replacement name: " MODULE
      ! [[ " ${ALL_MODULES[*]} " =~ [[:space:]]${MODULE}[[:space:]] ]] || (echo "RTFM"; return 1)
      MODULES[i]="$MODULE"
    fi
  done

  # Loop over projects
  for PROJECT_NAME in "${PROJECT_NAMES[@]}"; do 
    SCAN_DIR="$SCANS_DIR/$PROJECT_NAME"

    # Run selected modules
    for m in "${MODULES[@]}"; do
      ask "Run $m" && "$m"
    done
  done

}

main "$@"

exit $?