#!/bin/bash

# Initialize DOSMA

#

# @usage (from terminal/command line):

# ./setup

#

# @initialization protocol:

#   1. Navigate to this folder in terminal/command line

#   2. Run "chmod +x setup" from command-line (Linux) or Terminal (MacOS)

#

# @author: Arjun Desai, Stanford University

#          (c) Stanford University, 2018

openURL() {

    if [[ "$OSTYPE" == "linux-gnu" ]]; then

            xdg-open $1

    elif [[ "$OSTYPE" == "darwin"* ]]; then

            # Mac OSX

            open $1

    else

        echo "Only Linux and MacOS are supported"

        exit 125

    fi

}

setBashFile() {

    if [[ "$OSTYPE" == "linux-gnu" ]]; then

            bash_file="$HOME/.bashrc"

    elif [[ "$OSTYPE" == "darwin"* ]]; then

            bash_file="$HOME/.bash_profile"

    else

        echo "Only Linux and MacOS are supported"

        exit 125

    fi

}

BIN_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"

DOSMA_DIR="$( cd "$( dirname "${BIN_DIR}" )" >/dev/null 2>&1 && pwd )"

ANACONDA_KEYWORD="anaconda"

ANACONDA_DOWNLOAD_URL="https://www.anaconda.com/distribution/"

MINICONDA_KEYWORD="miniconda"

DOSMA_ENV_NAME="dosma_env"

ENV_FILE=$DOSMA_DIR/environment.yml

GOOGLE_FORM_URL="https://forms.gle/sprthTC2swyt8dDb6"

DOSMA_SETUP_PATTERN="dosma setup|export PATH.*dosma\/bin"

hasAnaconda=0

updateEnv=1

updatePath=1

setBashFile

while getopts ":h" opt; do

    case ${opt} in

        h )

            echo "DOSMA setup"

            echo "     Create Anaconda virtual environment and add dosma executable to PATH variable"

            echo "Usage:"

            echo "    -h                Display this help message"

            exit 0

            ;;

        \? )

            echo "Usage: cmd [-h] [-u] [-e]"

            exit 0

            ;;

    esac

done

# Check if conda exists

if echo $PATH | grep -q $ANACONDA_KEYWORD; then

    hasAnaconda=1

    echo "Conda found in path"

fi

if echo $PATH | grep -q $MINICONDA_KEYWORD

then

    hasAnaconda=1

    echo "Miniconda found in path"

fi

if [[ $hasAnaconda -eq 0 ]]; then

    echo "Anaconda/Miniconda not installed - install from $ANACONDA_DOWNLOAD_URL"

    openURL $ANACONDA_DOWNLOAD_URL

    exit 125

fi

# Check if OS is supported

if [[ "$OSTYPE" != "linux-gnu" && "$OSTYPE" != "darwin"* ]]; then

    echo "Only Linux and MacOS are supported"

    exit 125

fi

# Create Anaconda environment (dosma_env)

if [[ `conda env list | grep $DOSMA_ENV_NAME` ]]; then

    if [[ ${updateEnv} -eq 0 ]]; then

        echo "Environment 'dosma_env' found. Run 'conda activate dosma_env' to get started."

    else

        conda env remove -n $DOSMA_ENV_NAME

        conda env create -f $ENV_FILE

    fi

else

    conda env create -f $ENV_FILE

fi

# If DOSMA executable already exists as a shortcut and updating DOSMA, then remove the path lines

if [[ ! -z `cat ${bash_file} | egrep -i "${DOSMA_SETUP_PATTERN}"` && ${updatePath} -ne 0 ]]; then

    echo ""

    echo "Overwriting DOSMA executable path"

    echo ""

    cp $bash_file $bash_file"-dosma.bak"

    tempFile="$HOME/.bash_profile_temp"

    egrep -iv "${DOSMA_SETUP_PATTERN}" $bash_file >> $tempFile

    cp $tempFile $bash_file

fi

# Add dosma to path

if [[ -z `cat ${bash_file} | egrep -i "${DOSMA_SETUP_PATTERN}"` ]]; then

    cp $bash_file $bash_file"-dosma.bak"

    echo "Adding dosma to path - changes made in $bash_file"

    echo "" >> $bash_file

    echo "# Added by DOSMA setup" >> $bash_file

    echo 'export PATH='$BIN_DIR':$PATH' >> $bash_file

fi

echo ""

echo ""

echo "DOSMA Usage"

echo "------------"

echo "For command line help menu: 'dosma -h'"

echo "For GUI (user interface): 'dosma --app'"

echo ""

echo "For help with DOSMA, see documetation:"

echo "    https://ad12.github.io/DOSMA"

echo ""

echo "Please also complete the DOSMA questionnaire if not previously completed"

echo "    ${GOOGLE_FORM_URL}"

echo ""

echo ""

# Launch google form

openURL $GOOGLE_FORM_URL