install_bootstrap

#! /bin/bash
set -e
PANCANCER_LAUNCHER_VERSION=3.2.2
PANCANCER_CLI_VERSION=0.1.2
WORKFLOW_LISTING_URL=https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/cli/${PANCANCER_CLI_VERSION}/config/workflowlist.json

cat <<MSG
PANCANCER COMMAND LINE INTERFACE - INSTALLATION
-----------------------------------------------
This tool will setup a "launcher" host which has all of the tools we used to align and variant call
the PanCancer donors.  This launcher host can then launch one or more worker VMs with our Docker
workflows installed on them for processing one or more genomes specified by the user.

This system requires the following:
* Docker support in your Linux distribution (Ub1untu 14.04 is officially supported by the Pancancer Launcher).
* AWS credentials, if you are using Amazon EC2.
* A GNOS key (or keys) which are used to both download Docker images for our workflows, dependencies, as well as data from from GNOS servers used in the project.
  Please ensure that these files are in ~/.gnos
* Alternatively (or in addition to) the GNOS keys, a token for downloading workflows, dependencies, as well as donor data files from S3.
MSG

# Ask the user a question and save the answer.
# They MUST give an answer, they cannot leave their answer blank. In the future, that could be parameterized...
# $1 - the question string
# $2 - the previous value
# $3 - the name of the value
# $4 - reference to the user's answer.
function ask_question()
{
	question_str=$1
	prev_val=$2
	val_name=$3
	answer=''
	
    while [[ -z ${answer// /} ]] ; do
        if [[ -n $prev_val ]] ; then
			read -ep "${question_str} Previous value: "$'\n' -i "$prev_val" answer
        else
            read -ep "$question_str"$'\n' answer
        fi
        if [[ -z ${answer// /} ]] ; then
            echo "$val_name name cannot be blank."
        fi
    done
    # Set the user's value in the reference. See here: http://stackoverflow.com/a/14852461/192801 to get an idea of how this works.
	eval "${!4}=\"$answer\""
}

user_pancancer_version=latest
#FYI: The weird "^^" is to make the user input into uppercase so that if they enter "y" the installer will still run.
install_pancancer_launcher=''
while [[ "${install_pancancer_launcher^^}" != 'Y' &&  "${install_pancancer_launcher^^}" != 'N' ]] ; do
	echo "DO YOU WISH TO CONTINUE [Y/N]:"
	read install_pancancer_launcher
	if [ "${install_pancancer_launcher^^}" = 'Y' ] ; then
		user_install_docker=''
		set +e
		DOCKER_PATH="$(which docker)"
		set -e
		if [ -z "$DOCKER_PATH" ] ; then
			user_install_docker='Y'
		else
			while [[ "${user_install_docker^^}" != 'Y' &&  "${user_install_docker^^}" != 'N' ]] ; do
				echo "It looks like docker may already be installed. Would you like to run this step anyway, which may attempt to upgrade docker? [Y/N]"
				read user_install_docker
			done
		fi
		if [ "${user_install_docker^^}" = 'Y' ] ; then
			# Remove eXecute permission from /etc/grub.d/30_os-prober because sometimes the docker installer will hang when this hangs. This has happened in OpenStack
			# and could happen elsewhere.
			if [ -f /etc/grub.d/30_os-prober ] ; then
				sudo chmod a-x /etc/grub.d/30_os-prober
			fi

			echo "Installing docker..."
			
			set +e
			sudo apt-get install wget curl --yes &> install_wget_curl.log
			install_wget_result=$?
			set -e
			
			if [ $install_wget_result -ne  0 ] ; then
				echo "It looks like there may have been a problem installing or updated wget and curl:" 
				cat install_wget_curl.log
				exit 1
			fi
			
			set +e
			curl -sSL https://get.docker.com/ | sh &> install_docker.log
			install_docker_result=$?
			set -e
			
			if [ $install_docker_result -ne  0 ] ; then
				echo "It looks like there may have been a problem installing docker:" 
				cat install_wget_curl.log
				exit 1
			fi
			
			echo "Done installing docker!"
			DOCKER_PATH="$(which docker)"
		else
			echo "Skipping docker installation..."
		fi
		
		if [ -z "$DOCKER_PATH" ] ; then
			echo "You need to install docker before pulling docker images. Please ensure that docker is properly installed and then re-run this script with the command \"bash install_bootstrap\""
			exit 1
		else
			echo "Pulling pancancer_launcher image..."
			set +e
			sudo docker pull pancancer/pancancer_launcher:"${user_pancancer_version}" &> pull_image.log
			pull_result=$?
			set -e
			if [ $pull_result -ne  0 ] ; then
				echo "It looks like there might have been an error when pulling the docker image. The pancancer_launcher cannot be run until this is resolved. Error is:" 
				cat pull_image.log
				exit 1
			fi
			echo "Done pulling pancancer_launcher!"
		fi
	elif [ "${install_pancancer_launcher^^}" = 'N' ] ; then
		echo "You are exiting the installer now, but you can always run it again when you are ready."
		exit 0
	fi
done

run_pancancer_launcher=''
while [[ "${run_pancancer_launcher^^}" != 'Y' &&  "${run_pancancer_launcher^^}" != 'N' ]] ; do
    echo "Would you like to run the pancancer_launcher now? [Y/N]"
    read run_pancancer_launcher
    # If the user would like to run pancancer_launcher, then we have to get some config settings from them OR read them from an existing file
    if [ "${run_pancancer_launcher^^}" = 'Y' ] ; then
        #Read the config file if it exists and then show previous values...
        if [ -f ~/.pancancer/pancancer.config ] ; then
            source ~/.pancancer/pancancer.config
        fi

        user_cloud_env=''
		while [[ -z "${user_cloud_env// /}" ]] ; do
            if [ ! -z $CLOUD_ENV ] ; then
                read -ep $'What cloud environment are you working in? Allowed values are "AWS", "OpenStack", "Azure". Previous value: \n' -i "$CLOUD_ENV" user_cloud_env
            else
                read -ep $'What cloud environment are you working in? Allowed values are "AWS", "OpenStack", "Azure". \n' user_cloud_env
            fi
            if [[ -z "${user_cloud_env// /}" || ( ${user_cloud_env} != 'AWS' && ${user_cloud_env} != 'OpenStack' && ${user_cloud_env} != 'Azure' ) ]] ; then
                echo 'Cloud environment must be one of: "AWS", "OpenStack", "Azure".'
                user_cloud_env=''
            fi
        done

        user_pem_path=''
        while [[ ! -f $user_pem_path || ! -e $user_pem_path || -z "${user_pem_path// /}" ]] ; do
            if [ ! -z $PEM_PATH ] ; then
                read -ep $'What is the path to the pem key file you will use to authenticate in this environment? Previous value: \n' -i "$PEM_PATH" user_pem_path
                user_pem_path="${user_pem_path/#\~/$HOME}"
            else
                read -ep $'What is the path to the pem key file you will use to authenticate in this environment?\n' user_pem_path
                user_pem_path="${user_pem_path/#\~/$HOME}"
            fi
            if [[ ! -f $user_pem_path || ! -e $user_pem_path ]] ; then
                echo "The path you pass for the key file must be valid. Please ensure that \"$user_pem_path\" is a valid path."
            fi
        done

		user_key_name='user_key_name'
		ask_question "What is the name of this key?" "$KEY_NAME" "Key name" $user_key_name

        if [ $user_cloud_env == 'AWS' ] ; then
            ############################
            # AWS questions
            ############################
            if [ -f ~/.aws/config ] ; then
                AWS_KEY=$(grep aws_access_key_id ~/.aws/config | sed 's/\(.*=\)//g')
                AWS_SECRET_KEY=$(grep aws_secret_access_key ~/.aws/config | sed 's/\(.*=\)//g')
            fi

			user_aws_key='user_aws_key'
			ask_question "What is your AWS Key?" "$AWS_KEY" "AWS Key name" $user_aws_key
    
			user_aws_secret_key='user_aws_secret_key'
			ask_question "What is your AWS Secret Key?" "$AWS_SECRET_KEY" "AWS Secret Key name" $user_aws_secret_key

			user_sec_grp='user_sec_grp'
			ask_question "What is your Security Group?" "$SECURITY_GROUP" "Security Group" $user_sec_grp

            # Write the AWS config file, so that it will be available when the start_launcher_container script runs.
			# TODO: Parameterize "region" and "output", maybe...
            [[ -d ~/.aws ]] || mkdir ~/.aws
            cat >~/.aws/config <<AWS_CONFIG
[default]
aws_access_key_id=${user_aws_key}
aws_secret_access_key=${user_aws_secret_key}
region=us-east-1
output=json
AWS_CONFIG
        
        elif [ $user_cloud_env == 'Azure' ] ; then
	        ############################
	        # AZURE QUESTIONS
	        ############################        	
			user_azure_subscription_id='user_azure_subscription_id'
			ask_question "What is your Azure subscription?" "$AZURE_SUBSCRIPTION" "Azure subscription" $user_azure_subscription_id
            
			user_azure_storage_account_name='user_azure_storage_account_name'
			ask_question "What is your Azure storage account name?" "$AZURE_STORAGE_ACCOUNT" "Azure storage account name" $user_azure_storage_account_name

			user_azure_storage_account_key='user_azure_storage_account_key'
			ask_question "What is your Azure storage account key?" "$AZURE_STORAGE_ACCOUNT_KEY" "Azure storage account key" $user_azure_storage_account_key

			user_azure_AD_user='user_azure_AD_user'
			ask_question "What is your Azure Active Directory user name?" "$AZURE_AD_USER" "Azure Active Directory user name" $user_azure_AD_user

			user_azure_AD_passwd='user_azure_AD_passwd'
			ask_question "What is your Azure Active Directory password?" "$AZURE_AD_PASSWD" "Azure Active Directory user name" $user_azure_AD_passwd

			user_azure_AD_tenant='user_azure_AD_tenant'
			ask_question "What is your Azure Active Directory tenant?" "$AZURE_AD_TENANT" "Azure Active Directory tenant" $user_azure_AD_tenant

			user_azure_AD_client='user_azure_AD_client'
			ask_question "What is your Azure Active Directory client?" "$AZURE_AD_CLIENT" "Azure Active Directory client" $user_azure_AD_client

			user_azure_virtual_network='user_azure_virtual_network'
			ask_question "What is the name of the Virtual Network for this fleet?" "$AZURE_VIRTUAL_NETWORK" "Azure Virtual Network Name" $user_azure_virtual_network
			
			user_azure_location='user_azure_location'
			ask_question "What Location do you want to use for this fleet?" "$AZURE_LOCATION" "Location" $user_azure_location

            # TODO: Get public and private Azure IP addresses, or ask the user to provide them since it seems rather difficult to get them from the Azure API directly.

        elif [ $user_cloud_env == 'OpenStack' ] ; then
            ############################
            # OpenStack questions
            ############################
			user_os_username='user_os_username'
			ask_question "What is your OpenStack username (formatted as <tenant>:<username>)?" "$OS_USERNAME" "OpenStack username" $user_os_username

			user_os_password='user_os_password'
			ask_question "What is your OpenStack password?" "$OS_PASSWORD" "OpenStack password" $user_os_password

			user_os_endpoint='user_os_endpoint'
			ask_question "What is your OpenStack endpoint?" "$OS_ENDPOINT" "OpenStack endpoint" $user_os_endpoint

			user_os_region='user_os_region'
			ask_question "What is your OpenStack region?" "$OS_REGION" "OpenStack region" $user_os_region

            user_sec_grp='user_sec_grp'
            ask_question "What is your Security Group?" "$SECURITY_GROUP" "Security Group" $user_sec_grp

            user_os_network_id='user_os_network_id'
            ask_question "What is your OpenStack network ID?" "$OS_NETWORK_ID" "Network ID" $user_os_network_id

            user_os_zone=''
            if [ ! -z $OS_ZONE ] ; then
                read -ep $'What is your OpenStack zone? Previous value: \n' -i $OS_REGION user_os_zone
            else
                read -ep $'What is your OpenStack zone?\n' user_os_zone
            fi
        else
        	 # Just in case some other value somehow gets in to $user_cloud_env 
            echo "Unrecognized cloud environment: $user_cloud_env, exiting..."
            exit 1
        fi
        # echo "What version of the pancancer_launcher do you wish to run (default will be \"latest\")?"
        # read user_pancancer_version
        # They already pulled "latest", earlier in this script, so just stick with that. Future versions could ask this question, if necessary...
        user_pancancer_version="latest"


		user_fleet_name=''

        if [ $user_cloud_env == 'Azure' ] ; then
        	# In Azure, the fleet name also gets used for the storage account name which may only contain lowercase letters, numbers, and dashes.
	        if [ ! -z "$FLEET_NAME" ] ; then
	            read -ep $'What would you like to name your fleet? Azure fleet names may only contain lowercase letter, numbers, and dashes. If you do not specify a name, a name will be generated randomly for you. Previous value: \n' -i "$FLEET_NAME" user_fleet_name
	        else
	            read -ep $'What would you like to name your fleet? Azure fleet names may only contain lowercase letter, numbers, and dashes. If you do not specify a name, a name will be generated randomly for you.\n' user_fleet_name
	        fi
	        user_fleet_name=${user_fleet_name,,}
       		user_fleet_name=${user_fleet_name//[^[:alnum:]]/}
       		# If the user didn't specify a fleet name we need to do it HERE because the start_launcher_container.sh script may generate fleet names
			# that are not Azure-friendly.
       		if [ -z $user_fleet_name ] ; then
       			user_fleet_name=$(cat /dev/urandom | tr -dc 'a-z0-9-' | fold -w 10 | head -n 1)
       		fi
       		echo "Your Azure fleet name: $user_fleet_name"
        else
	        if [ ! -z "$FLEET_NAME" ] ; then
	            read -ep $'What would you like to name your fleet? If you do not specify a name, a name will be generated randomly for you. Previous value: \n' -i "$FLEET_NAME" user_fleet_name
	        else
	            read -ep $'What would you like to name your fleet? If you do not specify a name, a name will be generated randomly for you.\n' user_fleet_name
	        fi
       	fi 
        
        # Build a flag for fleet names to get passed to the next script...
        FLEET_NAME_STR=''
        if [ ! -z "$user_fleet_name" ] ; then
            # remove quotes from the fleet names, could have come from quoted previous fleet name in config
            user_fleet_name=${user_fleet_name//\"/}
            # replace space with underscore so we can pass to the next script without having to surround in quotes because that
            # causes problems for other systems.
            user_fleet_name=${user_fleet_name// /_}
            FLEET_NAME_STR=" -f $user_fleet_name "
        fi

		user_fleet_size='user_fleet_size'
		# Loop until the user gives a valid integer.
		while [[ -n ${user_fleet_size//[0-9]/} ]] ; do
		  	user_fleet_size='user_fleet_size'  
			ask_question "What is the maximum number of worker VMs you want to run in your fleet?" "$FLEET_SIZE" "Maximum fleet size" $user_fleet_size
			if [[ -n ${user_fleet_size//[0-9]/} ]] ; then
				echo "Only positive integers are allowed."
			fi
		done

		workflow_listing_url='workflow_listing_url'
		ask_question "What is the URL that lists available workflows?" $WORKFLOW_LISTING_URL "Workflow listing URL" $workflow_listing_url

        # now wget the start_launcher_container script and call it with the values from above:
        #$(wget -q -O start_launcher_container.sh https://github.com/ICGC-TCGA-PanCancer/pancancer_launcher/releases/download/$PANCANCER_LAUNCHER_VERSION/start_launcher_container.sh)
		starter_script_url="https://github.com/ICGC-TCGA-PanCancer/pancancer_launcher/releases/download/$PANCANCER_LAUNCHER_VERSION/start_launcher_container.sh"

        set +e
        wget -O start_launcher_container.sh $starter_script_url 2>get_start_launcher_container.err
        get_starter_script_result=$?
        set -e
        if [ $get_starter_script_result -ne 0 ] ; then
            echo "There seems to have been a problem downloading the startup script from:   $starter_script_url"
            echo "Error is:"
            cat ./get_start_launcher_container.err
        fi
				
        chmod u+x start_launcher_container.sh
        CMD_STR="bash start_launcher_container.sh -p $user_pem_path -i $user_pancancer_version -e ${user_cloud_env^^} $FLEET_NAME_STR"

        # Now write a config for this file.
        [[ -d ~/.pancancer ]] || mkdir ~/.pancancer
		# Note: You can't have ANY blank lines in .pancancer/pancancer.config because the python library that will eventually process it does not like blank lines and will fail. 
        cat >~/.pancancer/pancancer.config <<CONFIG
PEM_PATH="${user_pem_path}"
KEY_NAME="${user_key_name}"
FLEET_NAME="${user_fleet_name}"
FLEET_SIZE="${user_fleet_size}"
WORKFLOW_LISTING_URL="${workflow_listing_url}"
CLOUD_ENV="${user_cloud_env}"
SECURITY_GROUP="${user_sec_grp}"
AZURE_SUBSCRIPTION="${user_azure_subscription_id}"
AZURE_STORAGE_ACCOUNT="${user_azure_storage_account_name}"
AZURE_STORAGE_ACCOUNT_KEY="${user_azure_storage_account_key}"
AZURE_AD_USER="${user_azure_AD_user}"
AZURE_AD_PASSWD="${user_azure_AD_passwd}"
AZURE_AD_TENANT="${user_azure_AD_tenant}"
AZURE_AD_CLIENT="${user_azure_AD_client}"
AZURE_VIRTUAL_NETWORK="${user_azure_virtual_network}"
AZURE_LOCATION="${user_azure_location}"
OS_USERNAME="${user_os_username}"
OS_PASSWORD="${user_os_password}"
OS_ENDPOINT="${user_os_endpoint}"
OS_NETWORK_ID="${user_os_network_id}"
OS_REGION="${user_os_region}"
OS_ZONE="${user_os_zone}"
CONFIG
    [[ -d "/home/$USER/pancancer_launcher_config" ]] || mkdir "/home/$USER/pancancer_launcher_config"
    cp ~/.pancancer/pancancer.config /home/$USER/pancancer_launcher_config/pancancer.config
        echo $CMD_STR > start_launcher_container.cmd
        $(echo -e $CMD_STR)
    elif [ "${run_pancancer_launcher^^}" = 'N' ] ; then
        echo "You can run this script at another time to run the pancancer launcher"
        exit 0
    fi
done
echo "Exiting now."
set +e