EAreport

#!/usr/bin/env bash
# EAreport generates a bookdown summary of the current project

if [[ -n "$1" ]]; then
    src="$(dirname $0)/src"
    if [[ ! -f "$src/.env" ]]; then
        echo "EAreport: Please run ./install to setup necessary env variables"
        exit
    fi

    source $src/.env
    eval $condaEnv
    
    workingdir=$(dirname $1)
    configdir=$1

    if [[ $workingdir = ..* ]];then 
        CurrentPath=`pwd`"/"
        workingdir=$CurrentPath$workingdir
        configdir=$CurrentPath$configdir
    fi

    if [[ $workingdir = .* ]];then 
        CurrentPath=`pwd`
        RestPath=`echo $workingdir|sed 's/^\.//'`
        RestConfigPath=`echo $1|sed 's/^\.//'`
        workingdir=$CurrentPath$RestPath
        if [[ ! $RestConfigPath = /* ]];then
            configdir=$CurrentPath"/"$RestConfigPath
        else
            configdir=$CurrentPath$RestConfigPath
        fi
    fi

    if [[ ! $workingdir = /* ]];then
        CurrentPath=`pwd`
        workingdir=$CurrentPath"/"$workingdir
        configdir=$CurrentPath"/"$configdir
    fi

    echo -e "Building bookdown report in: \n    "$workingdir/BookdownReport/
    rm -rf $workingdir/BookdownReport && cp -r $(dirname $0)/src/BookdownTemplates $workingdir/BookdownReport

    #Create a bookdown.info.txt file
    echo -e "Source_code\t"$(dirname $0)/src/ > $workingdir/BookdownReport/bookdown.info.txt
    echo -e "Working_dir\t"$workingdir/BookdownReport/ >> $workingdir/BookdownReport/bookdown.info.txt
    echo -e "Config_file\t"$configdir >> $workingdir/BookdownReport/bookdown.info.txt
    ProjName=`awk '{if ($1=="prj_name:") print $2}' $configdir`

    echo "Running the following command:"
    echo -e "Rscript $(dirname $0)/src/BookdownReport.R \ \n    $(dirname $0)/src/ \ \n    $workingdir/BookdownReport/ \ \n    $configdir"
    Rscript $(dirname $0)/src/BookdownReport.R $(dirname $0)/src/ $workingdir/BookdownReport/ $configdir && \
        echo -e "Done building report ..." && \
	echo -e "Please find the report in: \n    "$workingdir/BookdownReport/docs/index.html && \
        mkdir $workingdir/${ProjName}_BookdownReport && \
        cp -r $workingdir/BookdownReport/docs/* $workingdir/${ProjName}_BookdownReport && \
        cd $workingdir && \
        tar -czf ${ProjName}_BookdownReport.tar.gz ${ProjName}_BookdownReport && \
        rm -rf ${ProjName}_BookdownReport && \
        echo -e "The tarball containing the full report is ready: \n    "$workingdir/${ProjName}_BookdownReport.tar.gz
	
else
    echo "=============== EAreport path/to/config/file"
    echo "EAreport generates a bookdown summary of the current project"
    exePath=$(dirname $0)
    echo "An example config file can be found: $exePath/example/config.yml"
    echo "'EAinit' can be used to create a config file for a RNAseq project downloaded from DNAnexus"
    echo "==============="
    exit 0
fi