#!/bin/bash

# The MIT License (MIT)
# Copyright (c) 2019-2022 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including without limitation the rights to
# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
# the Software, and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#

set -e

# Arguments to the script
#  $1 - BUILD_DISTRIBUTABLE_LIBRARY, if true will build/install OpenSSL/CURL/UUID/Intel zlib libs
#  $2 - 'full' if build prerequisites should be installed, 'release' if only runtime prerequisites should be installed

OPENSSL_VERSION=1.1.1o
MAVEN_VERSION=3.6.3
CURL_VERSION=7.83.1
UUID_VERSION=1.0.3

# Check for the following overriding env variables
#    $INSTALL_PREFIX allows for dependencies maven/protobuf/etc. that are built to be installed to $INSTALL_PREFIX for user installs
#    $PREREQS_ENV will set up file that can be sourced to set up the ENV for building GenomicsDB
if [[ `uname` == "Darwin" || `id -u` -ne 0 ]]; then
  INSTALL_PREFIX=${INSTALL_PREFIX:-$HOME/genomicsdb_prereqs}
  MAVEN_INSTALL_PREFIX=$INSTALL_PREFIX
  PREREQS_ENV=${PREREQS_ENV:-$HOME/genomicsdb_prereqs.sh}
  echo "GenomicsDB dependencies(e.g. maven, protobuf, etc. that are built from source will be installed to \$INSTALL_PREFIX=$INSTALL_PREFIX"
  echo "GenomicsDB environment will be persisted to \$PREREQS_ENV=$PREREQS_ENV"
  echo "Sleeping for 10 seconds. Ctrl-C if you want to change or setup \$INSTALL_PREFIX or \$PREREQS_ENV"
  sleep 10
else
  INSTALL_PREFIX=${INSTALL_PREFIX:-/usr/local}
  MAVEN_INSTALL_PREFIX=/opt
  PREREQS_ENV=${PREREQS_ENV:-/etc/profile.d/genomicsdb_prereqs.sh}
fi
if [ -f $PREREQS_ENV ]; then
  echo "Found PREREQS_ENV=$PREREQS_ENV from a previous run"
  source $PREREQS_ENV
  rm -f $PREREQS_ENV
fi
touch $PREREQS_ENV

BUILD_DISTRIBUTABLE_LIBRARY=${1:-false}

if [[ `uname` == "Darwin" && $BUILD_DISTRIBUTABLE_LIBRARY == true ]]; then
  export MACOSX_DEPLOYMENT_TARGET=10.13
  echo "export MACOSX_DEPLOYMENT_TARGET=10.13" >> $PREREQS_ENV
fi

################################# Should not have to change anything below ############################

CENTOS_VERSION=0
WGET_NO_CERTIFICATE=""
PARENT_DIR="$(dirname $0)"

# $1 - path variable name
# $2 - path variable value
add_to_env() {
  SEP=":"
  if [[ $1 != *PATH ]]; then
    echo "export $1=$2" >> $PREREQS_ENV
  elif grep -q -w $1 $PREREQS_ENV; then
    VALUE=`grep -w $1 $PREREQS_ENV`
    if [[ $VALUE == *$2* ]]; then
      return 0
    fi
    NEW_VALUE="export $1=$2$SEP${VALUE/export $1=/}"
    sed -i "s|$VALUE\$||g" $PREREQS_ENV
    echo $NEW_VALUE >> $PREREQS_ENV
  elif [[ -z $1 ]]; then
    echo "export $1=$2" >> $PREREQS_ENV
  else
    echo "export $1=$2$SEP\$$1" >> $PREREQS_ENV
  fi
}

install_mvn() {
  MVN=`which mvn`
  if [ -z $MVN ]; then
    if [ ! -d $MAVEN_INSTALL_PREFIX/apache-maven-$MAVEN_VERSION ]; then
      echo "Installing Maven"
      wget $WGET_NO_CERTIFICATE -nv https://downloads.apache.org/maven/maven-3/$MAVEN_VERSION/binaries/apache-maven-$MAVEN_VERSION-bin.tar.gz -P /tmp &&
        tar xf /tmp/apache-maven-*.tar.gz -C $MAVEN_INSTALL_PREFIX &&
        rm /tmp/apache-maven-*.tar.gz
      echo "Installing Maven DONE"
    fi
    rm -f $MAVEN_INSTALL_PREFIX/maven
    ln -s $MAVEN_INSTALL_PREFIX/apache-maven-$MAVEN_VERSION $MAVEN_INSTALL_PREFIX/maven &&
      MVN=$MAVEN_INSTALL_PREFIX/maven/bin/mvn &&
      test -f $MVN
  fi
  MVN_BIN_DIR=`dirname ${MVN}`
  M2_HOME=`dirname ${MVN_BIN_DIR}`
  test -d $M2_HOME  &&
    add_to_env M2_HOME $M2_HOME &&
    add_to_env PATH "\${M2_HOME}/bin"
}

OPENSSL_PREFIX=$INSTALL_PREFIX/ssl
install_openssl() {
  if [[ ! -d $OPENSSL_PREFIX ]]; then
    echo "Installing OpenSSL"
    pushd /tmp
    wget $WGET_NO_CERTIFICATE https://www.openssl.org/source/openssl-$OPENSSL_VERSION.tar.gz &&
      tar -xvzf openssl-$OPENSSL_VERSION.tar.gz &&
      cd openssl-$OPENSSL_VERSION &&
      if [[ `uname` == "Linux" ]]; then
	  CFLAGS=-fPIC ./config -fPIC no-shared --prefix=$OPENSSL_PREFIX --openssldir=$OPENSSL_PREFIX
      else
	  ./Configure darwin64-x86_64-cc no-shared -fPIC --prefix=$OPENSSL_PREFIX
      fi
      make && make install && echo "Installing OpenSSL DONE"
    rm -fr /tmp/openssl*
    popd
  fi
  add_to_env OPENSSL_ROOT_DIR $OPENSSL_PREFIX
  add_to_env LD_LIBRARY_PATH $OPENSSL_PREFIX/lib
}

CURL_PREFIX=$INSTALL_PREFIX
install_curl() {
  if [[ `uname` == "Darwin" ]]; then
    # curl is supported natively in macOS
    return 0
  fi
  if [[ ! -f $CURL_PREFIX/libcurl.a ]]; then
    echo "Installing CURL into $CURL_PREFIX"
    pushd /tmp
    CURL_VERSION_=$(echo $CURL_VERSION | sed -r 's/\./_/g')
    wget https://github.com/curl/curl/releases/download/curl-$CURL_VERSION_/curl-$CURL_VERSION.tar.gz &&
    tar xzf curl-$CURL_VERSION.tar.gz &&
    cd curl-$CURL_VERSION &&
      ./configure --disable-shared --with-pic -without-zstd --with-ssl=$OPENSSL_PREFIX --prefix $CURL_PREFIX &&
      make && make install && echo "Installing CURL DONE"
    rm -fr /tmp/curl
    popd
  fi
  add_to_env LD_LIBRARY_PATH $CURL_PREFIX/lib
}

UUID_PREFIX=$INSTALL_PREFIX
install_uuid() {
  if [[ `uname` == "Darwin" ]]; then
    # libuuid comes via brew install ossp-uuid; it might even be supported natively in macOS now
    return 0
  fi
  if [[ ! -f $UUID_PREFIX/libuuid.a ]]; then
    echo "Installing libuuid into $UUID_PREFIX"
    pushd /tmp
    wget $WGET_NO_CERTIFICATE https://sourceforge.net/projects/libuuid/files/libuuid-$UUID_VERSION.tar.gz &&
      tar -xvzf libuuid-$UUID_VERSION.tar.gz &&
      cd libuuid-$UUID_VERSION &&
      sed -i s/2.69/2.63/ configure.ac &&
      aclocal &&
      automake --add-missing &&
      ./configure --with-pic CFLAGS="-I/usr/include/x86_64-linux-gnu" --disable-shared --enable-static --prefix $UUID_PREFIX &&
      autoreconf -i -f &&
      make && make install && echo "Installing libuuid DONE"
    rm -fr /tmp/libuuid*
    popd
  fi
  add_to_env LD_LIBRARY_PATH $UUID_PREFIX/lib
}

ZLIB_PREFIX=$INSTALL_PREFIX
install_intel_zlib() {
  echo "Installing Intel optimized zlib"

  yum install -y yum-utils &&
	yum-config-manager --add-repo https://yum.repos.intel.com/ipp/setup/intel-ipp.repo &&
		rpm --import https://yum.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB &&
		yum -y install intel-ipp-2018.2-046 &&
	  if [ ! -f /opt/intel/compilers_and_libraries_2018.2.199/linux/ipp/bin/ippvars.sh ]; then
		  echo "Could not find ippvars.sh. Aborting installing Intel optimized zlib"
		  exit 1
	  fi &&
	  wget http://zlib.net/fossils/zlib-1.2.8.tar.gz &&
		tar -xvzf zlib-1.2.8.tar.gz &&
	  source /opt/intel/compilers_and_libraries_2018.2.199/linux/ipp/bin/ippvars.sh intel64 &&
  	echo "source /opt/intel/compilers_and_libraries_2018.2.199/linux/ipp/bin/ippvars.sh intel64" >> $PREREQS_ENV &&
	  pushd $IPPROOT/examples &&
		if [ ! -d components_and_examples_lin_ps ]; then
			sudo mkdir components_and_examples_lin_ps
		fi &&
	  cd components_and_examples_lin_ps &&
		tar -xzvf ../components_and_examples_lin_ps.tgz &&
		popd &&
		cd zlib-1.2.8 &&
		patch -p1 < $IPPROOT/examples/components_and_examples_lin_ps/components/interfaces/ipp_zlib/zlib-1.2.8.patch &&
		export CFLAGS="-m64 -DWITH_IPP -I$IPPROOT/include -fPIC" &&
		export LDFLAGS="$IPPROOT/lib/intel64/libippdc.a $IPPROOT/lib/intel64/libipps.a $IPPROOT/lib/intel64/libippcore.a" &&
		./configure &&
		make shared &&
		mkdir -p $HOME/intel_zlib/lib &&
		cp libz.a $HOME/intel_zlib/lib &&
		rm -fr $HOME/zlib* &&
	echo "Installing Intel optimized zlib done"
  add_to_env LD_LIBRARY_PATH $HOME/intel_zlib
}

centos_version() {
  CENTOS_RELEASE_FILE=/etc/centos-release
  if [[ ! -f $CENTOS_RELEASE_FILE ]]; then
    CENTOS_RELEASE_FILE=/etc/redhat-release
    if [[ ! -f $CENTOS_RELEASE_FILE ]]; then
      return 0
    fi
  fi
  if grep -q "release 6" $CENTOS_RELEASE_FILE; then
    CENTOS_VERSION=6
  elif grep -q "release 7" $CENTOS_RELEASE_FILE; then
    CENTOS_VERSION=7
  elif grep -q "release 8" $CENTOS_RELEASE_FILE; then
    CENTOS_VERSION=8
  fi
}

install_os_prerequisites() {
  case `uname` in
    Linux )
      if apt-get --version >/dev/null 2>&1; then
        export DEBIAN_FRONTEND=noninteractive
        source $PARENT_DIR/system/install_ubuntu_prereqs.sh
      else
        source $PARENT_DIR/system/install_centos_prereqs.sh
      fi
      if [[ $1 == "release" ]]; then
        install_nobuild_prerequisites
      else 
        install_system_prerequisites
      fi
      ;;
    Darwin )
      $PARENT_DIR/system/install_macos_prereqs.sh
      ;;
    * )
      echo "OS=`uname` not supported"
      exit 1
  esac
}

install_prerequisites() {
  PREREQS_ENV=$PREREQS_ENV install_os_prerequisites $1 && echo "Install OS prerequistes successful" &&
    source $PREREQS_ENV
  if [[ $1 == "full" ]]; then
    install_mvn
  fi
}

finalize() {
  echo
  echo "--"
  if [ $1 -ne 0 ]; then
    echo "Error(s) encountered! Please check stderr and correct the errors before proceeding."
  else
    echo "Installing prerequisites DONE. The GenomicsDB env is written out at $PREREQS_ENV for subsequent usage - "
    echo "    Invoke 'source $PREREQS_ENV' to setup environment for building GenomicsDB."
  fi
  return $1
}

centos_version
if [[ $BUILD_DISTRIBUTABLE_LIBRARY == false && $CENTOS_VERSION -eq 6 ]]; then
  echo "Centos 6 is supported only when build-arg distributable_jar=true"
  exit 1
elif [[ $CENTOS_VERSION -eq 6 ]]; then
  # Centos6 has EOL-ed so workaround to get yum to work
  curl https://www.getpagespeed.com/files/centos6-eol.repo --output /etc/yum.repos.d/CentOS-Base.repo
  yum -y install centos-release-scl
  curl https://www.getpagespeed.com/files/centos6-scl-eol.repo --output /etc/yum.repos.d/CentOS-SCLo-scl.repo
  curl https://www.getpagespeed.com/files/centos6-scl-rh-eol.repo --output /etc/yum.repos.d/CentOS-SCLo-scl-rh.repo
  sed -i 's/http/https/g' /etc/yum.repos.d/CentOS-Base.repo
  sed -i 's/http/https/g' /etc/yum.repos.d/CentOS-SCLo-scl.repo
  sed -i 's/http/https/g' /etc/yum.repos.d/CentOS-SCLo-scl-rh.repo
  WGET_NO_CERTIFICATE=" --no-check-certificate"
fi

RC=1
install_prerequisites $2 $3 &&
  if [[ $BUILD_DISTRIBUTABLE_LIBRARY == true ]]; then
    echo "Installing static libraries"
    install_openssl &&
      install_curl &&
      install_uuid &&
      if [[ $CENTOS_VERSION -eq 6 ]]; then
        install_intel_zlib
      fi
  fi && RC=0
finalize $RC