class MiGA::Cli::Action::Init

# File lib/miga/cli/action/init.rb, line 161
def ask_for_optional(symbol, name)
  cli[symbol] = cli[:optional] if !cli[:optional].nil? && cli[symbol].nil?
  return cli[symbol] unless cli[symbol].nil?

  cli[symbol] =
    cli.ask_user(
      "Should I include #{name} modules?",
      'yes', %w(yes no)
    ) == 'yes'
end

# File lib/miga/cli/action/init.rb, line 209
def check_and_install_library(paths, language, library)
  cli.print "Testing #{library}... "
  if test_library(cli, paths, language, library)
    cli.puts 'yes'
  else
    cli.puts 'no, installing'
    out = install_library(cli, paths, language, library)
    unless test_library(cli, paths, language, library)
      cli.puts out
      raise "Cannot install #{language.to_s.capitalize} library: #{library}"
    end
  end
end

# File lib/miga/cli/action/init.rb, line 193
def check_libraries(paths)
  req_libraries = {
    r: %w[ape cluster vegan],
    ruby: %w[sqlite3 daemons json],
    python: %w[numpy sqlite3 pyhmmer pyrodigal]
  }

  req_libraries.each do |language, libraries|
    cli.puts "Looking for #{language.to_s.capitalize} libraries:"
    libraries.each do |lib|
      check_and_install_library(paths, language, lib)
    end
    cli.puts ''
  end
end

# File lib/miga/cli/action/init.rb, line 121
def check_software_requirements(rc_fh)
  cli.puts 'Looking for requirements:'
  opt_groups = {
    mytaxa: 'MyTaxa',
    rdp: 'RDP classifier',
    reads: 'read processing'
  }
  opt_groups.each do |k, v|
    ask_for_optional(k, v)
    rc_fh.puts "export MIGA_#{k.to_s.upcase}='#{cli[k] ? 'yes' : 'no'}'"
  end
  paths = {}
  rc_fh.puts 'MIGA_PATH=""'
  req_path = File.expand_path('utils/requirements.txt', MiGA.root_path)
  File.open(req_path, 'r') do |fh|
    fh.each_line do |ln|
      r = define_software(ln) or next
      cli.print "Testing #{r[0]}#{" (#{r[3]})" if r[3]}... "
      if cli[:"path_to_#{r[1]}"]
        paths[r[1]] = cli[:"path_to_#{r[1]}"]
        cli.puts "user-provided: #{paths[r[1]]}"
      else
        path = find_software(r[1])
        paths[r[1]] = File.expand_path(r[1], path).shellescape
      end
    end
  end
  rc_fh.puts 'export PATH="$MIGA_PATH$PATH"'
  cli.puts ''
  paths
end

# File lib/miga/cli/action/init.rb, line 153
def define_software(ln)
  r = ln.chomp.split(/\t+/)
  return if %w[Software --------].include?(r[0])
  %[mytaxa rdp reads].each { |i| return if r[0] =~ /\(#{i}\)$/ && !cli[i] }

  r
end

# File lib/miga/cli/action/init.rb, line 89
def empty_action
end

# File lib/miga/cli/action/init.rb, line 172
def find_software(exec)
  path = nil
  loop do
    d_path = File.dirname(run_cmd(cli, ['which', exec], raise: false))
    if cli[:ask] || d_path == '.'
      path = cli.ask_user('Where can I find it?', d_path, nil, true)
    else
      path = d_path
      cli.puts path
    end
    if File.executable?(File.expand_path(exec, path))
      if d_path != path
        rc_fh.puts "MIGA_PATH=\"#{path}:$MIGA_PATH\" # #{exec}"
      end
      break
    end
    cli.print "I cannot find #{exec}. "
  end
  path
end

# File lib/miga/cli/action/init.rb, line 241
def install_library(cli, paths, language, pkg)
  case language
  when :r
    r_cmd = "install.packages('#{pkg}', repos='http://cran.rstudio.com/')"
    run_r_cmd(cli, paths, r_cmd)
  when :ruby
    # This hackey mess is meant to ensure the test and installation are done
    # on the configuration Ruby, not on the Ruby currently executing the
    # init action
    x = [
      paths['ruby'], '-r', 'rubygems', '-r', 'rubygems/gem_runner',
      '-e', "Gem::GemRunner.new.run %w(install --user #{pkg})"
    ]
    run_cmd(cli, x, err2out: true)
  when :python
    x = [paths['python3'], '-m', 'pip', 'install', '--user', pkg]
    run_cmd(cli, x, err2out: true)
  else
    raise "Unrecognized language: #{language}"
  end
end

# File lib/miga/cli/action/init.rb, line 105
def list_requirements
  if cli.ask_user(
    'Would you like to see all the requirements before starting?',
    'no', %w(yes no)
  ) == 'yes'
    cli.puts ''
    req_path = File.join(MiGA.root_path, 'utils', 'requirements.txt')
    File.open(req_path, 'r') do |fh|
      fh.each_line { |ln| cli.puts ln }
    end
    cli.puts ''
  end
end

# File lib/miga/cli/action/init.rb, line 12
def parse_cli
  cli.interactive = true
  cli.defaults = {
    mytaxa: nil,
    rdp: nil,
    reads: nil,
    optional: nil,
    config: File.join(ENV['MIGA_HOME'], '.miga_modules'),
    ask: false,
    auto: false,
    dtype: :bash
  }
  cli.parse do |opt|
    opt.on(
      '-c', '--config PATH',
      'Path to the Bash configuration file',
      "By default: #{cli[:config]}"
    ) { |v| cli[:config] = v }
    opt.on(
      '--[no-]mytaxa',
      'Should I try setting up MyTaxa and its dependencies?',
      'By default: interactive (true if --auto)'
    ) { |v| cli[:mytaxa] = v }
    opt.on(
      '--[no-]rdp',
      'Should I try setting up the RDP classifier?',
      'By default: interactive (true if --auto)'
    ) { |v| cli[:rdp] = v }
    opt.on(
      '--[no-]read-processing',
      'Should I try setting up read processing software?',
      'By default: interactive (true if --auto)'
    ) { |v| cli[:reads] = v }
    opt.on(
      '--[no-]optional',
      'Should I try setting up the optional software?',
      'Automatically sets answers for mytaxa, rdp, and reads'
    ) { |v| cli[:optional] = v }
    opt.on(
      '--daemon-type STRING',
      'Type of daemon launcher, one of: bash, ssh, qsub, msub, slurm',
      "By default: interactive (#{cli[:dtype]} if --auto)"
    ) { |v| cli[:dtype] = v.to_sym }
    %w[R ruby python].each do |bin|
      opt.on(
        "--path-to-#{bin} STRING",
        "Use this path to #{bin} instead of testing for executables"
      ) { |v| cli[:"path_to_#{bin}"] = v }
    end
    opt.on(
      '--ask-all',
      'Ask for the location of all software',
      'By default, only the locations missing in PATH are requested'
    ) { |v| cli[:ask] = v }
  end
end

# File lib/miga/cli/action/init.rb, line 69
  def perform
    cli.puts <<~BANNER
      ===[ Welcome to MiGA, the Microbial Genome Atlas ]===

      I'm the initialization script, and I'll sniff around your computer to
      make sure you have all the requirements for MiGA data processing.

    BANNER
    list_requirements
    rc_fh = open_rc_file
    check_configuration_script(rc_fh)
    paths = check_software_requirements(rc_fh)
    check_additional_files(paths)
    check_libraries(paths)
    configure_daemon
    close_rc_file(rc_fh)
    cli.puts 'Configuration complete. MiGA is ready to work!'
    cli.puts ''
  end

  def empty_action
  end

  def run_cmd(cli, cmd, opts = {})
    opts = { return: :output, source: cli[:config] }.merge(opts)
    MiGA::MiGA.run_cmd(cmd, opts)
  end

  def run_r_cmd(cli, paths, cmd, opts = {})
    run_cmd(
      cli,
      "echo #{cmd.shellescape} | #{paths['R'].shellescape} --vanilla -q",
      { err2out: true, stdout: '/dev/null' }.merge(opts)
    )
  end

  def list_requirements
    if cli.ask_user(
      'Would you like to see all the requirements before starting?',
      'no', %w(yes no)
    ) == 'yes'
      cli.puts ''
      req_path = File.join(MiGA.root_path, 'utils', 'requirements.txt')
      File.open(req_path, 'r') do |fh|
        fh.each_line { |ln| cli.puts ln }
      end
      cli.puts ''
    end
  end

  private

  def check_software_requirements(rc_fh)
    cli.puts 'Looking for requirements:'
    opt_groups = {
      mytaxa: 'MyTaxa',
      rdp: 'RDP classifier',
      reads: 'read processing'
    }
    opt_groups.each do |k, v|
      ask_for_optional(k, v)
      rc_fh.puts "export MIGA_#{k.to_s.upcase}='#{cli[k] ? 'yes' : 'no'}'"
    end
    paths = {}
    rc_fh.puts 'MIGA_PATH=""'
    req_path = File.expand_path('utils/requirements.txt', MiGA.root_path)
    File.open(req_path, 'r') do |fh|
      fh.each_line do |ln|
        r = define_software(ln) or next
        cli.print "Testing #{r[0]}#{" (#{r[3]})" if r[3]}... "
        if cli[:"path_to_#{r[1]}"]
          paths[r[1]] = cli[:"path_to_#{r[1]}"]
          cli.puts "user-provided: #{paths[r[1]]}"
        else
          path = find_software(r[1])
          paths[r[1]] = File.expand_path(r[1], path).shellescape
        end
      end
    end
    rc_fh.puts 'export PATH="$MIGA_PATH$PATH"'
    cli.puts ''
    paths
  end

  def define_software(ln)
    r = ln.chomp.split(/\t+/)
    return if %w[Software --------].include?(r[0])
    %[mytaxa rdp reads].each { |i| return if r[0] =~ /\(#{i}\)$/ && !cli[i] }

    r
  end

  def ask_for_optional(symbol, name)
    cli[symbol] = cli[:optional] if !cli[:optional].nil? && cli[symbol].nil?
    return cli[symbol] unless cli[symbol].nil?

    cli[symbol] =
      cli.ask_user(
        "Should I include #{name} modules?",
        'yes', %w(yes no)
      ) == 'yes'
  end

  def find_software(exec)
    path = nil
    loop do
      d_path = File.dirname(run_cmd(cli, ['which', exec], raise: false))
      if cli[:ask] || d_path == '.'
        path = cli.ask_user('Where can I find it?', d_path, nil, true)
      else
        path = d_path
        cli.puts path
      end
      if File.executable?(File.expand_path(exec, path))
        if d_path != path
          rc_fh.puts "MIGA_PATH=\"#{path}:$MIGA_PATH\" # #{exec}"
        end
        break
      end
      cli.print "I cannot find #{exec}. "
    end
    path
  end

  def check_libraries(paths)
    req_libraries = {
      r: %w[ape cluster vegan],
      ruby: %w[sqlite3 daemons json],
      python: %w[numpy sqlite3 pyhmmer pyrodigal]
    }

    req_libraries.each do |language, libraries|
      cli.puts "Looking for #{language.to_s.capitalize} libraries:"
      libraries.each do |lib|
        check_and_install_library(paths, language, lib)
      end
      cli.puts ''
    end
  end

  def check_and_install_library(paths, language, library)
    cli.print "Testing #{library}... "
    if test_library(cli, paths, language, library)
      cli.puts 'yes'
    else
      cli.puts 'no, installing'
      out = install_library(cli, paths, language, library)
      unless test_library(cli, paths, language, library)
        cli.puts out
        raise "Cannot install #{language.to_s.capitalize} library: #{library}"
      end
    end
  end

  def test_library(cli, paths, language, pkg)
    opts = { raise: false, return: :status, stderr: '/dev/null' }
    status =
      case language
      when :r
        run_r_cmd(cli, paths, "library('#{pkg}')", opts)
      when :ruby
        x = [paths['ruby'], '-r', pkg, '-e', '']
        run_cmd(cli, x, opts)
      when :python
        x = [paths['python3'], '-c', "import #{pkg}"]
        run_cmd(cli, x, opts)
      else
        raise "Unrecognized language: #{language}"
      end
    status.success?
  end

  def install_library(cli, paths, language, pkg)
    case language
    when :r
      r_cmd = "install.packages('#{pkg}', repos='http://cran.rstudio.com/')"
      run_r_cmd(cli, paths, r_cmd)
    when :ruby
      # This hackey mess is meant to ensure the test and installation are done
      # on the configuration Ruby, not on the Ruby currently executing the
      # init action
      x = [
        paths['ruby'], '-r', 'rubygems', '-r', 'rubygems/gem_runner',
        '-e', "Gem::GemRunner.new.run %w(install --user #{pkg})"
      ]
      run_cmd(cli, x, err2out: true)
    when :python
      x = [paths['python3'], '-m', 'pip', 'install', '--user', pkg]
      run_cmd(cli, x, err2out: true)
    else
      raise "Unrecognized language: #{language}"
    end
  end
end

# File lib/miga/cli/action/init.rb, line 92
def run_cmd(cli, cmd, opts = {})
  opts = { return: :output, source: cli[:config] }.merge(opts)
  MiGA::MiGA.run_cmd(cmd, opts)
end

# File lib/miga/cli/action/init.rb, line 97
def run_r_cmd(cli, paths, cmd, opts = {})
  run_cmd(
    cli,
    "echo #{cmd.shellescape} | #{paths['R'].shellescape} --vanilla -q",
    { err2out: true, stdout: '/dev/null' }.merge(opts)
  )
end

# File lib/miga/cli/action/init.rb, line 223
def test_library(cli, paths, language, pkg)
  opts = { raise: false, return: :status, stderr: '/dev/null' }
  status =
    case language
    when :r
      run_r_cmd(cli, paths, "library('#{pkg}')", opts)
    when :ruby
      x = [paths['ruby'], '-r', pkg, '-e', '']
      run_cmd(cli, x, opts)
    when :python
      x = [paths['python3'], '-c', "import #{pkg}"]
      run_cmd(cli, x, opts)
    else
      raise "Unrecognized language: #{language}"
    end
  status.success?
end