# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack import *
import os
import glob
import llnl.util.tty as tty


# This application uses cmake to build, but they wrap it with a
# configure script that performs dark magic.  This package does it
# their way.
class Bcl2fastq2(Package):
    """The bcl2fastq2 Conversion Software converts base
       call (BCL) files from a sequencing run into FASTQ
       files."""

    homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html"

    version('2.20.0.422', sha256='8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3')
    version('2.19.1.403', sha256='cf13580f2c1ebcc3642b4d98a02ad01e41a44e644db7d31730f9767b25521806')

    conflicts('platform=darwin',
              msg='malloc.h/etc requirements break build on macs')

    depends_on('boost@1.54.0')
    depends_on('cmake@2.8.9:')
    depends_on('libxml2@2.7.8')
    depends_on('libxslt@1.1.26~crypto')
    depends_on('libgcrypt')
    depends_on('zlib')

    # Their cmake macros don't set the flag when they find a library
    # that makes them happy.
    patch('cmake-macros.patch')
    # After finding the libxslt bits, cmake still needs to wire in the
    # libexslt bits.
    patch('cxxConfigure-cmake.patch')

    root_cmakelists_dir = 'src'

    # v2.17.1.14 and v2.18.0.12 were available via HTTP.
    # v2.19.1.403 is only available via ftp.
    # who knows what the future will hold.
    def url_for_version(self, version):
        url = "ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip"
        if version.string == '2.19.1.403':
            return url.format(version.up_to(3).dotted)
        else:
            return url.format(version.up_to(3).dashed)

    # Illumina tucks the source inside a gzipped tarball inside a zip
    # file.  We let the normal Spack expansion bit unzip the zip file,
    # then follow it with a function untars the tarball after Spack's
    # done it's bit.
    def do_stage(self, mirror_only=False):
        # wrap (decorate) the standard expand_archive step with a
        # helper, then call the real do_stage().
        self.stage.expand_archive = self.unpack_it(self.stage.expand_archive)
        super(Bcl2fastq2, self).do_stage(mirror_only)

    def unpack_it(self, f):
        def wrap():
            f()                 # call the original expand_archive()

            # The tarfile should now reside in the well-known source
            # directory (i.e., self.stage.source_path).
            with working_dir(self.stage.path):
                source_subdir = os.path.relpath(self.stage.source_path,
                                                self.stage.path)
                files = glob.glob(os.path.join(source_subdir,
                                               'bcl2fastq2*.tar.gz'))
                if len(files) == 1:
                    # Rename the tarball so it resides in self.stage.path
                    # alongside the original zip file before unpacking it.
                    tarball = files[0]
                    basename = os.path.basename(tarball)
                    os.rename(tarball, basename)
                    tty.msg("Unpacking bcl2fastq2 tarball")
                    tar = which('tar')
                    tar('-xf', basename)

                    # Rename the unpacked directory to the well-known
                    # source path self.stage.source_path.
                    os.rename('bcl2fastq', source_subdir)
                    tty.msg("Finished unpacking bcl2fastq2 tarball")

                elif self.stage.expanded:
                    # The unpacked files already reside in the "well known"
                    # source directory (i.e., self.stage.source_path).
                    tty.msg("The tarball has already been unpacked.")

        return wrap

    def install(self, spec, prefix):
        bash = which('bash')
        bash("src/configure", "--prefix={0}".format(prefix),
             "--with-cmake={0}".format(join_path(spec['cmake'].prefix.bin,
                                                 "cmake")))
        make()
        make("install")