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"""Tests for make_examples_somatic."""

import os


from absl import flags
from absl import logging
from absl.testing import absltest
from absl.testing import flagsaver
from absl.testing import parameterized

from deepvariant import make_examples_core
from deepvariant import make_examples_somatic
from deepvariant import testdata
from third_party.nucleus.testing import test_utils


FLAGS = flags.FLAGS


def setUpModule():
  logging.set_verbosity(logging.FATAL)
  testdata.init()


class MakeExamplesSomaticEnd2EndTest(parameterized.TestCase):

  @flagsaver.flagsaver
  def test_options_and_sample_names(self):
    FLAGS.ref = testdata.CHR20_FASTA
    FLAGS.reads_normal = testdata.CHR20_BAM
    FLAGS.reads_tumor = testdata.CHR20_BAM
    FLAGS.sample_name_normal = 'NORMAL'
    FLAGS.sample_name_tumor = 'TUMOR'
    FLAGS.mode = 'calling'
    FLAGS.examples = ''
    options = make_examples_somatic.default_options(add_flags=True)
    self.assertLen(options.sample_options, 2)
    normal_sample_options = options.sample_options[
        make_examples_somatic.NORMAL_SAMPLE_INDEX
    ]
    tumor_sample_options = options.sample_options[
        make_examples_somatic.MAIN_SAMPLE_INDEX
    ]
    self.assertEqual(normal_sample_options.name, 'NORMAL')
    self.assertEqual(tumor_sample_options.name, 'TUMOR')

  @flagsaver.flagsaver
  def test_make_examples_somatic_end2end_check_calling_examples_suffixes(self):
    FLAGS.ref = testdata.CHR20_FASTA
    FLAGS.reads_normal = testdata.CHR20_BAM
    FLAGS.reads_tumor = testdata.CHR20_BAM
    FLAGS.sample_name_normal = 'NORMAL'
    FLAGS.sample_name_tumor = 'TUMOR'
    FLAGS.mode = 'calling'
    FLAGS.examples = test_utils.test_tmpfile('TEST_SUFFIX.tfrecord.gz')
    with_normal_suffix = test_utils.test_tmpfile(
        'TEST_SUFFIX_normal.tfrecord.gz'
    )
    with_tumor_suffix = test_utils.test_tmpfile('TEST_SUFFIX_tumor.tfrecord.gz')
    options = make_examples_somatic.default_options(add_flags=True)
    FLAGS.regions = 'chr20:10,000,000-10,010,000'
    options = make_examples_somatic.default_options(add_flags=True)
    make_examples_core.make_examples_runner(options)
    # This shows that tumor examples in calling mode are generated without the
    # _tumor suffixes, because it's the only samples generating output.
    self.assertFalse(os.path.exists(with_normal_suffix))
    self.assertFalse(os.path.exists(with_tumor_suffix))
    self.assertTrue(os.path.exists(FLAGS.examples))


if __name__ == '__main__':
  absltest.main()