"""Test cases for procedures defined in computations.gemma"""
import unittest
from unittest import mock

import pytest

from gn3.computations.gemma import generate_gemma_cmd
from gn3.computations.gemma import generate_hash_of_string
from gn3.computations.gemma import generate_pheno_txt_file


class TestGemma(unittest.TestCase):
    """Test cases for computations.gemma module"""
    @pytest.mark.unit_test
    def test_generate_pheno_txt_file(self):
        """Test that the pheno text file is generated correctly"""
        open_mock = mock.mock_open()
        with mock.patch("gn3.computations.gemma.open", open_mock, create=True):
            _file = generate_pheno_txt_file(tmpdir="/tmp",
                                            trait_filename="phenotype.txt",
                                            values=["x", "x", "BXD07 438.700"])
            self.assertEqual(_file, ("/tmp/gn2/phenotype_"
                                     "P7y6QWnwBPedSZdL0+m/GQ.txt"))
        open_mock.assert_called_with(("/tmp/gn2/phenotype_"
                                      "P7y6QWnwBPedSZdL0+m/GQ.txt"), "w", encoding="utf-8")
        open_mock.return_value.write.assert_has_calls([
            mock.call("NA\n"),
            mock.call("NA\n"),
            mock.call("BXD07 438.700\n")
        ])

    @pytest.mark.unit_test
    def test_generate_hash_of_string(self):
        """Test that a string is hashed correctly"""
        self.assertEqual(generate_hash_of_string("I^iQP&TlSR^z"),
                         "hMVRw8kbEp49rOmoIkhMjA")

    @pytest.mark.unit_test
    @mock.patch("gn3.computations.gemma.get_hash_of_files")
    def test_compute_k_values_without_loco(self, mock_get_hash):
        """Test computing k values without loco"""
        mock_get_hash.return_value = "my-hash"
        self.assertEqual(
            generate_gemma_cmd(gemma_cmd="gemma-wrapper",
                               output_dir="/tmp",
                               token="my-token",
                               gemma_kwargs={
                                   "g": "genofile",
                                   "p": "phenofile",
                                   "a": "snpsfile"
                               }), {
                                   "output_file":
                                   "my-hash-output.json",
                                   "gemma_cmd":
                                   ("gemma-wrapper --json -- -g genofile "
                                    "-p phenofile -a snpsfile "
                                    "-gk > /tmp/my-token/my-hash-output.json")
                               })

    @pytest.mark.unit_test
    @mock.patch("gn3.computations.gemma.get_hash_of_files")
    def test_generate_gemma_cmd_with_loco(self, mock_get_hash):
        """Test computing k values with loco"""
        mock_get_hash.return_value = "my-hash"
        self.assertEqual(
            generate_gemma_cmd(gemma_cmd="gemma-wrapper",
                               output_dir="/tmp",
                               token="my-token",
                               chromosomes="1,2,3,4,5",
                               gemma_kwargs={
                                   "g": "genofile",
                                   "p": "phenofile",
                                   "a": "snpsfile"
                               }), {
                                   "output_file":
                                   "my-hash-r+gF5a-output.json",
                                   "gemma_cmd": ("gemma-wrapper --json "
                                                 "--loco 1,2,3,4,5 "
                                                 "-- -g genofile "
                                                 "-p phenofile -a snpsfile "
                                                 "-gk > /tmp/my-token/"
                                                 "my-hash-r+gF5a-output.json")
                               })