# Copyright 2009 by Cymon J. Cox.  All rights reserved.
# Revisions 2009 copyright by Peter Cock.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.
"""Unittests for Bio.Align.Applications interface for DIALIGN2-2."""

import sys
import os
import unittest
import warnings

from Bio import MissingExternalDependencyError
from Bio import BiopythonDeprecationWarning

with warnings.catch_warnings():
    warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
    from Bio.Align.Applications import DialignCommandline

# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"

dialign_exe = None
if sys.platform == "win32":
    raise MissingExternalDependencyError("DIALIGN2-2 not available on Windows")
else:
    from subprocess import getoutput

    output = getoutput("dialign2-2")
    if "not found" not in output and "not recognized" not in output:
        if "dialign2-2" in output.lower():
            dialign_exe = "dialign2-2"
            if "DIALIGN2_DIR" not in os.environ:
                raise MissingExternalDependencyError(
                    "Environment variable DIALIGN2_DIR for DIALIGN2-2 missing."
                )
            if not os.path.isdir(os.environ["DIALIGN2_DIR"]):
                raise MissingExternalDependencyError(
                    "Environment variable DIALIGN2_DIR for DIALIGN2-2 is not a valid directory."
                )
            if not os.path.isfile(os.path.join(os.environ["DIALIGN2_DIR"], "BLOSUM")):
                raise MissingExternalDependencyError(
                    "Environment variable DIALIGN2_DIR directory missing BLOSUM file."
                )
            # TODO - check for tp400_dna, tp400_prot and tp400_trans too?

if not dialign_exe:
    raise MissingExternalDependencyError(
        "Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper."
    )


class DialignApplication(unittest.TestCase):
    def setUp(self):
        self.infile1 = "Fasta/f002"
        # Standard output file
        self.outfile1 = "Fasta/f002.ali"
        # MSF output
        self.outfile2 = "Fasta/f002.ms"

    def tearDown(self):
        if os.path.isfile(self.outfile1):
            os.remove(self.outfile1)
        if os.path.isfile(self.outfile2):
            os.remove(self.outfile2)

    def test_Dialign_simple(self):
        """Simple round-trip through app with infile."""
        # Test using keyword arguments:
        cmdline = DialignCommandline(dialign_exe, input=self.infile1)
        self.assertEqual(str(cmdline), dialign_exe + " Fasta/f002")
        stdout, stderr = cmdline()
        self.assertEqual(stderr, "")
        self.assertEqual(stdout, "")
        self.assertTrue(os.path.exists(self.outfile1))

    def test_Dialign_simple_with_options(self):
        """Simple round-trip through app with infile and options."""
        cmdline = DialignCommandline(dialign_exe)
        cmdline.set_parameter("input", self.infile1)
        cmdline.set_parameter("-max_link", True)
        cmdline.set_parameter("stars", 4)
        self.assertEqual(str(cmdline), dialign_exe + " -max_link -stars 4 Fasta/f002")
        stdout, stderr = cmdline()
        self.assertEqual(stderr, "")
        self.assertEqual(stdout, "")
        self.assertTrue(os.path.exists(self.outfile1))

    def test_Dialign_simple_with_MSF_output(self):
        """Simple round-trip through app with infile, output MSF."""
        cmdline = DialignCommandline(dialign_exe)
        # Test with properties
        cmdline.input = self.infile1
        cmdline.msf = True
        self.assertEqual(str(cmdline), dialign_exe + " -msf Fasta/f002")
        stdout, stderr = cmdline()
        self.assertEqual(stderr, "")
        self.assertEqual(stdout, "")
        self.assertTrue(os.path.exists(self.outfile1))
        self.assertTrue(os.path.exists(self.outfile2))

    def test_Dialign_complex_command_line(self):
        """Round-trip through app with complex command line."""
        cmdline = DialignCommandline(dialign_exe)
        cmdline.set_parameter("input", self.infile1)
        cmdline.set_parameter("-nt", True)
        cmdline.set_parameter("-thr", 4)
        cmdline.set_parameter("stars", 9)
        cmdline.set_parameter("-ow", True)
        cmdline.set_parameter("mask", True)
        cmdline.set_parameter("-cs", True)
        self.assertEqual(
            str(cmdline), dialign_exe + " -cs -mask -nt -ow -stars 9 -thr 4 Fasta/f002"
        )
        stdout, stderr = cmdline()
        self.assertEqual(stderr, "")
        self.assertTrue(os.path.exists(self.outfile1))
        self.assertTrue(stdout.startswith(" e_len = 633"))


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)
