# Copyright 2010 by Thomas Schmitt.  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.
"""Tests for SeqIO SeqXML module."""

import unittest
import sys

from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio._py3k import StringIO

test_files = {
    "dna": ["SeqXML/dna_example.xml", 4],
    "rna": ["SeqXML/rna_example.xml", 5],
    "protein": ["SeqXML/protein_example.xml", 5],
    "globalSpecies": ["SeqXML/global_species_example.xml", 2],
}

corrupt_files = [
    "SeqXML/corrupt_example1.xml",
    "SeqXML/corrupt_example2.xml",
]


def assert_equal_records(testCase, record_a, record_b):
    testCase.assertEqual(record_a.id, record_b.id)
    testCase.assertEqual(record_a.name, record_b.name)
    testCase.assertEqual(record_a.description, record_b.description)
    testCase.assertEqual(str(record_a.seq), str(record_b.seq))
    testCase.assertEqual(record_a.dbxrefs, record_b.dbxrefs)
    testCase.assertEqual(record_a.annotations, record_a.annotations)


class TestSimpleRead(unittest.TestCase):

    def test_check_SeqIO(self):
        """Files readable using parser via SeqIO."""
        for key in test_files:
            records = list(SeqIO.parse(test_files[key][0], "seqxml"))
            self.assertEqual(len(records), test_files[key][1])


class TestDetailedRead(unittest.TestCase):

    records = {}

    def setUp(self):
        for key in test_files:
            self.records[key] = list(SeqIO.parse(test_files[key][0], "seqxml"))

    def test_special_characters_desc(self):
        """Read special XML characters in description."""
        self.assertEqual(self.records["dna"][2].description, u'some special characters in the description\n<tag> "quoted string"')

    # TODO - Fix this failure under Windows with Python 3.1 and 3.2
    if not (sys.platform == "win32" and sys.version_info[0] >= 3):
        def test_unicode_characters_desc(self):
            """Test special unicode characters in the description."""
            self.assertEqual(self.records["rna"][2].description, u"\u00E5\u00C5\u00FC\u00F6\u00D6\u00DF\u00F8\u00E4\u00A2\u00A3$\u20AC\u9999\u80A0")

    def test_full_characters_set_read(self):
        """Read full characters set for each type."""
        self.assertEqual(str(self.records["dna"][1].seq), "ACGTMRWSYKVHDBXN.-")
        self.assertEqual(str(self.records["rna"][1].seq), "ACGUMRWSYKVHDBXN.-")
        self.assertEqual(str(self.records["protein"][1].seq), "ABCDEFGHIJKLMNOPQRSTUVWXYZ.-*")

    def test_duplicated_property(self):
        """Read property with multiple values."""
        self.assertEqual(self.records["protein"][2].annotations["test"], [u"1", u"2", u"3"])

    def test_duplicated_dbxref(self):
        """Read multiple cross references to a single source."""
        self.assertEqual(self.records["protein"][2].dbxrefs, [u"someDB:G001", u"someDB:G002"])

    def test_read_minimal_required(self):
        """Check minimal record."""
        minimalRecord = SeqRecord(id="test", seq=Seq("abc"))
        minimalRecord.annotations["source"] = u"Ensembl"

        self.assertEqual(self.records["rna"][3].name, minimalRecord.name)
        self.assertEqual(self.records["dna"][3].annotations, minimalRecord.annotations)
        self.assertEqual(self.records["rna"][3].dbxrefs, minimalRecord.dbxrefs)
        self.assertEqual(self.records["protein"][3].description, minimalRecord.description)

    def test_local_species(self):
        """Check local species."""
        self.assertEqual(self.records["rna"][1].annotations["organism"], "Mus musculus")
        self.assertEqual(self.records["rna"][1].annotations["ncbi_taxid"], "10090")

        self.assertEqual(self.records["rna"][0].annotations["organism"], "Gallus gallus")
        self.assertEqual(self.records["rna"][0].annotations["ncbi_taxid"], "9031")

    def test_global_species(self):
        """Check global species."""
        self.assertEqual(self.records["globalSpecies"][0].annotations["organism"], "Mus musculus")
        self.assertEqual(self.records["globalSpecies"][0].annotations["ncbi_taxid"], "10090")

        self.assertEqual(self.records["globalSpecies"][1].annotations["organism"], "Homo sapiens")
        self.assertEqual(self.records["globalSpecies"][1].annotations["ncbi_taxid"], "9606")

    def test_local_source_definition(self):
        """Check local source."""
        self.assertEqual(self.records["protein"][4].annotations["source"], u"Uniprot")

    def test_empty_description(self):
        """Check empty description."""
        self.assertEqual(self.records["rna"][4].description, SeqRecord(id="", seq=Seq("")).description)


class TestReadAndWrite(unittest.TestCase):

    def test_read_write_rna(self):
        """Read and write RNA."""
        read1_records = list(SeqIO.parse(test_files["rna"][0], "seqxml"))
        self._write_parse_and_compare(read1_records)

    def test_read_write_dna(self):
        """Read and write DNA."""
        read1_records = list(SeqIO.parse(test_files["dna"][0], "seqxml"))
        self._write_parse_and_compare(read1_records)

    def test_read_write_protein(self):
        """Read and write protein."""
        read1_records = list(SeqIO.parse(test_files["protein"][0], "seqxml"))
        self._write_parse_and_compare(read1_records)

    def test_read_write_globalSpecies(self):
        """Read and write global species."""
        read1_records = list(SeqIO.parse(test_files["globalSpecies"][0], "seqxml"))
        self._write_parse_and_compare(read1_records)

    def _write_parse_and_compare(self, read1_records):

        handle = StringIO()

        SeqIO.write(read1_records, handle, "seqxml")

        handle.seek(0)
        read2_records = list(SeqIO.parse(handle, "seqxml"))

        self.assertEqual(len(read1_records), len(read2_records))

        for record1, record2 in zip(read1_records, read2_records):
            assert_equal_records(self, record1, record2)

    def test_write_species(self):
        """Test writing species from annotation tags."""
        record = SeqIO.read("SwissProt/sp016", "swiss")
        self.assertEqual(record.annotations["organism"], "Homo sapiens (Human)")
        self.assertEqual(record.annotations["ncbi_taxid"], ["9606"])
        handle = StringIO()
        SeqIO.write(record, handle, "seqxml")
        handle.seek(0)
        output = handle.getvalue()
        self.assertIn("Homo sapiens (Human)", output)
        self.assertIn("9606", output)
        if '<species name="Homo sapiens (Human)" ncbiTaxID="9606"/>' in output:
            # Good, but don't get this (do we?)
            pass
        elif '<species name="Homo sapiens (Human)" ncbiTaxID="9606"></species>' in output:
            # Not as concise, but fine (seen on C Python)
            pass
        elif '<species ncbiTaxID="9606" name="Homo sapiens (Human)"></species>' in output:
            # Jython uses a different order
            pass
        elif '<species ncbiTaxID="9606" name="Homo sapiens (Human)"/>' in output:
            # This would be fine too, but don't get this (do we?)
            pass
        else:
            raise ValueError("Mising expected <species> tag: %r" % output)


class TestReadCorruptFiles(unittest.TestCase):

    def test_for_errors(self):
        """Handling of corrupt files."""
        for filename in corrupt_files:
            iterator = SeqIO.parse(filename, "seqxml")
            self.assertRaises(ValueError, next, iterator)


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