# Copyright 2009-2017 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.
"""Unit tests for Bio.SeqIO.index(...) and index_db() functions."""

try:
    import sqlite3
except ImportError:
    # Try to run what tests we can in case sqlite3 was not installed
    sqlite3 = None

import os
import unittest
import tempfile
import threading
import gzip
import warnings
from io import BytesIO
from io import StringIO

from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
from Bio.SeqIO._index import _FormatToRandomAccess

from Bio import BiopythonParserWarning
from Bio import MissingPythonDependencyError

from seq_tests_common import SeqRecordTestBaseClass
from test_SeqIO import SeqIOTestBaseClass


CUR_DIR = os.getcwd()


if sqlite3:

    def raw_filenames(index_filename):
        """Open SQLite index and extract filenames (as is).

        Returns a 2-tuple, holding a list of strings, and the value
        of the meta_data.filenames_relative_to_index (or None).
        """
        con = sqlite3.dbapi2.connect(index_filename)

        filenames = [
            row[0]
            for row in con.execute(
                "SELECT name FROM file_data ORDER BY file_number;"
            ).fetchall()
        ]

        try:
            (filenames_relative_to_index,) = con.execute(
                "SELECT value FROM meta_data WHERE key=?;",
                ("filenames_relative_to_index",),
            ).fetchone()
            filenames_relative_to_index = filenames_relative_to_index.upper() == "TRUE"
        except TypeError:
            filenames_relative_to_index = None

        con.close()
        return filenames, filenames_relative_to_index

    class OldIndexTest(unittest.TestCase):
        """Testing a pre-built index (make sure cross platform etc).

        >>> from Bio import SeqIO
        >>> d = SeqIO.index_db("triple_sff.idx", ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"], "sff")
        >>> len(d)
        54
        """

        def setUp(self):
            os.chdir(CUR_DIR)

        def tearDown(self):
            os.chdir(CUR_DIR)

        def test_old(self):
            """Load existing index with no options (from parent directory)."""
            d = SeqIO.index_db("Roche/triple_sff.idx")
            self.assertEqual(54, len(d))
            self.assertRaises(FileNotFoundError, d.get_raw, "alpha")

        def test_old_check_same_thread(self):
            """Setting check_same_thread to False doesn't raise an exception."""
            d = SeqIO.index_db("Roche/triple_sff_rel_paths.idx")

            def reader_thread():
                try:
                    d["alpha"]
                except sqlite3.ProgrammingError:
                    self.fail(
                        "Raised sqlite3.ProgrammingError in violation of check_same_thread=False"
                    )

            reader = threading.Thread(target=reader_thread)
            reader.start()
            reader.join()

        def test_old_rel(self):
            """Load existing index (with relative paths) with no options (from parent directory)."""
            d = SeqIO.index_db("Roche/triple_sff_rel_paths.idx")
            self.assertEqual(54, len(d))
            self.assertEqual(395, len(d["alpha"]))

        def test_old_contents(self):
            """Check actual filenames in existing indexes."""
            filenames, flag = raw_filenames("Roche/triple_sff.idx")
            self.assertIsNone(flag)
            self.assertEqual(
                filenames, ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"]
            )

            filenames, flag = raw_filenames("Roche/triple_sff_rel_paths.idx")
            self.assertTrue(flag)
            self.assertEqual(
                filenames, ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"]
            )

        def test_old_same_dir(self):
            """Load existing index with no options (from same directory)."""
            os.chdir("Roche")
            d = SeqIO.index_db("triple_sff.idx")
            self.assertEqual(54, len(d))
            self.assertEqual(395, len(d["alpha"]))

        def test_old_same_dir_rel(self):
            """Load existing index (with relative paths) with no options (from same directory)."""
            os.chdir("Roche")
            d = SeqIO.index_db("triple_sff_rel_paths.idx")
            self.assertEqual(54, len(d))
            self.assertEqual(395, len(d["alpha"]))

        def test_old_format(self):
            """Load existing index with correct format."""
            d = SeqIO.index_db("Roche/triple_sff.idx", format="sff")
            self.assertEqual(54, len(d))

        def test_old_format_wrong(self):
            """Load existing index with wrong format."""
            self.assertRaises(
                ValueError, SeqIO.index_db, "Roche/triple_sff.idx", format="fasta"
            )

        def test_old_files(self):
            """Load existing index with correct files (from parent directory)."""
            d = SeqIO.index_db(
                "Roche/triple_sff.idx",
                ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"],
            )
            self.assertEqual(54, len(d))
            self.assertRaises(FileNotFoundError, d.get_raw, "alpha")

        def test_old_files_same_dir(self):
            """Load existing index with correct files (from same directory)."""
            os.chdir("Roche")
            d = SeqIO.index_db(
                "triple_sff.idx",
                ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"],
            )
            self.assertEqual(54, len(d))
            self.assertEqual(395, len(d["alpha"]))

        def test_old_files_wrong(self):
            """Load existing index with wrong files."""
            self.assertRaises(
                ValueError,
                SeqIO.index_db,
                "Roche/triple_sff.idx",
                ["a.sff", "b.sff", "c.sff"],
            )

        def test_old_files_wrong2(self):
            """Load existing index with wrong number of files."""
            self.assertRaises(
                ValueError,
                SeqIO.index_db,
                "Roche/triple_sff.idx",
                ["E3MFGYR02_no_manifest.sff", "greek.sff"],
            )

    class NewIndexTest(unittest.TestCase):
        """Check paths etc in newly built index."""

        def setUp(self):
            os.chdir(CUR_DIR)

        def tearDown(self):
            os.chdir(CUR_DIR)
            for i in ["temp.idx", "Roche/temp.idx"]:
                if os.path.isfile(i):
                    os.remove(i)

        def check(self, index_file, sff_files, expt_sff_files):
            if os.path.isfile(index_file):
                os.remove(index_file)
            # Build index...
            d = SeqIO.index_db(index_file, sff_files, "sff")
            self.assertEqual(395, len(d["alpha"]))
            d._con.close()  # hack for PyPy
            d.close()
            self.assertEqual(
                [os.path.abspath(f) for f in sff_files],
                [os.path.abspath(f) for f in d._filenames],
            )

            # Now directly check the filenames inside the SQLite index:
            filenames, flag = raw_filenames(index_file)
            self.assertTrue(flag)
            self.assertEqual(filenames, expt_sff_files)

            # Load index...
            d = SeqIO.index_db(index_file, sff_files)
            self.assertEqual(395, len(d["alpha"]))
            d._con.close()  # hack for PyPy
            d.close()
            self.assertEqual([os.path.abspath(f) for f in sff_files], d._filenames)

            os.remove(index_file)

        def test_child_folder_rel(self):
            """Check relative links to child folder."""
            # Note we expect relative paths recorded with Unix slashs!
            expt_sff_files = [
                "Roche/E3MFGYR02_no_manifest.sff",
                "Roche/greek.sff",
                "Roche/paired.sff",
            ]

            self.check("temp.idx", expt_sff_files, expt_sff_files)
            # Here index is given as abs
            self.check(
                os.path.abspath("temp.idx"),
                [
                    "Roche/E3MFGYR02_no_manifest.sff",
                    os.path.abspath("Roche/greek.sff"),
                    "Roche/paired.sff",
                ],
                expt_sff_files,
            )
            # Here index is given as relative path
            self.check(
                "temp.idx",
                [
                    "Roche/E3MFGYR02_no_manifest.sff",
                    os.path.abspath("Roche/greek.sff"),
                    "Roche/paired.sff",
                ],
                expt_sff_files,
            )

        def test_same_folder(self):
            """Check relative links in same folder."""
            os.chdir("Roche")
            expt_sff_files = ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"]

            # Here everything is relative,
            self.check("temp.idx", expt_sff_files, expt_sff_files)
            self.check(
                os.path.abspath("temp.idx"),
                [
                    "E3MFGYR02_no_manifest.sff",
                    os.path.abspath("greek.sff"),
                    "../Roche/paired.sff",
                ],
                expt_sff_files,
            )
            self.check(
                "temp.idx",
                [
                    "E3MFGYR02_no_manifest.sff",
                    os.path.abspath("greek.sff"),
                    "../Roche/paired.sff",
                ],
                expt_sff_files,
            )
            self.check(
                "../Roche/temp.idx",
                [
                    "E3MFGYR02_no_manifest.sff",
                    os.path.abspath("greek.sff"),
                    "../Roche/paired.sff",
                ],
                expt_sff_files,
            )

        def test_some_abs(self):
            """Check absolute filenames in index.

            Unless the repository and tests themselves are under the temp
            directory (as detected by ``tempfile``), we expect the index to
            use absolute filenames.
            """
            h, t = tempfile.mkstemp(prefix="index_test_", suffix=".idx")
            os.close(h)
            os.remove(t)

            abs_sff_files = [
                os.path.abspath("Roche/E3MFGYR02_no_manifest.sff"),
                os.path.abspath("Roche/greek.sff"),
                os.path.abspath(os.path.join("Roche", "paired.sff")),
            ]

            if os.getcwd().startswith(os.path.dirname(t)):
                # The tests are being run from within the temp directory,
                # e.g. index filename /tmp/index_test_XYZ.idx
                # and working directory of /tmp/biopython/Tests/
                # This means the indexing will use a RELATIVE path
                # e.g. biopython/Tests/Roche/E3MFGYR02_no_manifest.sff
                # not /tmp/biopython/Tests/Roche/E3MFGYR02_no_manifest.sff
                expt_sff_files = [
                    os.path.relpath(f, os.path.dirname(t)) for f in abs_sff_files
                ]
            else:
                expt_sff_files = abs_sff_files

            # Providing absolute paths...
            self.check(t, abs_sff_files, expt_sff_files)
            # Now try with mix of abs and relative paths...
            self.check(
                t,
                [
                    os.path.abspath("Roche/E3MFGYR02_no_manifest.sff"),
                    os.path.join("Roche", "greek.sff"),
                    os.path.abspath("Roche/paired.sff"),
                ],
                expt_sff_files,
            )


class IndexDictTests(SeqRecordTestBaseClass, SeqIOTestBaseClass):

    tests = [
        ("Ace/contig1.ace", "ace"),
        ("Ace/consed_sample.ace", "ace"),
        ("Ace/seq.cap.ace", "ace"),
        ("Quality/wrapping_original_sanger.fastq", "fastq"),
        ("Quality/example.fastq", "fastq"),  # Unix newlines
        ("Quality/example.fastq", "fastq-sanger"),
        ("Quality/example_dos.fastq", "fastq"),  # DOS/Windows newlines
        ("Quality/tricky.fastq", "fastq"),
        ("Quality/sanger_faked.fastq", "fastq-sanger"),
        ("Quality/solexa_faked.fastq", "fastq-solexa"),
        ("Quality/illumina_faked.fastq", "fastq-illumina"),
        ("Quality/zero_length.fastq", "fastq"),
        ("EMBL/epo_prt_selection.embl", "embl"),
        ("EMBL/U87107.embl", "embl"),
        ("EMBL/TRBG361.embl", "embl"),
        ("EMBL/kipo_prt_sample.embl", "embl"),
        ("EMBL/A04195.imgt", "embl"),  # Not a proper EMBL file, an IMGT file
        ("EMBL/A04195.imgt", "imgt"),
        ("EMBL/hla_3260_sample.imgt", "imgt"),
        ("EMBL/patents.embl", "embl"),
        ("EMBL/AAA03323.embl", "embl"),
        ("GenBank/NC_000932.faa", "fasta"),
        ("GenBank/NC_005816.faa", "fasta"),
        ("GenBank/NC_005816.tsv", "tab"),
        ("GenBank/NC_005816.ffn", "fasta"),
        ("GenBank/NC_005816.fna", "fasta"),
        ("GenBank/NC_005816.gb", "gb"),
        ("GenBank/cor6_6.gb", "genbank"),
        ("GenBank/empty_accession.gbk", "gb"),
        ("GenBank/empty_version.gbk", "gb"),
        ("IntelliGenetics/vpu_nucaligned.txt", "ig"),
        ("IntelliGenetics/TAT_mase_nuc.txt", "ig"),
        ("IntelliGenetics/VIF_mase-pro.txt", "ig"),
        ("Phd/phd1", "phd"),
        ("Phd/phd2", "phd"),
        ("Phd/phd_solexa", "phd"),
        ("Phd/phd_454", "phd"),
        ("NBRF/B_nuc.pir", "pir"),
        ("NBRF/Cw_prot.pir", "pir"),
        ("NBRF/clustalw.pir", "pir"),
        ("SwissProt/sp001", "swiss"),
        ("SwissProt/sp010", "swiss"),
        ("SwissProt/sp016", "swiss"),
        ("SwissProt/multi_ex.txt", "swiss"),
        ("SwissProt/multi_ex.xml", "uniprot-xml"),
        ("SwissProt/multi_ex.fasta", "fasta"),
        ("Roche/E3MFGYR02_random_10_reads.sff", "sff"),
        ("Roche/E3MFGYR02_random_10_reads.sff", "sff-trim"),
        ("Roche/E3MFGYR02_index_at_start.sff", "sff"),
        ("Roche/E3MFGYR02_index_in_middle.sff", "sff"),
        ("Roche/E3MFGYR02_alt_index_at_start.sff", "sff"),
        ("Roche/E3MFGYR02_alt_index_in_middle.sff", "sff"),
        ("Roche/E3MFGYR02_alt_index_at_end.sff", "sff"),
        ("Roche/E3MFGYR02_no_manifest.sff", "sff"),
        ("Roche/greek.sff", "sff"),
        ("Roche/greek.sff", "sff-trim"),
        ("Roche/paired.sff", "sff"),
        ("Roche/paired.sff", "sff-trim"),
    ]

    def setUp(self):
        os.chdir(CUR_DIR)
        h, self.index_tmp = tempfile.mkstemp("_idx.tmp")
        os.close(h)

    def tearDown(self):
        os.chdir(CUR_DIR)
        if os.path.isfile(self.index_tmp):
            os.remove(self.index_tmp)

    def check_dict_methods(self, rec_dict, keys, ids, msg):
        self.assertCountEqual(keys, rec_dict.keys(), msg=msg)
        # This is redundant, I just want to make sure len works:
        self.assertEqual(len(keys), len(rec_dict), msg=msg)
        # Make sure boolean evaluation works
        self.assertEqual(bool(keys), bool(rec_dict), msg=msg)
        for key, id in zip(keys, ids):
            self.assertIn(key, rec_dict, msg=msg)
            self.assertEqual(id, rec_dict[key].id, msg=msg)
            self.assertEqual(id, rec_dict.get(key).id, msg=msg)
        # Check non-existant keys,
        assert chr(0) not in keys, "Bad example in test"
        with self.assertRaises(KeyError, msg=msg):
            rec = rec_dict[chr(0)]
        self.assertIsNone(rec_dict.get(chr(0)), msg=msg)
        self.assertEqual(rec_dict.get(chr(0), chr(1)), chr(1), msg=msg)
        with self.assertRaises(AttributeError, msg=msg):
            rec_dict.iteritems
        for key, rec in rec_dict.items():
            self.assertIn(key, keys, msg=msg)
            self.assertIsInstance(rec, SeqRecord, msg=msg)
            self.assertIn(rec.id, ids, msg=msg)
        for rec in rec_dict.values():
            self.assertIn(key, keys, msg=msg)
            self.assertIsInstance(rec, SeqRecord, msg=msg)
            self.assertIn(rec.id, ids, msg=msg)

    def simple_check(self, filename, fmt, comp):
        """Check indexing (without a key function)."""
        msg = "Test failure parsing file %s with format %s" % (filename, fmt)
        if comp:
            mode = "r" + self.get_mode(fmt)
            with gzip.open(filename, mode) as handle:
                id_list = [rec.id for rec in SeqIO.parse(handle, fmt)]
        else:
            id_list = [rec.id for rec in SeqIO.parse(filename, fmt)]

        with warnings.catch_warnings():
            if "_alt_index_" in filename:
                # BiopythonParserWarning: Could not parse the SFF index:
                # Unknown magic number b'.diy' in SFF index header:
                # b'.diy1.00'
                warnings.simplefilter("ignore", BiopythonParserWarning)

            rec_dict = SeqIO.index(filename, fmt)
            self.check_dict_methods(rec_dict, id_list, id_list, msg=msg)
            rec_dict.close()

            if not sqlite3:
                return

            # In memory,
            # note here give filenames as list of strings
            rec_dict = SeqIO.index_db(":memory:", [filename], fmt)
            self.check_dict_methods(rec_dict, id_list, id_list, msg=msg)
            rec_dict.close()

            # check error conditions
            with self.assertRaises(ValueError, msg=msg):
                SeqIO.index_db(":memory:", format="dummy")
            with self.assertRaises(ValueError, msg=msg):
                SeqIO.index_db(":memory:", filenames=["dummy"])

            # Saving to file...
            index_tmp = self.index_tmp
            if os.path.isfile(index_tmp):
                os.remove(index_tmp)

            # To disk,
            # note here we give the filename as a single string
            # to confirm that works too.
            rec_dict = SeqIO.index_db(index_tmp, filename, fmt)
            self.check_dict_methods(rec_dict, id_list, id_list, msg=msg)
            rec_dict.close()
            rec_dict._con.close()  # hack for PyPy

            # Now reload it...
            rec_dict = SeqIO.index_db(index_tmp, [filename], fmt)
            self.check_dict_methods(rec_dict, id_list, id_list, msg=msg)
            rec_dict.close()
            rec_dict._con.close()  # hack for PyPy

            # Now reload without passing filenames and format
            # and switch directory to check  paths still work
            index_tmp = os.path.abspath(index_tmp)
            os.chdir(os.path.dirname(filename))
            try:
                rec_dict = SeqIO.index_db(index_tmp)
            finally:
                os.chdir(CUR_DIR)
            self.check_dict_methods(rec_dict, id_list, id_list, msg=msg)
            rec_dict.close()
            rec_dict._con.close()  # hack for PyPy

            os.remove(index_tmp)

    def add_prefix(self, key):
        """Sample key_function for testing index code."""
        return "id_" + key

    def key_check(self, filename, fmt, comp):
        """Check indexing with a key function."""
        msg = "Test failure parsing file %s with format %s" % (filename, fmt)
        if comp:
            mode = "r" + self.get_mode(fmt)
            with gzip.open(filename, mode) as handle:
                id_list = [rec.id for rec in SeqIO.parse(handle, fmt)]
        else:
            id_list = [rec.id for rec in SeqIO.parse(filename, fmt)]

        key_list = [self.add_prefix(id) for id in id_list]

        with warnings.catch_warnings():
            if "_alt_index_" in filename:
                # BiopythonParserWarning: Could not parse the SFF index:
                # Unknown magic number b'.diy' in SFF index header:
                # b'.diy1.00'
                warnings.simplefilter("ignore", BiopythonParserWarning)

            rec_dict = SeqIO.index(filename, fmt, key_function=self.add_prefix)
            self.check_dict_methods(rec_dict, key_list, id_list, msg=msg)
            rec_dict.close()

            if not sqlite3:
                return

            # In memory,
            rec_dict = SeqIO.index_db(
                ":memory:", [filename], fmt, key_function=self.add_prefix
            )
            self.check_dict_methods(rec_dict, key_list, id_list, msg=msg)
            # check error conditions
            with self.assertRaises(ValueError, msg=msg):
                SeqIO.index_db(":memory:", format="dummy", key_function=self.add_prefix)
            with self.assertRaises(ValueError, msg=msg):
                SeqIO.index_db(
                    ":memory:", filenames=["dummy"], key_function=self.add_prefix
                )
            rec_dict.close()

            # Saving to file...
            index_tmp = filename + ".key.idx"
            if os.path.isfile(index_tmp):
                os.remove(index_tmp)
            rec_dict = SeqIO.index_db(
                index_tmp, [filename], fmt, key_function=self.add_prefix
            )
            self.check_dict_methods(rec_dict, key_list, id_list, msg=msg)
            rec_dict.close()
            rec_dict._con.close()  # hack for PyPy

            # Now reload it...
            rec_dict = SeqIO.index_db(
                index_tmp, [filename], fmt, key_function=self.add_prefix
            )
            self.check_dict_methods(rec_dict, key_list, id_list, msg=msg)
            rec_dict.close()
            rec_dict._con.close()  # hack for PyPy

            # Now reload without passing filenames and format
            rec_dict = SeqIO.index_db(index_tmp, key_function=self.add_prefix)
            self.check_dict_methods(rec_dict, key_list, id_list, msg=msg)
            rec_dict.close()
            rec_dict._con.close()  # hack for PyPy
            os.remove(index_tmp)
            # Done

    def get_raw_check(self, filename, fmt, comp):
        # Also checking the key_function here
        msg = "Test failure parsing file %s with format %s" % (filename, fmt)
        if comp:
            with gzip.open(filename, "rb") as handle:
                raw_file = handle.read()
            mode = "r" + self.get_mode(fmt)
            with gzip.open(filename, mode) as handle:
                id_list = [rec.id.lower() for rec in SeqIO.parse(handle, fmt)]
        else:
            with open(filename, "rb") as handle:
                raw_file = handle.read()
            id_list = [rec.id.lower() for rec in SeqIO.parse(filename, fmt)]

        if fmt in ["sff"]:
            with warnings.catch_warnings():
                warnings.simplefilter("ignore", BiopythonParserWarning)
                rec_dict = SeqIO.index(filename, fmt, key_function=str.lower)
                if sqlite3:
                    rec_dict_db = SeqIO.index_db(
                        ":memory:", filename, fmt, key_function=str.lower,
                    )
        else:
            rec_dict = SeqIO.index(filename, fmt, key_function=str.lower)
            if sqlite3:
                rec_dict_db = SeqIO.index_db(
                    ":memory:", filename, fmt, key_function=str.lower,
                )

        self.assertCountEqual(id_list, rec_dict.keys(), msg=msg)
        if sqlite3:
            self.assertCountEqual(id_list, rec_dict_db.keys(), msg=msg)
        for key in id_list:
            self.assertIn(key, rec_dict, msg=msg)
            self.assertEqual(key, rec_dict[key].id.lower(), msg=msg)
            self.assertEqual(key, rec_dict.get(key).id.lower(), msg=msg)
            raw = rec_dict.get_raw(key)
            self.assertIsInstance(raw, bytes, msg=msg)
            self.assertTrue(raw.strip(), msg=msg)
            self.assertIn(raw, raw_file, msg=msg)

            if sqlite3:
                raw_db = rec_dict_db.get_raw(key)
                # Via index using format-specific get_raw which scans the file,
                # Via index_db in general using raw length found when indexing.
                self.assertEqual(raw, raw_db, msg=msg)

            rec1 = rec_dict[key]
            # Following isn't very elegant, but it lets me test the
            # __getitem__ SFF code is working.
            mode = self.get_mode(fmt)
            if mode == "b":
                handle = BytesIO(raw)
            elif mode == "t":
                handle = StringIO(raw.decode())
            else:
                raise RuntimeError("Unexpected mode %s" % mode)
            if fmt == "sff":
                rec2 = SeqIO.SffIO._sff_read_seq_record(
                    handle,
                    rec_dict._proxy._flows_per_read,
                    rec_dict._proxy._flow_chars,
                    rec_dict._proxy._key_sequence,
                    trim=False,
                )
            elif fmt == "sff-trim":
                rec2 = SeqIO.SffIO._sff_read_seq_record(
                    handle,
                    rec_dict._proxy._flows_per_read,
                    rec_dict._proxy._flow_chars,
                    rec_dict._proxy._key_sequence,
                    trim=True,
                )
            elif fmt == "uniprot-xml":
                self.assertTrue(raw.startswith(b"<entry "), msg=msg)
                self.assertTrue(raw.endswith(b"</entry>"), msg=msg)
                # Currently the __getitem__ method uses this
                # trick too, but we hope to fix that later
                raw = (
                    """<?xml version='1.0' encoding='UTF-8'?>
                <uniprot xmlns="http://uniprot.org/uniprot"
                xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                xsi:schemaLocation="http://uniprot.org/uniprot
                http://www.uniprot.org/support/docs/uniprot.xsd">
                %s
                </uniprot>
                """
                    % raw.decode()
                )
                handle = StringIO(raw)
                rec2 = SeqIO.read(handle, fmt)
            else:
                rec2 = SeqIO.read(handle, fmt)
            self.compare_record(rec1, rec2)
        rec_dict.close()
        del rec_dict

    if sqlite3:

        def test_alpha_fails_db(self):
            """Reject alphabet argument in Bio.SeqIO.index_db()."""
            # In historic usage, alphabet=... would be a Bio.Alphabet object.
            self.assertRaises(
                ValueError,
                SeqIO.index_db,
                ":memory:",
                ["Fasta/dups.fasta"],
                "fasta",
                alphabet="XXX",
            )

    def test_alpha_fails(self):
        """Reject alphabet argument in Bio.SeqIO.index()."""
        # In historic usage, alphabet=... would be a Bio.Alphabet object.
        self.assertRaises(
            ValueError, SeqIO.index, "Fasta/dups.fasta", "fasta", alphabet="XXX"
        )

    if sqlite3:

        def test_duplicates_index_db(self):
            """Index file with duplicate identifiers with Bio.SeqIO.index_db()."""
            self.assertRaises(
                ValueError, SeqIO.index_db, ":memory:", ["Fasta/dups.fasta"], "fasta"
            )

    def test_duplicates_index(self):
        """Index file with duplicate identifiers with Bio.SeqIO.index()."""
        self.assertRaises(ValueError, SeqIO.index, "Fasta/dups.fasta", "fasta")

    def test_duplicates_to_dict(self):
        """Index file with duplicate identifiers with Bio.SeqIO.to_dict()."""
        with open("Fasta/dups.fasta") as handle:
            iterator = SeqIO.parse(handle, "fasta")
            self.assertRaises(ValueError, SeqIO.to_dict, iterator)

    def test_simple_checks(self):
        for filename1, fmt in self.tests:
            assert fmt in _FormatToRandomAccess
            tasks = [(filename1, None)]
            if os.path.isfile(filename1 + ".bgz"):
                tasks.append((filename1 + ".bgz", "bgzf"))
            for filename2, comp in tasks:
                self.simple_check(filename2, fmt, comp)

    def test_key_checks(self):
        for filename1, fmt in self.tests:
            assert fmt in _FormatToRandomAccess
            tasks = [(filename1, None)]
            if os.path.isfile(filename1 + ".bgz"):
                tasks.append((filename1 + ".bgz", "bgzf"))
            for filename2, comp in tasks:
                self.key_check(filename2, fmt, comp)

    def test_raw_checks(self):
        for filename1, fmt in self.tests:
            assert fmt in _FormatToRandomAccess
            tasks = [(filename1, None)]
            if os.path.isfile(filename1 + ".bgz"):
                tasks.append((filename1 + ".bgz", "bgzf"))
            for filename2, comp in tasks:
                self.get_raw_check(filename2, fmt, comp)


class IndexOrderingSingleFile(unittest.TestCase):
    f = "GenBank/NC_000932.faa"
    ids = [r.id for r in SeqIO.parse(f, "fasta")]

    def test_order_to_dict(self):
        """Check to_dict preserves order in indexed file."""
        d = SeqIO.to_dict(SeqIO.parse(self.f, "fasta"))
        self.assertEqual(self.ids, list(d))

    def test_order_index(self):
        """Check index preserves order in indexed file."""
        d = SeqIO.index(self.f, "fasta")
        self.assertEqual(self.ids, list(d))

    if sqlite3:

        def test_order_index_db(self):
            """Check index_db preserves ordering indexed file."""
            d = SeqIO.index_db(":memory:", [self.f], "fasta")
            self.assertEqual(self.ids, list(d))


if sqlite3:

    class IndexOrderingManyFiles(unittest.TestCase):
        def test_order_index_db(self):
            """Check index_db preserves order in multiple indexed files."""
            files = ["GenBank/NC_000932.faa", "GenBank/NC_005816.faa"]
            ids = []
            for f in files:
                ids.extend(r.id for r in SeqIO.parse(f, "fasta"))
            d = SeqIO.index_db(":memory:", files, "fasta")
            self.assertEqual(ids, list(d))


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