biopython/Tests/test_SearchIO_legacy.py

# Copyright 1999 by Jeffrey Chang.  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 SearchIO legacy module."""


import string
import unittest

from io import StringIO


import warnings
from Bio import BiopythonDeprecationWarning

with warnings.catch_warnings():
    warnings.simplefilter("ignore", BiopythonDeprecationWarning)
    from Bio.SearchIO._legacy import ParserSupport


class UndoHandleTests(unittest.TestCase):
    """Tests for the UndoHandle."""

    def test_one(self):
        """First test."""
        data = """\
This
is
a multi-line
file"""
        h = ParserSupport.UndoHandle(StringIO(data))
        self.assertEqual(h.readline(), "This\n")
        self.assertEqual(h.peekline(), "is\n")
        self.assertEqual(h.readline(), "is\n")
        # TODO - Meaning of saveline lacking \n?
        h.saveline("saved\n")
        self.assertEqual(h.peekline(), "saved\n")
        h.saveline("another\n")
        self.assertEqual(h.readline(), "another\n")
        self.assertEqual(h.readline(), "saved\n")
        # Test readlines after saveline
        h.saveline("saved again\n")
        lines = h.readlines()
        self.assertEqual(len(lines), 3)
        self.assertEqual(lines[0], "saved again\n")
        self.assertEqual(lines[1], "a multi-line\n")
        self.assertEqual(lines[2], "file")  # no trailing \n
        # should be empty now
        self.assertEqual(h.readline(), "")
        h.saveline("save after empty\n")
        self.assertEqual(h.readline(), "save after empty\n")
        self.assertEqual(h.readline(), "")

    def test_read(self):
        """Test read method."""
        h = ParserSupport.UndoHandle(StringIO("some text"))
        h.saveline("more text")
        self.assertEqual(h.read(), "more textsome text")

    def test_undohandle_read_block(self):
        """Test reading in blocks."""
        data = """\
This
is
a multi-line
file"""
        for block in [1, 2, 10]:
            s = StringIO(data)
            h = ParserSupport.UndoHandle(s)
            h.peekline()
            new = ""
            while True:
                tmp = h.read(block)
                if not tmp:
                    break
                new += tmp
            self.assertEqual(data, new)
            h.close()


class TestParserSupport(unittest.TestCase):
    def test_TaggingConsumer(self):
        h = StringIO()
        tc = ParserSupport.TaggingConsumer(handle=h, colwidth=5)
        tc.start_section()
        self.assertEqual(h.getvalue(), "***** start_section\n")
        h.seek(0)
        h.truncate(0)
        tc.test1("myline")
        self.assertEqual(h.getvalue(), "test1: myline\n")
        h.seek(0)
        h.truncate(0)
        tc.end_section()
        self.assertEqual(h.getvalue(), "***** end_section\n")

    def test_is_blank_line(self):
        is_blank_line = ParserSupport.is_blank_line
        self.assertTrue(is_blank_line("\n"))
        self.assertTrue(is_blank_line("\r\n"))
        self.assertTrue(is_blank_line("\r"))
        self.assertTrue(is_blank_line(""))
        self.assertTrue(is_blank_line("", allow_spaces=1))
        self.assertTrue(is_blank_line("", allow_spaces=0))
        self.assertTrue(is_blank_line(string.whitespace, allow_spaces=1))
        self.assertFalse(is_blank_line("hello"))
        self.assertFalse(is_blank_line("hello", allow_spaces=1))
        self.assertFalse(is_blank_line("hello", allow_spaces=0))
        self.assertFalse(is_blank_line(string.whitespace, allow_spaces=0))

    def test_safe_readline(self):
        data = """\
This
file"""
        h = ParserSupport.UndoHandle(StringIO(data))
        safe_readline = ParserSupport.safe_readline
        self.assertEqual(safe_readline(h), "This\n")
        self.assertEqual(safe_readline(h), "file")
        self.assertRaises(ValueError, safe_readline, h)

    def test_safe_peekline(self):
        safe_peekline = ParserSupport.safe_peekline
        data = """\
This
file"""
        h = ParserSupport.UndoHandle(StringIO(data))
        self.assertEqual(safe_peekline(h), "This\n")
        h.readline()
        self.assertEqual(safe_peekline(h), "file")
        h.readline()
        self.assertRaises(ValueError, safe_peekline, h)
        h.saveline("hello")
        self.assertEqual(safe_peekline(h), "hello")

    def test_read_and_call(self):
        data = """\
>gi|132871|sp|P19947|RL30_BACSU 50S RIBOSOMAL PROTEIN L30 (BL27)
MAKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVSHLVSVKEQ
>gi|132679|sp|P19946|RL15_BACSU 50S RIBOSOMAL PROTEIN L15
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQRLPKRGFTNIN
RKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKKLTVKANKFSASAKEAVEAAG
GTAEVI


"""
        h = ParserSupport.UndoHandle(StringIO(data))
        lines = []
        rac = ParserSupport.read_and_call
        rac(h, lines.append)
        self.assertEqual(lines[-1][:10], ">gi|132871")
        rac(h, lines.append, start="MAKLE", end="KEQ", contains="SVIG")
        self.assertRaises(ValueError, rac, h, lines.append, blank=1)
        self.assertRaises(ValueError, rac, h, lines.append, start="foobar")
        self.assertRaises(ValueError, rac, h, lines.append, end="foobar")
        self.assertRaises(ValueError, rac, h, lines.append, contains="foobar")
        self.assertRaises(ValueError, rac, h, lines.append, blank=0)

    def test_attempt_read_and_call(self):
        data = """\
>gi|132871|sp|P19947|RL30_BACSU 50S RIBOSOMAL PROTEIN L30 (BL27)
MAKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVSHLVSVKEQ
>gi|132679|sp|P19946|RL15_BACSU 50S RIBOSOMAL PROTEIN L15
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQRLPKRGFTNIN
RKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKKLTVKANKFSASAKEAVEAAG
GTAEVI"""
        h = ParserSupport.UndoHandle(StringIO(data))
        lines = []
        arac = ParserSupport.attempt_read_and_call
        self.assertTrue(arac(h, lines.append, contains="RIBOSOMAL PROTEIN"))
        self.assertFalse(arac(h, lines.append, start="foobar"))
        self.assertFalse(arac(h, lines.append, blank=1))
        self.assertTrue(arac(h, lines.append, end="LVSVKEQ"))


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