Example #1
0
def test_file_gz():
    src = get_fn('tz2_2.pdb.gz')
    fh = FileManager(src)
    nt.assert_true(fh.use_filename)
    nt.assert_true(fh.is_compressed)
    nt.assert_equal(fh.compressed_ext, 'gz')

    nt.assert_true(fh.ext, 'pdb')
    nt.assert_true(fh.is_filename)

    with open(src, 'rb') as src2:
        fh2 = FileManager(src2, compressed=True)
        nt.assert_false(fh2.is_filename)
        nt.assert_true(fh.is_compressed)

        def func():
            fh2.ext
        nt.assert_raises(ValueError, func)

    with open(src, 'rb') as src3:
        fh3 = FileManager(src3, compressed=True, ext='pdb')
        nt.assert_true(fh3.ext, 'pdb')

    # specify compression
    fh4 = FileManager(src, compressed=True)
    nt.assert_true(fh4.is_compressed)

    content = gzip.open(src).read() 
    nt.assert_equal(fh4.read(force_buffer=True), content)
Example #2
0
def test_file_gz():
    src = get_fn('tz2_2.pdb.gz')
    fh = FileManager(src)
    assert fh.use_filename
    assert fh.is_compressed
    assert_equal(fh.compressed_ext, 'gz')

    assert fh.ext.endswith('pdb')
    assert fh.is_filename

    with open(src, 'rb') as src2:
        fh2 = FileManager(src2, compressed=True)
        assert not fh2.is_filename
        assert fh.is_compressed

        def func():
            fh2.ext

        with pytest.raises(ValueError):
            func()

    with open(src, 'rb') as src3:
        fh3 = FileManager(src3, compressed=True, ext='pdb')
        assert fh3.ext.endswith('pdb')

    # specify compression
    fh4 = FileManager(src, compressed=True)
    assert fh4.is_compressed

    content = gzip.open(src).read() 
    assert_equal(fh4.read(force_buffer=True), content)
Example #3
0
def test_file_current_folder():
    src = get_fn('tz2.pdb')
    fh = FileManager(src)
    nt.assert_true(fh.use_filename)
    nt.assert_false(fh.is_compressed)

    nt.assert_true(fh.ext, 'pdb')
    nt.assert_true(fh.is_filename)
    nt.assert_true(fh.read(), fh.src)

    with open(src) as src2:
        fh2 = FileManager(src2)
        nt.assert_false(fh2.is_filename)
        nt.assert_true(fh2.read(), src2.read())

    with open(src) as src2:
        nt.assert_true(fh.read(), src2.read())

    fh3 = FileManager(src)
    content = open(src, 'rb').read() 
    nt.assert_equal(fh3.read(force_buffer=True), content)

    # blob
    fh4 = FileManager(content)
    nt.assert_equal(fh4.read(force_buffer=True), content)
Example #4
0
def test_file_current_folder():
    src = get_fn('tz2.pdb')
    fh = FileManager(src)
    assert fh.use_filename
    assert not fh.is_compressed

    assert fh.ext.endswith('pdb')
    assert fh.is_filename
    assert fh.read() == fh.src

    with open(src) as src2:
        fh2 = FileManager(src2)
        assert not fh2.is_filename
        fh2_content = fh2.read()
        src2.seek(0)
        assert fh2_content == src2.read()

    with open(src) as src2:
        fh_content = fh.read()
        src2.seek(0)
        assert fh_content != src2.read()

    fh3 = FileManager(src)
    content = open(src, 'rb').read() 
    assert_equal(fh3.read(force_buffer=True), content)

    # blob
    fh4 = FileManager(content)
    assert_equal(fh4.read(force_buffer=True), content)
Example #5
0
def test_file_not_use_filename():
    src = os.path.abspath(nglview.__file__)
    fh = FileManager(src)
    nt.assert_false(fh.is_compressed)

    nt.assert_true(fh.ext, 'py')
    nt.assert_true(fh.is_filename)

    with open(src) as src2:
        fh2 = FileManager(src2)
        nt.assert_false(fh2.is_filename)
        nt.assert_true(fh2.read(), src2.read())
Example #6
0
def test_file_not_use_filename():
    src = os.path.abspath(nglview.__file__)
    fh = FileManager(src)
    nt.assert_false(fh.is_compressed)

    nt.assert_true(fh.ext, 'py')
    nt.assert_true(fh.is_filename)

    with open(src) as src2:
        fh2 = FileManager(src2)
        nt.assert_false(fh2.is_filename)
        nt.assert_true(fh2.read(), src2.read())
Example #7
0
def test_file_manager_use_url():
    fh = FileManager('rcsb://1tsu.pdb')
    nt.assert_true(fh.is_url)
    nt.assert_equal(fh.ext, 'pdb')
    nt.assert_false(fh.is_compressed)

    fh = FileManager('http://dummy.com/1tsu.pdb')
    nt.assert_true(fh.is_url)
    nt.assert_equal(fh.ext, 'pdb')

    fh = FileManager('http://dummy.com/1tsu.pdb.gz')
    nt.assert_true(fh.is_url)
    nt.assert_equal(fh.ext, 'pdb')
    nt.assert_true(fh.is_compressed)
def test_file_not_use_filename():
    src = os.path.join(os.path.dirname(nglview.__file__), '__init__.py')
    fh = FileManager(src)
    assert not fh.is_compressed

    assert fh.ext.endswith('py')
    assert fh.is_filename

    with open(src) as src2:
        fh2 = FileManager(src2)
        assert not fh2.is_filename
        fh2_content = fh2.read()
        src2.seek(0)
        assert fh2_content == src2.read()
Example #9
0
def test_file_not_use_filename():
    src = os.path.join(os.path.dirname(nglview.__file__), '__init__.py')
    fh = FileManager(src)
    assert not fh.is_compressed

    assert fh.ext.endswith('py')
    assert fh.is_filename

    with open(src) as src2:
        fh2 = FileManager(src2)
        assert not fh2.is_filename
        fh2_content = fh2.read()
        src2.seek(0)
        assert fh2_content == src2.read()
Example #10
0
def test_file_manager_use_url():
    fh = FileManager('rcsb://1tsu.pdb')
    assert fh.is_url
    assert_equal(fh.ext, 'pdb')
    assert not fh.is_compressed

    fh = FileManager('http://dummy.com/1tsu.pdb')
    assert fh.is_url
    assert_equal(fh.ext, 'pdb')

    fh = FileManager('http://dummy.com/1tsu.pdb.gz')
    assert fh.is_url
    assert_equal(fh.ext, 'pdb')
    assert fh.is_compressed
Example #11
0
def test_file_passing_blob():
    src = get_fn('tz2.pdb')
    blob = open(src).read()

    fm = FileManager(blob)
    nt.assert_false(fm.is_filename)
    nt.assert_raises(ValueError, lambda: fm.ext)
Example #12
0
def test_file_passing_blob():
    src = get_fn('tz2.pdb')
    blob = open(src).read()

    fm = FileManager(blob)
    assert not fm.is_filename
    with pytest.raises(ValueError):
        fm.ext
Example #13
0
def test_file_passing_blob_from_gzip():
    import gzip
    src = get_fn('tz2_2.pdb.gz')
    blob = gzip.open(src).read()

    fm = FileManager(blob)
    nt.assert_false(fm.is_filename)

    nt.assert_raises(ValueError, lambda: fm.ext)
Example #14
0
def test_file_passing_blob_from_gzip():
    import gzip
    src = get_fn('tz2_2.pdb.gz')
    blob = gzip.open(src).read()

    fm = FileManager(blob)
    assert not fm.is_filename

    with pytest.raises(ValueError):
        fm.ext
Example #15
0
def test_file_gz():
    src = get_fn('tz2_2.pdb.gz')
    fh = FileManager(src)
    assert fh.use_filename
    assert fh.is_compressed
    assert_equal(fh.compressed_ext, 'gz')

    assert fh.ext.endswith('pdb')
    assert fh.is_filename

    with open(src, 'rb') as src2:
        fh2 = FileManager(src2, compressed=True)
        assert not fh2.is_filename
        assert fh.is_compressed

        def func():
            fh2.ext

        with pytest.raises(ValueError):
            func()

    with open(src, 'rb') as src3:
        fh3 = FileManager(src3, compressed=True, ext='pdb')
        assert fh3.ext.endswith('pdb')

    # specify compression
    fh4 = FileManager(src, compressed=True)
    assert fh4.is_compressed

    content = gzip.open(src).read()
    assert_equal(fh4.read(force_buffer=True), content)
Example #16
0
def test_file_gz():
    src = get_fn('tz2_2.pdb.gz')
    fh = FileManager(src)
    nt.assert_true(fh.use_filename)
    nt.assert_true(fh.is_compressed)
    nt.assert_equal(fh.compressed_ext, 'gz')

    nt.assert_true(fh.ext, 'pdb')
    nt.assert_true(fh.is_filename)

    with open(src, 'rb') as src2:
        fh2 = FileManager(src2, compressed=True)
        nt.assert_false(fh2.is_filename)
        nt.assert_true(fh.is_compressed)

        def func():
            fh2.ext

        nt.assert_raises(ValueError, func)

    with open(src, 'rb') as src3:
        fh3 = FileManager(src3, compressed=True, ext='pdb')
        nt.assert_true(fh3.ext, 'pdb')

    # specify compression
    fh4 = FileManager(src, compressed=True)
    nt.assert_true(fh4.is_compressed)

    content = gzip.open(src).read()
    nt.assert_equal(fh4.read(force_buffer=True), content)
Example #17
0
def test_file_current_folder():
    src = get_fn('tz2.pdb')
    fh = FileManager(src)
    assert fh.use_filename
    assert not fh.is_compressed

    assert fh.ext.endswith('pdb')
    assert fh.is_filename
    assert fh.read() == os.path.relpath(fh.src)

    with open(src) as src2:
        fh2 = FileManager(src2)
        assert not fh2.is_filename
        fh2_content = fh2.read()
        src2.seek(0)
        assert fh2_content == src2.read()

    with open(src) as src2:
        fh_content = fh.read()
        src2.seek(0)
        assert fh_content != src2.read()

    fh3 = FileManager(src)
    content = open(src, 'r').read()
    assert_equal(fh3.read(force_buffer=True), content)

    # blob
    fh4 = FileManager(content)
    assert_equal(fh4.read(force_buffer=True), content)
Example #18
0
def test_file_current_folder():
    src = get_fn('tz2.pdb')
    fh = FileManager(src)
    nt.assert_true(fh.use_filename)
    nt.assert_false(fh.is_compressed)

    nt.assert_true(fh.ext, 'pdb')
    nt.assert_true(fh.is_filename)
    nt.assert_true(fh.read(), fh.src)

    with open(src) as src2:
        fh2 = FileManager(src2)
        nt.assert_false(fh2.is_filename)
        nt.assert_true(fh2.read(), src2.read())

    with open(src) as src2:
        nt.assert_true(fh.read(), src2.read())

    fh3 = FileManager(src)
    content = open(src, 'rb').read()
    nt.assert_equal(fh3.read(force_buffer=True), content)

    # blob
    fh4 = FileManager(content)
    nt.assert_equal(fh4.read(force_buffer=True), content)