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)
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)
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)
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)
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())
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())
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()
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()
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
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)
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
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)
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
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)
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)
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)
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)