def test_blocksize(self):
""" Core driver supports variable block size """
fname = self.mktemp()
fid = File(fname, 'w', driver='core', block_size=1024,
backing_store=False)
self.assert_(fid)
fid.close()
class BaseGroup(TestCase):
def setUp(self):
self.f = File(self.mktemp(), "w")
def tearDown(self):
if self.f:
self.f.close()
class TestVisit(TestCase):
"""
Feature: The .visit and .visititems methods allow iterative access to
group and subgroup members
"""
def setUp(self):
self.f = File(self.mktemp(), "w")
self.groups = ["grp1", "grp1/sg1", "grp1/sg2", "grp2", "grp2/sg1", "grp2/sg1/ssg1"]
for x in self.groups:
self.f.create_group(x)
def tearDown(self):
self.f.close()
def test_visit(self):
""" All subgroups are visited """
l = []
self.f.visit(l.append)
self.assertSameElements(l, self.groups)
def test_visititems(self):
""" All subgroups and contents are visited """
l = []
comp = [(x, self.f[x]) for x in self.groups]
self.f.visititems(lambda x, y: l.append((x, y)))
self.assertSameElements(comp, l)
def test_bailout(self):
""" Returning a non-None value immediately aborts iteration """
x = self.f.visit(lambda x: x)
self.assertEqual(x, self.groups[0])
x = self.f.visititems(lambda x, y: (x, y))
self.assertEqual(x, (self.groups[0], self.f[self.groups[0]]))
class BaseDataset(TestCase):
def setUp(self):
self.f = File(self.mktemp(), 'w')
def tearDown(self):
if self.f:
self.f.close()
class BaseDataset(TestCase):
"""
data is a 3-dimensional dataset with dimensions [z, y, x]
The z dimension is labeled. It does not have any attached scales.
The y dimension is not labeled. It has one attached scale.
The x dimension is labeled. It has two attached scales.
data2 is a 3-dimensional dataset with no associated dimension scales.
"""
def setUp(self):
self.f = File(self.mktemp(), 'w')
self.f['data'] = np.ones((4, 3, 2), 'f')
self.f['data2'] = np.ones((4, 3, 2), 'f')
self.f['x1'] = np.ones((2), 'f')
h5py.h5ds.set_scale(self.f['x1'].id)
h5py.h5ds.attach_scale(self.f['data'].id, self.f['x1'].id, 2)
self.f['x2'] = np.ones((2), 'f')
h5py.h5ds.set_scale(self.f['x2'].id, b'x2 name')
h5py.h5ds.attach_scale(self.f['data'].id, self.f['x2'].id, 2)
self.f['y1'] = np.ones((3), 'f')
h5py.h5ds.set_scale(self.f['y1'].id, b'y1 name')
h5py.h5ds.attach_scale(self.f['data'].id, self.f['y1'].id, 1)
self.f['z1'] = np.ones((4), 'f')
h5py.h5ds.set_label(self.f['data'].id, 0, b'z')
h5py.h5ds.set_label(self.f['data'].id, 2, b'x')
def tearDown(self):
if self.f:
self.f.close()
def test_core(self):
""" Core driver is supported (no backing store) """
fname = self.mktemp()
fid = File(fname, 'w', driver='core', backing_store=False)
self.assert_(fid)
self.assertEqual(fid.driver, 'core')
fid.close()
self.assertFalse(os.path.exists(fname))
def test_mode(self):
""" Retrieved File objects have a meaningful mode attribute """
hfile = File(self.mktemp(),'w')
try:
grp = hfile.create_group('foo')
self.assertEqual(grp.file.mode, hfile.mode)
finally:
hfile.close()
def test_create_exclusive(self):
""" Mode 'w-' opens file in exclusive mode """
fname = self.mktemp()
fid = File(fname, 'w-')
self.assert_(fid)
fid.close()
with self.assertRaises(IOError):
File(fname, 'w-')
def test_iter_zero(self):
""" Iteration works properly for the case with no group members """
hfile = File(self.mktemp(), 'w')
try:
lst = [x for x in hfile]
self.assertEqual(lst, [])
finally:
hfile.close()
def test_property(self):
""" File object can be retrieved from subgroup """
fname = self.mktemp()
hfile = File(fname, 'w')
try:
hfile2 = hfile['/'].file
self.assertEqual(hfile, hfile2)
finally:
hfile.close()
def test_filename(self):
""" .filename behaves properly for string data """
fname = self.mktemp()
fid = File(fname, 'w')
try:
self.assertEqual(fid.filename, fname)
self.assertIsInstance(fid.filename, unicode)
finally:
fid.close()
def test_unicode(self):
""" Unicode filenames can be used, and retrieved properly via .filename
"""
fname = self.mktemp(prefix=six.unichr(0x201A))
fid = File(fname, "w")
try:
self.assertEqual(fid.filename, fname)
self.assertIsInstance(fid.filename, six.text_type)
finally:
fid.close()
def test_unicode(self):
""" Unicode filenames can be used, and retrieved properly via .filename
"""
fname = self.mktemp(prefix = u'\u201a')
fid = File(fname, 'w')
try:
self.assertEqual(fid.filename, fname)
self.assertIsInstance(fid.filename, unicode)
finally:
fid.close()
def test_mode_external(self):
""" Mode property works for files opened via external links
Issue 190.
"""
fname1 = self.mktemp()
fname2 = self.mktemp()
f1 = File(fname1,'w')
f1.close()
f2 = File(fname2,'w')
try:
f2['External'] = h5py.ExternalLink(fname1, '/')
f3 = f2['External'].file
self.assertEqual(f3.mode, 'r+')
finally:
f2.close()
f3.close()
f2 = File(fname2,'r')
try:
f3 = f2['External'].file
self.assertEqual(f3.mode, 'r')
finally:
f2.close()
f3.close()
def test_mode_external(self):
""" Mode property works for files opened via external links
Issue 190.
"""
fname1 = self.mktemp()
fname2 = self.mktemp()
f1 = File(fname1, "w")
f1.close()
f2 = File(fname2, "w")
try:
f2["External"] = h5py.ExternalLink(fname1, "/")
f3 = f2["External"].file
self.assertEqual(f3.mode, "r+")
finally:
f2.close()
f3.close()
f2 = File(fname2, "r")
try:
f3 = f2["External"].file
self.assertEqual(f3.mode, "r")
finally:
f2.close()
f3.close()
def test_readwrite(self):
""" Mode 'r+' opens existing file in readwrite mode """
fname = self.mktemp()
fid = File(fname, "w")
fid.create_group("foo")
fid.close()
fid = File(fname, "r+")
self.assert_("foo" in fid)
fid.create_group("bar")
self.assert_("bar" in fid)
fid.close()
def test_close(self):
""" All retrieved File objects are closed at the same time """
fname = self.mktemp()
hfile = File(fname, 'w')
grp = hfile.create_group('foo')
hfile2 = grp.file
hfile3 = hfile['/'].file
hfile2.close()
self.assertFalse(hfile)
self.assertFalse(hfile2)
self.assertFalse(hfile3)
def test_readwrite(self):
""" Mode 'r+' opens existing file in readwrite mode """
fname = self.mktemp()
fid = File(fname, 'w')
fid.create_group('foo')
fid.close()
fid = File(fname, 'r+')
self.assert_('foo' in fid)
fid.create_group('bar')
self.assert_('bar' in fid)
fid.close()
def test_write_only(self):
""" User block only allowed for write """
name = self.mktemp()
f = File(name, 'w')
f.close()
with self.assertRaises(ValueError):
f = h5py.File(name, 'r', userblock_size=512)
with self.assertRaises(ValueError):
f = h5py.File(name, 'r+', userblock_size=512)
def test_readonly(self):
""" Core driver can be used to open existing files """
fname = self.mktemp()
fid = File(fname, 'w')
fid.create_group('foo')
fid.close()
fid = File(fname, 'r', driver='core')
self.assert_(fid)
self.assert_('foo' in fid)
with self.assertRaises(ValueError):
fid.create_group('bar')
fid.close()
def test_readonly(self):
""" Core driver can be used to open existing files """
fname = self.mktemp()
fid = File(fname, "w")
fid.create_group("foo")
fid.close()
fid = File(fname, "r", driver="core")
self.assert_(fid)
self.assert_("foo" in fid)
with self.assertRaises(ValueError):
fid.create_group("bar")
fid.close()
def test_issue_212(self):
""" Issue 212
Fails with:
AttributeError: 'SharedConfig' object has no attribute 'lapl'
"""
def closer(x):
def w():
try:
if x:
x.close()
except IOError:
pass
return w
orig_name = self.mktemp()
new_name = self.mktemp()
f = File(orig_name, 'w')
self.addCleanup(closer(f))
f.create_group('a')
f.close()
g = File(new_name, 'w')
self.addCleanup(closer(g))
g['link'] = ExternalLink(orig_name, '/') # note root group
g.close()
h = File(new_name, 'r')
self.addCleanup(closer(h))
self.assertIsInstance(h['link']['a'], Group)
class BaseMapping(BaseGroup):
"""
Base class for mapping tests
"""
def setUp(self):
self.f = File(self.mktemp(), 'w')
self.groups = ('a','b','c','d')
for x in self.groups:
self.f.create_group(x)
def tearDown(self):
if self.f:
self.f.close()
class BaseMapping(BaseGroup):
"""
Base class for mapping tests
"""
def setUp(self):
self.f = File(self.mktemp(), "w")
self.groups = ("a", "b", "c", "d")
for x in self.groups:
self.f.create_group(x)
def tearDown(self):
if self.f:
self.f.close()
def setUp(self):
self.f = File(self.mktemp(), 'w')
self.groups = [
'grp1', 'grp1/sg1', 'grp1/sg2', 'grp2', 'grp2/sg1', 'grp2/sg1/ssg1'
]
for x in self.groups:
self.f.create_group(x)
class BaseMapping(BaseGroup):
"""
Base class for mapping tests
"""
def setUp(self):
self.f = File(self.mktemp(), 'w')
self.groups = ('a','b','c','d')
for x in self.groups:
self.f.create_group(x)
self.f['x'] = h5py.SoftLink('/mongoose')
self.groups = self.groups + ('x',)
def tearDown(self):
if self.f:
self.f.close()
def setUp(self):
self.f = File(self.mktemp(), "w")
self.groups = ("a", "b", "c", "d")
for x in self.groups:
self.f.create_group(x)
self.f["x"] = h5py.SoftLink("/mongoose")
self.groups = self.groups + ("x",)
def setUp(self):
self.f = File(self.mktemp(), 'w')
self.groups = ('a','b','c','d')
for x in self.groups:
self.f.create_group(x)
self.f['x'] = h5py.SoftLink('/mongoose')
self.groups = self.groups + ('x',)
def test_backing(self):
""" Core driver saves to file when backing store used """
fname = self.mktemp()
fid = File(fname, 'w', driver='core', backing_store=True)
fid.create_group('foo')
fid.close()
fid = File(fname, 'r')
self.assert_('foo' in fid)
fid.close()
def test_backing(self):
""" Core driver saves to file when backing store used """
fname = self.mktemp()
fid = File(fname, "w", driver="core", backing_store=True)
fid.create_group("foo")
fid.close()
fid = File(fname, "r")
self.assert_("foo" in fid)
fid.close()
def test_closed_file(self):
""" Trying to modify closed file raises ValueError """
fid = File(self.mktemp(), 'w')
fid.close()
with self.assertRaises(ValueError):
fid.create_group('foo')
def test_flush(self):
""" Flush via .flush method """
fid = File(self.mktemp(), 'w')
fid.flush()
fid.close()
def test_stdio(self):
""" Stdio driver is supported on posix """
fid = File(self.mktemp(), 'w', driver='stdio')
self.assertTrue(fid)
self.assertEqual(fid.driver, 'stdio')
fid.close()
def test_unicode_hdf5_python_consistent(self):
""" Unicode filenames can be used, and seen correctly from python
"""
fname = self.mktemp(prefix=six.unichr(0x201a))
with File(fname, 'w') as f:
self.assertTrue(os.path.exists(fname))
def test_pathlib_accepted_file(self):
""" Check that pathlib is accepted by h5py.File """
with closed_tempfile() as f:
path = pathlib.Path(f)
with File(path) as f2:
self.assertTrue(True)
def test_default(self):
""" Opening with no libver arg """
f = File(self.mktemp(), 'w')
self.assertEqual(f.libver, ('earliest', 'latest'))
f.close()
def test_context_manager(self):
""" File objects can be used in with statements """
with File(self.mktemp(), 'w') as fid:
self.assertTrue(fid)
self.assertTrue(not fid)
def test_multiple(self):
""" Opening with two libver args """
f = File(self.mktemp(), 'w', libver=('earliest', 'latest'))
self.assertEqual(f.libver, ('earliest', 'latest'))
f.close()
def test_readonly(self):
""" Core driver can be used to open existing files """
fname = self.mktemp()
fid = File(fname, 'w')
fid.create_group('foo')
fid.close()
fid = File(fname, 'r', driver='core')
self.assert_(fid)
self.assert_('foo' in fid)
with self.assertRaises(ValueError):
fid.create_group('bar')
fid.close()
def test_append(self):
""" Mode 'a' opens file in append/readwrite mode, creating if necessary """
fname = self.mktemp()
fid = File(fname, 'a')
try:
self.assert_(fid)
fid.create_group('foo')
self.assert_('foo' in fid)
finally:
fid.close()
fid = File(fname, 'a')
try:
self.assert_('foo' in fid)
fid.create_group('bar')
self.assert_('bar' in fid)
finally:
fid.close()
def test_invalid_mode(self):
""" Invalid modes raise ValueError """
with self.assertRaises(ValueError):
File(self.mktemp(), 'mongoose')
class TestAdditionalMappingFuncs(BaseMapping):
"""
Feature: Other dict methods (pop, pop_item, clear, update, setdefault) are
available.
"""
def setUp(self):
self.f = File(self.mktemp(), 'w')
for x in ('/test/a', '/test/b', '/test/c', '/test/d'):
self.f.create_group(x)
self.group = self.f['test']
def tearDown(self):
if self.f:
self.f.close()
def test_pop_item(self):
""".pop_item exists and removes item"""
key, val = self.group.popitem()
self.assertNotIn(key, self.group)
def test_pop(self):
""".pop exists and removes specified item"""
self.group.pop('a')
self.assertNotIn('a', self.group)
def test_pop_default(self):
""".pop falls back to default"""
# e shouldn't exist as a group
value = self.group.pop('e', None)
self.assertEqual(value, None)
def test_pop_raises(self):
""".pop raises KeyError for non-existence"""
# e shouldn't exist as a group
with self.assertRaises(KeyError):
key = self.group.pop('e')
def test_clear(self):
""".clear removes groups"""
self.group.clear()
self.assertEqual(len(self.group), 0)
def test_update_dict(self):
""".update works with dict"""
new_items = {'e': np.array([42])}
self.group.update(new_items)
self.assertIn('e', self.group)
def test_update_iter(self):
""".update works with list"""
new_items = [('e', np.array([42])), ('f', np.array([42]))]
self.group.update(new_items)
self.assertIn('e', self.group)
def test_update_kwargs(self):
""".update works with kwargs"""
new_items = {'e': np.array([42])}
self.group.update(**new_items)
self.assertIn('e', self.group)
def test_setdefault(self):
""".setdefault gets group if it exists"""
value = self.group.setdefault('a')
self.assertEqual(value, self.group.get('a'))
def test_setdefault_with_default(self):
""".setdefault gets default if group doesn't exist"""
# e shouldn't exist as a group
# 42 used as groups should be strings
value = self.group.setdefault('e', np.array([42]))
self.assertEqual(value, 42)
def test_setdefault_no_default(self):
"""
.setdefault gets None if group doesn't exist, but as None isn't defined
as data for a dataset, this should raise a TypeError.
"""
# e shouldn't exist as a group
with self.assertRaises(TypeError):
self.group.setdefault('e')
def test_close(self):
""" Close file via .close method """
fid = File(self.mktemp())
self.assert_(fid)
fid.close()
self.assert_(not fid)
def test_sec2(self):
""" Sec2 driver is supported on posix """
fid = File(self.mktemp(), 'w', driver='sec2')
self.assert_(fid)
self.assertEqual(fid.driver, 'sec2')
fid.close()
def setUp(self):
self.f1 = File(self.mktemp(), 'w')
self.f2 = File(self.mktemp(), 'w')
def test_issue_212(self):
""" Issue 212
Fails with:
AttributeError: 'SharedConfig' object has no attribute 'lapl'
"""
def closer(x):
def w():
try:
if x:
x.close()
except IOError:
pass
return w
orig_name = self.mktemp()
new_name = self.mktemp()
f = File(orig_name, 'w')
self.addCleanup(closer(f))
f.create_group('a')
f.close()
g = File(new_name, 'w')
self.addCleanup(closer(g))
g['link'] = ExternalLink(orig_name, '/') # note root group
g.close()
h = File(new_name, 'r')
self.addCleanup(closer(h))
self.assertIsInstance(h['link']['a'], Group)
def test_none(self):
""" Omitting libver arg results in maximum compatibility """
f = File(self.mktemp(), 'w')
self.assertEqual(f.libver, ('earliest', 'latest'))
f.close()
def test_single(self):
""" Opening with single libver arg """
f = File(self.mktemp(), 'w', libver='latest')
self.assertEqual(f.libver, ('latest', 'latest'))
f.close()
class TestCopy(TestCase):
def setUp(self):
self.f1 = File(self.mktemp(), 'w')
self.f2 = File(self.mktemp(), 'w')
def tearDown(self):
if self.f1:
self.f1.close()
if self.f2:
self.f2.close()
@ut.skipIf(h5py.version.hdf5_version_tuple < (1, 8, 9),
"Bug in HDF5<1.8.8 prevents copying open dataset")
def test_copy_path_to_path(self):
foo = self.f1.create_group('foo')
foo['bar'] = [1, 2, 3]
self.f1.copy('foo', 'baz')
baz = self.f1['baz']
self.assertIsInstance(baz, Group)
self.assertArrayEqual(baz['bar'], np.array([1, 2, 3]))
@ut.skipIf(h5py.version.hdf5_version_tuple < (1, 8, 9),
"Bug in HDF5<1.8.8 prevents copying open dataset")
def test_copy_path_to_group(self):
foo = self.f1.create_group('foo')
foo['bar'] = [1, 2, 3]
baz = self.f1.create_group('baz')
self.f1.copy('foo', baz)
baz = self.f1['baz']
self.assertIsInstance(baz, Group)
self.assertArrayEqual(baz['foo/bar'], np.array([1, 2, 3]))
self.f1.copy('foo', self.f2['/'])
self.assertIsInstance(self.f2['/foo'], Group)
self.assertArrayEqual(self.f2['foo/bar'], np.array([1, 2, 3]))
@ut.skipIf(h5py.version.hdf5_version_tuple < (1, 8, 9),
"Bug in HDF5<1.8.8 prevents copying open dataset")
def test_copy_group_to_path(self):
foo = self.f1.create_group('foo')
foo['bar'] = [1, 2, 3]
self.f1.copy(foo, 'baz')
baz = self.f1['baz']
self.assertIsInstance(baz, Group)
self.assertArrayEqual(baz['bar'], np.array([1, 2, 3]))
self.f2.copy(foo, 'foo')
self.assertIsInstance(self.f2['/foo'], Group)
self.assertArrayEqual(self.f2['foo/bar'], np.array([1, 2, 3]))
@ut.skipIf(h5py.version.hdf5_version_tuple < (1, 8, 9),
"Bug in HDF5<1.8.8 prevents copying open dataset")
def test_copy_group_to_group(self):
foo = self.f1.create_group('foo')
foo['bar'] = [1, 2, 3]
baz = self.f1.create_group('baz')
self.f1.copy(foo, baz)
baz = self.f1['baz']
self.assertIsInstance(baz, Group)
self.assertArrayEqual(baz['foo/bar'], np.array([1, 2, 3]))
self.f1.copy(foo, self.f2['/'])
self.assertIsInstance(self.f2['/foo'], Group)
self.assertArrayEqual(self.f2['foo/bar'], np.array([1, 2, 3]))
@ut.skipIf(h5py.version.hdf5_version_tuple < (1, 8, 9),
"Bug in HDF5<1.8.8 prevents copying open dataset")
def test_copy_dataset(self):
self.f1['foo'] = [1, 2, 3]
foo = self.f1['foo']
self.f1.copy(foo, 'bar')
self.assertArrayEqual(self.f1['bar'], np.array([1, 2, 3]))
self.f1.copy('foo', 'baz')
self.assertArrayEqual(self.f1['baz'], np.array([1, 2, 3]))
self.f1.copy('foo', self.f2)
self.assertArrayEqual(self.f2['foo'], np.array([1, 2, 3]))
self.f2.copy(self.f1['foo'], self.f2, 'bar')
self.assertArrayEqual(self.f2['bar'], np.array([1, 2, 3]))
@ut.skipIf(h5py.version.hdf5_version_tuple < (1, 8, 9),
"Bug in HDF5<1.8.8 prevents copying open dataset")
def test_copy_shallow(self):
foo = self.f1.create_group('foo')
bar = foo.create_group('bar')
foo['qux'] = [1, 2, 3]
bar['quux'] = [4, 5, 6]
self.f1.copy(foo, 'baz', shallow=True)
baz = self.f1['baz']
self.assertIsInstance(baz, Group)
self.assertIsInstance(baz['bar'], Group)
self.assertEqual(len(baz['bar']), 0)
self.assertArrayEqual(baz['qux'], np.array([1, 2, 3]))
self.f2.copy(foo, 'foo', shallow=True)
self.assertIsInstance(self.f2['/foo'], Group)
self.assertIsInstance(self.f2['foo/bar'], Group)
self.assertEqual(len(self.f2['foo/bar']), 0)
self.assertArrayEqual(self.f2['foo/qux'], np.array([1, 2, 3]))
@ut.skipIf(h5py.version.hdf5_version_tuple < (1, 8, 9),
"Bug in HDF5<1.8.8 prevents copying open dataset")
def test_copy_without_attributes(self):
self.f1['foo'] = [1, 2, 3]
foo = self.f1['foo']
foo.attrs['bar'] = [4, 5, 6]
self.f1.copy(foo, 'baz', without_attrs=True)
self.assertArrayEqual(self.f1['baz'], np.array([1, 2, 3]))
self.assert_('bar' not in self.f1['baz'].attrs)
self.f2.copy(foo, 'baz', without_attrs=True)
self.assertArrayEqual(self.f2['baz'], np.array([1, 2, 3]))
self.assert_('bar' not in self.f2['baz'].attrs)
@ut.skipIf(h5py.version.hdf5_version_tuple < (1, 8, 9),
"Bug in HDF5<1.8.8 prevents copying open dataset")
def test_copy_soft_links(self):
self.f1['bar'] = [1, 2, 3]
foo = self.f1.create_group('foo')
foo['baz'] = SoftLink('/bar')
self.f1.copy(foo, 'qux', expand_soft=True)
self.f2.copy(foo, 'foo', expand_soft=True)
del self.f1['bar']
self.assertIsInstance(self.f1['qux'], Group)
self.assertArrayEqual(self.f1['qux/baz'], np.array([1, 2, 3]))
self.assertIsInstance(self.f2['/foo'], Group)
self.assertArrayEqual(self.f2['foo/baz'], np.array([1, 2, 3]))
@ut.skipIf(h5py.version.hdf5_version_tuple < (1, 8, 9),
"Bug in HDF5<1.8.8 prevents copying open dataset")
def test_copy_external_links(self):
filename = self.f1.filename
self.f1['foo'] = [1, 2, 3]
self.f2['bar'] = ExternalLink(filename, 'foo')
self.f1.close()
self.f1 = None
self.assertArrayEqual(self.f2['bar'], np.array([1, 2, 3]))
self.f2.copy('bar', 'baz', expand_external=True)
os.unlink(filename)
self.assertArrayEqual(self.f2['baz'], np.array([1, 2, 3]))
@ut.skipIf(h5py.version.hdf5_version_tuple < (1, 8, 9),
"Bug in HDF5<1.8.8 prevents copying open dataset")
def test_copy_refs(self):
self.f1['foo'] = [1, 2, 3]
self.f1['bar'] = [4, 5, 6]
foo = self.f1['foo']
bar = self.f1['bar']
foo.attrs['bar'] = bar.ref
self.f1.copy(foo, 'baz', expand_refs=True)
self.assertArrayEqual(self.f1['baz'], np.array([1, 2, 3]))
baz_bar = self.f1['baz'].attrs['bar']
self.assertArrayEqual(self.f1[baz_bar], np.array([4, 5, 6]))
# The reference points to a copy of bar, not to bar itself.
self.assertNotEqual(self.f1[baz_bar].name, bar.name)
self.f1.copy('foo', self.f2, 'baz', expand_refs=True)
self.assertArrayEqual(self.f2['baz'], np.array([1, 2, 3]))
baz_bar = self.f2['baz'].attrs['bar']
self.assertArrayEqual(self.f2[baz_bar], np.array([4, 5, 6]))
self.f1.copy('/', self.f2, 'root', expand_refs=True)
self.assertArrayEqual(self.f2['root/foo'], np.array([1, 2, 3]))
self.assertArrayEqual(self.f2['root/bar'], np.array([4, 5, 6]))
foo_bar = self.f2['root/foo'].attrs['bar']
self.assertArrayEqual(self.f2[foo_bar], np.array([4, 5, 6]))
# There's only one copy of bar, which the reference points to.
self.assertEqual(self.f2[foo_bar], self.f2['root/bar'])
def test_readwrite(self):
""" Mode 'r+' opens existing file in readwrite mode """
fname = self.mktemp()
fid = File(fname, 'w')
fid.create_group('foo')
fid.close()
fid = File(fname, 'r+')
self.assert_('foo' in fid)
fid.create_group('bar')
self.assert_('bar' in fid)
fid.close()
def test_create_blocksize(self):
""" User blocks created with w, w-, x and properties work correctly """
f = File(self.mktemp(),'w-', userblock_size=512)
try:
self.assertEqual(f.userblock_size, 512)
finally:
f.close()
f = File(self.mktemp(),'x', userblock_size=512)
try:
self.assertEqual(f.userblock_size, 512)
finally:
f.close()
f = File(self.mktemp(),'w', userblock_size=512)
try:
self.assertEqual(f.userblock_size, 512)
finally:
f.close()
class TestExternalLinks(TestCase):
"""
Feature: Create and manage external links
"""
def setUp(self):
self.f = File(self.mktemp(), 'w')
self.ename = self.mktemp()
self.ef = File(self.ename, 'w')
self.ef.create_group('external')
self.ef.close()
def tearDown(self):
if self.f:
self.f.close()
if self.ef:
self.ef.close()
def test_epath(self):
""" External link paths attributes """
el = ExternalLink('foo.hdf5', '/foo')
self.assertEqual(el.filename, 'foo.hdf5')
self.assertEqual(el.path, '/foo')
def test_erepr(self):
""" External link repr """
el = ExternalLink('foo.hdf5', '/foo')
self.assertIsInstance(repr(el), six.string_types)
def test_create(self):
""" Creating external links """
self.f['ext'] = ExternalLink(self.ename, '/external')
grp = self.f['ext']
self.ef = grp.file
self.assertNotEqual(self.ef, self.f)
self.assertEqual(grp.name, '/external')
def test_exc(self):
""" KeyError raised when attempting to open broken link """
self.f['ext'] = ExternalLink(self.ename, '/missing')
with self.assertRaises(KeyError):
self.f['ext']
# I would prefer IOError but there's no way to fix this as the exception
# class is determined by HDF5.
def test_exc_missingfile(self):
""" KeyError raised when attempting to open missing file """
self.f['ext'] = ExternalLink('mongoose.hdf5', '/foo')
with self.assertRaises(KeyError):
self.f['ext']
def test_close_file(self):
""" Files opened by accessing external links can be closed
Issue 189.
"""
self.f['ext'] = ExternalLink(self.ename, '/')
grp = self.f['ext']
f2 = grp.file
f2.close()
self.assertFalse(f2)
@ut.skipIf(NO_FS_UNICODE, "No unicode filename support")
def test_unicode_encode(self):
"""
Check that external links encode unicode filenames properly
Testing issue #732
"""
ext_filename = os.path.join(mkdtemp(), u"α.hdf5")
with File(ext_filename, "w") as ext_file:
ext_file.create_group('external')
self.f['ext'] = ExternalLink(ext_filename, '/external')
@ut.skipIf(NO_FS_UNICODE, "No unicode filename support")
def test_unicode_decode(self):
"""
Check that external links decode unicode filenames properly
Testing issue #732
"""
ext_filename = os.path.join(mkdtemp(), u"α.hdf5")
with File(ext_filename, "w") as ext_file:
ext_file.create_group('external')
ext_file["external"].attrs["ext_attr"] = "test"
self.f['ext'] = ExternalLink(ext_filename, '/external')
self.assertEqual(self.f["ext"].attrs["ext_attr"], "test")
def setUp(self):
self.f = File(self.mktemp(), 'w')
self.arr = np.arange(10)
self.dset = self.f.create_dataset('x', data=self.arr)
def test_repr(self):
""" __repr__ behaves itself when files are open and closed """
fid = File(self.mktemp())
self.assertIsInstance(repr(fid), basestring)
fid.close()
self.assertIsInstance(repr(fid), basestring)
def setUp(self):
self.f = File(self.mktemp(), 'w')
self.ename = self.mktemp()
self.ef = File(self.ename, 'w')
self.ef.create_group('external')
self.ef.close()
def setUp(self):
self.f = File(self.mktemp(), 'w')
def test_fid(self):
""" File objects provide a .fid attribute aliased to the file ID """
with File(self.mktemp(), 'w') as hfile:
self.assertIs(hfile.fid, hfile.id)
def test_mode_external(self):
""" Mode property works for files opened via external links
Issue 190.
"""
fname1 = self.mktemp()
fname2 = self.mktemp()
f1 = File(fname1, 'w')
f1.close()
f2 = File(fname2, 'w')
try:
f2['External'] = h5py.ExternalLink(fname1, '/')
f3 = f2['External'].file
self.assertEqual(f3.mode, 'r+')
finally:
f2.close()
f3.close()
f2 = File(fname2, 'r')
try:
f3 = f2['External'].file
self.assertEqual(f3.mode, 'r')
finally:
f2.close()
f3.close()
def test_pathlib_accepted_file(self):
""" Check that pathlib is accepted by h5py.File """
with tempfile.NamedTemporaryFile() as f:
path = pathlib.Path(f.name)
with File(path) as f2:
self.assertTrue(True)
def setUp(self):
self.f = File(self.mktemp(), 'w')
for x in ('/test/a', '/test/b', '/test/c', '/test/d'):
self.f.create_group(x)
self.group = self.f['test']