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# This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Tests the h5py.File object.
"""
import h5py
from h5py._hl.files import _drivers
from h5py import File
from .common import ut, TestCase
import pytest
import io
import tempfile
import os
def nfiles():
return h5py.h5f.get_obj_count(h5py.h5f.OBJ_ALL, h5py.h5f.OBJ_FILE)
def ngroups():
return h5py.h5f.get_obj_count(h5py.h5f.OBJ_ALL, h5py.h5f.OBJ_GROUP)
class TestDealloc(TestCase):
"""
Behavior on object deallocation. Note most of this behavior is
delegated to FileID.
"""
def test_autoclose(self):
""" File objects close automatically when out of scope, but
other objects remain open. """
start_nfiles = nfiles()
start_ngroups = ngroups()
fname = self.mktemp()
f = h5py.File(fname, 'w')
g = f['/']
self.assertEqual(nfiles(), start_nfiles+1)
self.assertEqual(ngroups(), start_ngroups+1)
del f
self.assertTrue(g)
self.assertEqual(nfiles(), start_nfiles)
self.assertEqual(ngroups(), start_ngroups+1)
f = g.file
self.assertTrue(f)
self.assertEqual(nfiles(), start_nfiles+1)
self.assertEqual(ngroups(), start_ngroups+1)
del g
self.assertEqual(nfiles(), start_nfiles+1)
self.assertEqual(ngroups(), start_ngroups)
del f
self.assertEqual(nfiles(), start_nfiles)
self.assertEqual(ngroups(), start_ngroups)
class TestDriverRegistration(TestCase):
def test_register_driver(self):
called_with = [None]
def set_fapl(plist, *args, **kwargs):
called_with[0] = args, kwargs
return _drivers['sec2'](plist)
h5py.register_driver('new-driver', set_fapl)
self.assertIn('new-driver', h5py.registered_drivers())
fname = self.mktemp()
h5py.File(fname, driver='new-driver', driver_arg_0=0, driver_arg_1=1,
mode='w')
self.assertEqual(
called_with,
[((), {'driver_arg_0': 0, 'driver_arg_1': 1})],
)
def test_unregister_driver(self):
h5py.register_driver('new-driver', lambda plist: None)
self.assertIn('new-driver', h5py.registered_drivers())
h5py.unregister_driver('new-driver')
self.assertNotIn('new-driver', h5py.registered_drivers())
with self.assertRaises(ValueError) as e:
fname = self.mktemp()
h5py.File(fname, driver='new-driver', mode='w')
self.assertEqual(str(e.exception), 'Unknown driver type "new-driver"')
class TestCache(TestCase):
def test_defaults(self):
fname = self.mktemp()
f = h5py.File(fname, 'w')
self.assertEqual(list(f.id.get_access_plist().get_cache()),
[0, 521, 1048576, 0.75])
def test_nbytes(self):
fname = self.mktemp()
f = h5py.File(fname, 'w', rdcc_nbytes=1024)
self.assertEqual(list(f.id.get_access_plist().get_cache()),
[0, 521, 1024, 0.75])
def test_nslots(self):
fname = self.mktemp()
f = h5py.File(fname, 'w', rdcc_nslots=125)
self.assertEqual(list(f.id.get_access_plist().get_cache()),
[0, 125, 1048576, 0.75])
def test_w0(self):
fname = self.mktemp()
f = h5py.File(fname, 'w', rdcc_w0=0.25)
self.assertEqual(list(f.id.get_access_plist().get_cache()),
[0, 521, 1048576, 0.25])
class TestFileObj(TestCase):
def check_write(self, fileobj):
f = h5py.File(fileobj, 'w')
self.assertEqual(f.driver, 'fileobj')
self.assertEqual(f.filename, repr(fileobj))
f.create_dataset('test', data=list(range(12)))
self.assertEqual(list(f), ['test'])
self.assertEqual(list(f['test'][:]), list(range(12)))
f.close()
def check_read(self, fileobj):
f = h5py.File(fileobj, 'r')
self.assertEqual(list(f), ['test'])
self.assertEqual(list(f['test'][:]), list(range(12)))
self.assertRaises(Exception, f.create_dataset, 'another.test', data=list(range(3)))
f.close()
def test_BytesIO(self):
with io.BytesIO() as fileobj:
self.assertEqual(len(fileobj.getvalue()), 0)
self.check_write(fileobj)
self.assertGreater(len(fileobj.getvalue()), 0)
self.check_read(fileobj)
def test_file(self):
fname = self.mktemp()
try:
with open(fname, 'wb+') as fileobj:
self.assertEqual(os.path.getsize(fname), 0)
self.check_write(fileobj)
self.assertGreater(os.path.getsize(fname), 0)
self.check_read(fileobj)
with open(fname, 'rb') as fileobj:
self.check_read(fileobj)
finally:
os.remove(fname)
def test_TemporaryFile(self):
# in this test, we check explicitly that temp file gets
# automatically deleted upon h5py.File.close()...
fileobj = tempfile.NamedTemporaryFile()
fname = fileobj.name
f = h5py.File(fileobj, 'w')
del fileobj
# ... but in your code feel free to simply
# f = h5py.File(tempfile.TemporaryFile())
f.create_dataset('test', data=list(range(12)))
self.assertEqual(list(f), ['test'])
self.assertEqual(list(f['test'][:]), list(range(12)))
self.assertTrue(os.path.isfile(fname))
f.close()
self.assertFalse(os.path.isfile(fname))
def test_exception_open(self):
self.assertRaises(Exception, h5py.File, None,
driver='fileobj', mode='x')
self.assertRaises(Exception, h5py.File, 'rogue',
driver='fileobj', mode='x')
self.assertRaises(Exception, h5py.File, self,
driver='fileobj', mode='x')
def test_exception_read(self):
class BrokenBytesIO(io.BytesIO):
def readinto(self, b):
raise Exception('I am broken')
f = h5py.File(BrokenBytesIO(), 'w')
f.create_dataset('test', data=list(range(12)))
self.assertRaises(Exception, list, f['test'])
def test_exception_write(self):
class BrokenBytesIO(io.BytesIO):
allow_write = False
def write(self, b):
if self.allow_write:
return super().write(b)
else:
raise Exception('I am broken')
bio = BrokenBytesIO()
f = h5py.File(bio, 'w')
try:
self.assertRaises(Exception, f.create_dataset, 'test',
data=list(range(12)))
finally:
# Un-break writing so we can close: errors while closing get messy.
bio.allow_write = True
f.close()
@ut.skip("Incompletely closed files can cause segfaults")
def test_exception_close(self):
fileobj = io.BytesIO()
f = h5py.File(fileobj, 'w')
fileobj.close()
self.assertRaises(Exception, f.close)
def test_exception_writeonly(self):
# HDF5 expects read & write access to a file it's writing;
# check that we get the correct exception on a write-only file object.
fileobj = open(os.path.join(self.tempdir, 'a.h5'), 'wb')
with self.assertRaises(io.UnsupportedOperation):
f = h5py.File(fileobj, 'w')
group = f.create_group("group")
group.create_dataset("data", data='foo', dtype=h5py.string_dtype())
def test_method_vanish(self):
fileobj = io.BytesIO()
f = h5py.File(fileobj, 'w')
f.create_dataset('test', data=list(range(12)))
self.assertEqual(list(f['test'][:]), list(range(12)))
fileobj.readinto = None
self.assertRaises(Exception, list, f['test'])
class TestTrackOrder(TestCase):
def populate(self, f):
for i in range(100):
# Mix group and dataset creation.
if i % 10 == 0:
f.create_group(str(i))
else:
f[str(i)] = [i]
def test_track_order(self):
fname = self.mktemp()
f = h5py.File(fname, 'w', track_order=True) # creation order
self.populate(f)
self.assertEqual(list(f),
[str(i) for i in range(100)])
def test_no_track_order(self):
fname = self.mktemp()
f = h5py.File(fname, 'w', track_order=False) # name alphanumeric
self.populate(f)
self.assertEqual(list(f),
sorted([str(i) for i in range(100)]))
class TestFileMetaBlockSize(TestCase):
"""
Feature: The meta block size can be manipulated, changing how metadata
is aggregated and the offset of the first dataset.
"""
def test_file_create_with_meta_block_size_4096(self):
# Test a large meta block size of 4 kibibytes
meta_block_size = 4096
with File(
self.mktemp(), 'w',
meta_block_size=meta_block_size,
libver="latest"
) as f:
f["test"] = 5
self.assertEqual(f.meta_block_size, meta_block_size)
# Equality is expected for HDF5 1.10
self.assertGreaterEqual(f["test"].id.get_offset(), meta_block_size)
def test_file_create_with_meta_block_size_512(self):
# Test a small meta block size of 512 bytes
# The smallest verifiable meta_block_size is 463
meta_block_size = 512
libver = "latest"
with File(
self.mktemp(), 'w',
meta_block_size=meta_block_size,
libver=libver
) as f:
f["test"] = 3
self.assertEqual(f.meta_block_size, meta_block_size)
# Equality is expected for HDF5 1.10
self.assertGreaterEqual(f["test"].id.get_offset(), meta_block_size)
# Default meta_block_size is 2048. This should fail if meta_block_size is not set.
self.assertLess(f["test"].id.get_offset(), meta_block_size*2)
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