/usr/lib/python2.7/dist-packages/tables/tests/test_create.py is in python-tables 3.1.1-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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-*- coding: utf-8 -*-
"""This test unit checks object creation funtions, like open_file,
create_table, create_array or create_group.
It also checks:
- name identifiers in tree objects
- title character limit for objects (255)
- limit in number in table fields (255)
"""
from __future__ import print_function
import os
import sys
import hashlib
import unittest
import tempfile
import warnings
import numpy
from tables import *
# important objects to test
from tables import Group, Leaf, Table, Array, hdf5_version
from tables.tests import common
from tables.parameters import MAX_COLUMNS
from tables.hdf5extension import HAVE_DIRECT_DRIVER, HAVE_WINDOWS_DRIVER
from tables.utils import quantize
import tables
# To delete the internal attributes automagically
unittest.TestCase.tearDown = common.cleanup
class Record(IsDescription):
var1 = StringCol(itemsize=4) # 4-character String
var2 = IntCol() # integer
var3 = Int16Col() # short integer
var4 = FloatCol() # double (double-precision)
var5 = Float32Col() # float (single-precision)
class createTestCase(unittest.TestCase):
file = "test.h5"
title = "This is the table title"
expectedrows = 100
maxshort = 2 ** 15
maxint = 2147483648 # (2 ** 31)
compress = 0
def setUp(self):
# Create an instance of HDF5 Table
self.fileh = open_file(self.file, mode="w")
self.root = self.fileh.root
# Create a table object
self.table = self.fileh.create_table(self.root, 'atable',
Record, "Table title")
# Create an array object
self.array = self.fileh.create_array(self.root, 'anarray',
[1], "Array title")
# Create a group object
self.group = self.fileh.create_group(self.root, 'agroup',
"Group title")
def tearDown(self):
self.fileh.close()
os.remove(self.file)
common.cleanup(self)
#----------------------------------------
def test00_isClass(self):
"""Testing table creation."""
self.assertTrue(isinstance(self.table, Table))
self.assertTrue(isinstance(self.array, Array))
self.assertTrue(isinstance(self.array, Leaf))
self.assertTrue(isinstance(self.group, Group))
def test01_overwriteNode(self):
"""Checking protection against node overwriting."""
try:
self.array = self.fileh.create_array(self.root, 'anarray',
[1], "Array title")
except NodeError:
if common.verbose:
(type, value, traceback) = sys.exc_info()
print("\nGreat!, the next NameError was catched!")
print(value)
else:
self.fail("expected a NodeError")
def test02_syntaxname(self):
"""Checking syntax in object tree names."""
# Now, try to attach an array to the object tree with
# a not allowed Python variable name
warnings.filterwarnings("error", category=NaturalNameWarning)
try:
self.array = self.fileh.create_array(self.root, ' array',
[1], "Array title")
except NaturalNameWarning:
if common.verbose:
(type, value, traceback) = sys.exc_info()
print("\nGreat!, the next NaturalNameWarning was catched!")
print(value)
else:
self.fail("expected a NaturalNameWarning")
# another name error
try:
self.array = self.fileh.create_array(self.root, '$array',
[1], "Array title")
except NaturalNameWarning:
if common.verbose:
(type, value, traceback) = sys.exc_info()
print("\nGreat!, the next NaturalNameWarning was catched!")
print(value)
else:
self.fail("expected a NaturalNameWarning")
# Finally, test a reserved word
try:
self.array = self.fileh.create_array(self.root, 'for',
[1], "Array title")
except NaturalNameWarning:
if common.verbose:
(type, value, traceback) = sys.exc_info()
print("\nGreat!, the next NaturalNameWarning was catched!")
print(value)
else:
self.fail("expected a NaturalNameWarning")
# Reset the warning
warnings.filterwarnings("default", category=NaturalNameWarning)
def test03a_titleAttr(self):
"""Checking the self.title attr in nodes."""
# Close the opened file to destroy the object tree
self.fileh.close()
# Open the file again to re-create the objects
self.fileh = open_file(self.file, "r")
# Now, test that self.title exists and is correct in all the nodes
self.assertEqual(self.fileh.root.agroup._v_title, "Group title")
self.assertEqual(self.fileh.root.atable.title, "Table title")
self.assertEqual(self.fileh.root.anarray.title, "Array title")
def test03b_titleLength(self):
"""Checking large title character length limit (1023)"""
titlelength = 1023
# Try to put a very long title on a group object
group = self.fileh.create_group(self.root, 'group',
"t" * titlelength)
self.assertEqual(group._v_title, "t" * titlelength)
self.assertEqual(group._f_getattr('TITLE'), "t" * titlelength)
# Now, try with a table object
table = self.fileh.create_table(self.root, 'table',
Record, "t" * titlelength)
self.assertEqual(table.title, "t" * titlelength)
self.assertEqual(table.get_attr("TITLE"), "t" * titlelength)
# Finally, try with an Array object
arr = self.fileh.create_array(self.root, 'arr',
[1], "t" * titlelength)
self.assertEqual(arr.title, "t" * titlelength)
self.assertEqual(arr.get_attr("TITLE"), "t" * titlelength)
def test04_maxFields(self):
"Checking a large number of fields in tables"
# The number of fields for a table
varnumber = MAX_COLUMNS
varnames = []
for i in range(varnumber):
varnames.append('int%d' % i)
# Build a dictionary with the types as values and varnames as keys
recordDict = {}
i = 0
for varname in varnames:
recordDict[varname] = Col.from_type("int32", dflt=1, pos=i)
i += 1
# Append this entry to indicate the alignment!
recordDict['_v_align'] = "="
table = self.fileh.create_table(self.root, 'table',
recordDict, "MetaRecord instance")
row = table.row
listrows = []
# Write 10 records
for j in range(10):
rowlist = []
for i in range(len(table.colnames)):
row[varnames[i]] = i * j
rowlist.append(i * j)
row.append()
listrows.append(tuple(rowlist))
# write data on disk
table.flush()
# Read all the data as a list
listout = table.read().tolist()
# Compare the input rowlist and output row list. They should
# be equal.
if common.verbose:
print("Original row list:", listrows[-1])
print("Retrieved row list:", listout[-1])
self.assertEqual(listrows, listout)
# The next limitation has been released. A warning is still there, though
def test05_maxFieldsExceeded(self):
"Checking an excess of the maximum number of fields in tables"
# The number of fields for a table
varnumber = MAX_COLUMNS + 1
varnames = []
for i in range(varnumber):
varnames.append('int%d' % i)
# Build a dictionary with the types as values and varnames as keys
recordDict = {}
i = 0
for varname in varnames:
recordDict[varname] = Col.from_type("int32", dflt=1)
i += 1
# Now, create a table with this record object
# This way of creating node objects has been deprecated
# table = Table(recordDict, "MetaRecord instance")
# Attach the table to object tree
warnings.filterwarnings("error", category=PerformanceWarning)
# Here, a PerformanceWarning should be raised!
try:
self.fileh.create_table(self.root, 'table',
recordDict, "MetaRecord instance")
except PerformanceWarning:
if common.verbose:
(type, value, traceback) = sys.exc_info()
print("\nGreat!, the next PerformanceWarning was catched!")
print(value)
else:
self.fail("expected an PerformanceWarning")
# Reset the warning
warnings.filterwarnings("default", category=PerformanceWarning)
# The next limitation has been released
def _test06_maxColumnNameLengthExceeded(self):
"Checking an excess (256) of the maximum length in column names"
# Build a dictionary with the types as values and varnames as keys
recordDict = {}
recordDict["a" * 255] = IntCol(dflt=1)
recordDict["b" * 256] = IntCol(dflt=1) # Should trigger a ValueError
# Now, create a table with this record object
# This way of creating node objects has been deprecated
table = Table(recordDict, "MetaRecord instance")
self.assertTrue(table is not None)
# Attach the table to object tree
# Here, ValueError should be raised!
try:
self.fileh.create_table(self.root, 'table',
recordDict, "MetaRecord instance")
except ValueError:
if common.verbose:
(type, value, traceback) = sys.exc_info()
print("\nGreat!, the next ValueError was catched!")
print(value)
else:
self.fail("expected an ValueError")
def test06_noMaxColumnNameLength(self):
"Checking unlimited length in column names"
# Build a dictionary with the types as values and varnames as keys
recordDict = {}
recordDict["a" * 255] = IntCol(dflt=1, pos=0)
recordDict["b" * 1024] = IntCol(dflt=1, pos=1) # Should work well
# Attach the table to object tree
# Here, IndexError should be raised!
table = self.fileh.create_table(self.root, 'table',
recordDict, "MetaRecord instance")
self.assertEqual(table.colnames[0], "a" * 255)
self.assertEqual(table.colnames[1], "b" * 1024)
class Record2(IsDescription):
var1 = StringCol(itemsize=4) # 4-character String
var2 = IntCol() # integer
var3 = Int16Col() # short integer
class FiltersTreeTestCase(unittest.TestCase):
title = "A title"
nrows = 10
def setUp(self):
# Create a temporary file
self.file = tempfile.mktemp(".h5")
# Create an instance of HDF5 Table
self.h5file = open_file(self.file, "w", filters=self.filters)
self.populateFile()
def populateFile(self):
group = self.h5file.root
# Create a tree with three levels of depth
for j in range(5):
# Create a table
table = self.h5file.create_table(group, 'table1', Record2,
title=self.title,
filters=None)
# Get the record object associated with the new table
d = table.row
# Fill the table
for i in xrange(self.nrows):
d['var1'] = '%04d' % (self.nrows - i)
d['var2'] = i
d['var3'] = i * 2
d.append() # This injects the Record values
# Flush the buffer for this table
table.flush()
# Create a couple of arrays in each group
var1List = [x['var1'] for x in table.iterrows()]
var3List = [x['var3'] for x in table.iterrows()]
self.h5file.create_array(group, 'array1', var1List, "col 1")
self.h5file.create_array(group, 'array2', var3List, "col 3")
# Create a couple of EArrays as well
ea1 = self.h5file.create_earray(group, 'earray1',
StringAtom(itemsize=4), (0,),
"col 1")
ea2 = self.h5file.create_earray(group, 'earray2',
Int16Atom(), (0,), "col 3")
# And fill them with some values
ea1.append(var1List)
ea2.append(var3List)
# Finally a couple of VLArrays too
vla1 = self.h5file.create_vlarray(group, 'vlarray1',
StringAtom(itemsize=4), "col 1")
vla2 = self.h5file.create_vlarray(group, 'vlarray2',
Int16Atom(), "col 3")
# And fill them with some values
vla1.append(var1List)
vla2.append(var3List)
# Create a new group (descendant of group)
if j == 1: # The second level
group2 = self.h5file.create_group(group, 'group' + str(j),
filters=self.gfilters)
elif j == 2: # third level
group2 = self.h5file.create_group(group, 'group' + str(j))
else: # The rest of levels
group2 = self.h5file.create_group(group, 'group' + str(j),
filters=self.filters)
# Iterate over this new group (group2)
group = group2
def tearDown(self):
# Close the file
if self.h5file.isopen:
self.h5file.close()
os.remove(self.file)
common.cleanup(self)
#----------------------------------------
def test00_checkFilters(self):
"Checking inheritance of filters on trees (open file version)"
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test00_checkFilters..." %
self.__class__.__name__)
# First level check
if common.verbose:
print("Test filter:", repr(self.filters))
print("Filters in file:", repr(self.h5file.filters))
if self.filters is None:
filters = Filters()
else:
filters = self.filters
self.assertEqual(repr(filters), repr(self.h5file.filters))
# The next nodes have to have the same filter properties as
# self.filters
nodelist = [
'/table1', '/group0/earray1', '/group0/vlarray1', '/group0',
]
for node in nodelist:
object = self.h5file.get_node(node)
if isinstance(object, Group):
self.assertEqual(repr(filters), repr(object._v_filters))
else:
self.assertEqual(repr(filters), repr(object.filters))
# Second and third level check
group1 = self.h5file.root.group0.group1
if self.gfilters is None:
if self.filters is None:
gfilters = Filters()
else:
gfilters = self.filters
else:
gfilters = self.gfilters
if common.verbose:
print("Test gfilter:", repr(gfilters))
print("Filters in file:", repr(group1._v_filters))
self.assertEqual(repr(gfilters), repr(group1._v_filters))
# The next nodes have to have the same filter properties as
# gfilters
nodelist = ['/group0/group1', '/group0/group1/earray1',
'/group0/group1/vlarray1',
'/group0/group1/table1', '/group0/group1/group2/table1']
for node in nodelist:
object = self.h5file.get_node(node)
if isinstance(object, Group):
self.assertEqual(repr(gfilters), repr(object._v_filters))
else:
self.assertEqual(repr(gfilters), repr(object.filters))
# Fourth and fifth level check
if self.filters is None:
# If None, the filters are inherited!
if self.gfilters is None:
filters = Filters()
else:
filters = self.gfilters
else:
filters = self.filters
group3 = self.h5file.root.group0.group1.group2.group3
if common.verbose:
print("Test filter:", repr(filters))
print("Filters in file:", repr(group3._v_filters))
self.assertEqual(repr(filters), repr(group3._v_filters))
# The next nodes have to have the same filter properties as
# self.filter
nodelist = ['/group0/group1/group2/group3',
'/group0/group1/group2/group3/earray1',
'/group0/group1/group2/group3/vlarray1',
'/group0/group1/group2/group3/table1',
'/group0/group1/group2/group3/group4']
for node in nodelist:
object = self.h5file.get_node(node)
if isinstance(object, Group):
self.assertEqual(repr(filters), repr(object._v_filters))
else:
self.assertEqual(repr(filters), repr(object.filters))
# Checking the special case for Arrays in which the compression
# should always be the empty Filter()
# The next nodes have to have the same filter properties as
# Filter()
nodelist = ['/array1',
'/group0/array1',
'/group0/group1/array1',
'/group0/group1/group2/array1',
'/group0/group1/group2/group3/array1']
for node in nodelist:
object = self.h5file.get_node(node)
self.assertEqual(repr(Filters()), repr(object.filters))
def test01_checkFilters(self):
"Checking inheritance of filters on trees (close file version)"
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test01_checkFilters..." %
self.__class__.__name__)
# Close the file
self.h5file.close()
# And open it again
self.h5file = open_file(self.file, "r")
# First level check
if self.filters is None:
filters = Filters()
else:
filters = self.filters
if common.verbose:
print("Test filter:", repr(filters))
print("Filters in file:", repr(self.h5file.filters))
self.assertEqual(repr(filters), repr(self.h5file.filters))
# The next nodes have to have the same filter properties as
# self.filters
nodelist = [
'/table1', '/group0/earray1', '/group0/vlarray1', '/group0',
]
for node in nodelist:
object_ = self.h5file.get_node(node)
if isinstance(object_, Group):
self.assertEqual(repr(filters), repr(object_._v_filters))
else:
self.assertEqual(repr(filters), repr(object_.filters))
# Second and third level check
group1 = self.h5file.root.group0.group1
if self.gfilters is None:
if self.filters is None:
gfilters = Filters()
else:
gfilters = self.filters
else:
gfilters = self.gfilters
if common.verbose:
print("Test filter:", repr(gfilters))
print("Filters in file:", repr(group1._v_filters))
repr(gfilters) == repr(group1._v_filters)
# The next nodes have to have the same filter properties as
# gfilters
nodelist = ['/group0/group1', '/group0/group1/earray1',
'/group0/group1/vlarray1',
'/group0/group1/table1', '/group0/group1/group2/table1']
for node in nodelist:
object_ = self.h5file.get_node(node)
if isinstance(object_, Group):
self.assertEqual(repr(gfilters), repr(object_._v_filters))
else:
self.assertEqual(repr(gfilters), repr(object_.filters))
# Fourth and fifth level check
if self.filters is None:
if self.gfilters is None:
filters = Filters()
else:
filters = self.gfilters
else:
filters = self.filters
group3 = self.h5file.root.group0.group1.group2.group3
if common.verbose:
print("Test filter:", repr(filters))
print("Filters in file:", repr(group3._v_filters))
repr(filters) == repr(group3._v_filters)
# The next nodes have to have the same filter properties as
# self.filters
nodelist = ['/group0/group1/group2/group3',
'/group0/group1/group2/group3/earray1',
'/group0/group1/group2/group3/vlarray1',
'/group0/group1/group2/group3/table1',
'/group0/group1/group2/group3/group4']
for node in nodelist:
object = self.h5file.get_node(node)
if isinstance(object, Group):
self.assertEqual(repr(filters), repr(object._v_filters))
else:
self.assertEqual(repr(filters), repr(object.filters))
# Checking the special case for Arrays in which the compression
# should always be the empty Filter()
# The next nodes have to have the same filter properties as
# Filter()
nodelist = ['/array1',
'/group0/array1',
'/group0/group1/array1',
'/group0/group1/group2/array1',
'/group0/group1/group2/group3/array1']
for node in nodelist:
object = self.h5file.get_node(node)
self.assertEqual(repr(Filters()), repr(object.filters))
class FiltersCase1(FiltersTreeTestCase):
filters = Filters()
gfilters = Filters(complevel=1)
class FiltersCase2(FiltersTreeTestCase):
filters = Filters(complevel=1, complib="bzip2")
gfilters = Filters(complevel=1)
class FiltersCase3(FiltersTreeTestCase):
filters = Filters(shuffle=True, complib="zlib")
gfilters = Filters(complevel=1, shuffle=False, complib="lzo")
class FiltersCase4(FiltersTreeTestCase):
filters = Filters(shuffle=True)
gfilters = Filters(complevel=1, shuffle=False)
class FiltersCase5(FiltersTreeTestCase):
filters = Filters(fletcher32=True)
gfilters = Filters(complevel=1, shuffle=False)
class FiltersCase6(FiltersTreeTestCase):
filters = None
gfilters = Filters(complevel=1, shuffle=False)
class FiltersCase7(FiltersTreeTestCase):
filters = Filters(complevel=1)
gfilters = None
class FiltersCase8(FiltersTreeTestCase):
filters = None
gfilters = None
class FiltersCase9(FiltersTreeTestCase):
filters = Filters(shuffle=True, complib="zlib")
gfilters = Filters(complevel=5, shuffle=True, complib="bzip2")
class FiltersCase10(FiltersTreeTestCase):
filters = Filters(shuffle=False, complevel=1, complib="blosc")
gfilters = Filters(complevel=5, shuffle=True, complib="blosc")
class FiltersCaseBloscBloscLZ(FiltersTreeTestCase):
filters = Filters(shuffle=False, complevel=1, complib="blosc:blosclz")
gfilters = Filters(complevel=5, shuffle=True, complib="blosc:blosclz")
class FiltersCaseBloscLZ4(FiltersTreeTestCase):
filters = Filters(shuffle=False, complevel=1, complib="blosc:lz4")
gfilters = Filters(complevel=5, shuffle=True, complib="blosc:lz4")
class FiltersCaseBloscLZ4HC(FiltersTreeTestCase):
filters = Filters(shuffle=False, complevel=1, complib="blosc:lz4hc")
gfilters = Filters(complevel=5, shuffle=True, complib="blosc:lz4hc")
class FiltersCaseBloscSnappy(FiltersTreeTestCase):
filters = Filters(shuffle=False, complevel=1, complib="blosc:snappy")
gfilters = Filters(complevel=5, shuffle=True, complib="blosc:snappy")
class FiltersCaseBloscZlib(FiltersTreeTestCase):
filters = Filters(shuffle=False, complevel=1, complib="blosc:zlib")
gfilters = Filters(complevel=5, shuffle=True, complib="blosc:zlib")
class CopyGroupTestCase(unittest.TestCase):
title = "A title"
nrows = 10
def setUp(self):
# Create a temporary file
self.file = tempfile.mktemp(".h5")
self.file2 = tempfile.mktemp(".h5")
# Create the source file
self.h5file = open_file(self.file, "w")
# Create the destination
self.h5file2 = open_file(self.file2, "w")
self.populateFile()
def populateFile(self):
group = self.h5file.root
# Add some user attrs:
group._v_attrs.attr1 = "an string for root group"
group._v_attrs.attr2 = 124
# Create a tree
for j in range(5):
for i in range(2):
# Create a new group (brother of group)
group2 = self.h5file.create_group(group, 'bgroup' + str(i),
filters=None)
# Create a table
table = self.h5file.create_table(group2, 'table1', Record2,
title=self.title,
filters=None)
# Get the record object associated with the new table
d = table.row
# Fill the table
for i in xrange(self.nrows):
d['var1'] = '%04d' % (self.nrows - i)
d['var2'] = i
d['var3'] = i * 2
d.append() # This injects the Record values
# Flush the buffer for this table
table.flush()
# Add some user attrs:
table.attrs.attr1 = "an string"
table.attrs.attr2 = 234
# Create a couple of arrays in each group
var1List = [x['var1'] for x in table.iterrows()]
var3List = [x['var3'] for x in table.iterrows()]
self.h5file.create_array(group2, 'array1', var1List, "col 1")
self.h5file.create_array(group2, 'array2', var3List, "col 3")
# Create a couple of EArrays as well
ea1 = self.h5file.create_earray(group2, 'earray1',
StringAtom(itemsize=4), (0,),
"col 1")
ea2 = self.h5file.create_earray(group2, 'earray2',
Int16Atom(), (0,), "col 3")
# Add some user attrs:
ea1.attrs.attr1 = "an string for earray"
ea2.attrs.attr2 = 123
# And fill them with some values
ea1.append(var1List)
ea2.append(var3List)
# Create a new group (descendant of group)
group3 = self.h5file.create_group(group, 'group' + str(j),
filters=None)
# Iterate over this new group (group3)
group = group3
# Add some user attrs:
group._v_attrs.attr1 = "an string for group"
group._v_attrs.attr2 = 124
def tearDown(self):
# Close the file
if self.h5file.isopen:
self.h5file.close()
if self.h5file2.isopen:
self.h5file2.close()
os.remove(self.file)
os.remove(self.file2)
common.cleanup(self)
#----------------------------------------
def test00_nonRecursive(self):
"Checking non-recursive copy of a Group"
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test00_nonRecursive..." %
self.__class__.__name__)
# Copy a group non-recursively
srcgroup = self.h5file.root.group0.group1
# srcgroup._f_copy_children(self.h5file2.root,
# recursive=False,
# filters=self.filters)
self.h5file.copy_children(srcgroup, self.h5file2.root,
recursive=False, filters=self.filters)
if self.close:
# Close the destination file
self.h5file2.close()
# And open it again
self.h5file2 = open_file(self.file2, "r")
# Check that the copy has been done correctly
dstgroup = self.h5file2.root
nodelist1 = srcgroup._v_children.keys()
nodelist2 = dstgroup._v_children.keys()
# Sort the lists
nodelist1.sort()
nodelist2.sort()
if common.verbose:
print("The origin node list -->", nodelist1)
print("The copied node list -->", nodelist2)
self.assertEqual(srcgroup._v_nchildren, dstgroup._v_nchildren)
self.assertEqual(nodelist1, nodelist2)
def test01_nonRecursiveAttrs(self):
"Checking non-recursive copy of a Group (attributes copied)"
if common.verbose:
print('\n', '-=' * 30)
print(("Running %s.test01_nonRecursiveAttrs..." %
self.__class__.__name__))
# Copy a group non-recursively with attrs
srcgroup = self.h5file.root.group0.group1
srcgroup._f_copy_children(self.h5file2.root,
recursive=False,
filters=self.filters,
copyuserattrs=1)
if self.close:
# Close the destination file
self.h5file2.close()
# And open it again
self.h5file2 = open_file(self.file2, "r")
# Check that the copy has been done correctly
dstgroup = self.h5file2.root
for srcnode in srcgroup:
dstnode = getattr(dstgroup, srcnode._v_name)
if isinstance(srcnode, Group):
srcattrs = srcnode._v_attrs
srcattrskeys = srcattrs._f_list("all")
dstattrs = dstnode._v_attrs
dstattrskeys = dstattrs._f_list("all")
else:
srcattrs = srcnode.attrs
srcattrskeys = srcattrs._f_list("all")
dstattrs = dstnode.attrs
dstattrskeys = dstattrs._f_list("all")
# Filters may differ, do not take into account
if self.filters is not None:
dstattrskeys.remove('FILTERS')
# These lists should already be ordered
if common.verbose:
print("srcattrskeys for node %s: %s" % (srcnode._v_name,
srcattrskeys))
print("dstattrskeys for node %s: %s" % (dstnode._v_name,
dstattrskeys))
self.assertEqual(srcattrskeys, dstattrskeys)
if common.verbose:
print("The attrs names has been copied correctly")
# Now, for the contents of attributes
for srcattrname in srcattrskeys:
srcattrvalue = str(getattr(srcattrs, srcattrname))
dstattrvalue = str(getattr(dstattrs, srcattrname))
self.assertEqual(srcattrvalue, dstattrvalue)
if self.filters is not None:
self.assertEqual(dstattrs.FILTERS, self.filters)
if common.verbose:
print("The attrs contents has been copied correctly")
def test02_Recursive(self):
"Checking recursive copy of a Group"
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test02_Recursive..." % self.__class__.__name__)
# Create the destination node
group = self.h5file2.root
for groupname in self.dstnode.split("/"):
if groupname:
group = self.h5file2.create_group(group, groupname)
dstgroup = self.h5file2.get_node(self.dstnode)
# Copy a group non-recursively
srcgroup = self.h5file.get_node(self.srcnode)
self.h5file.copy_children(srcgroup, dstgroup,
recursive=True,
filters=self.filters)
lenSrcGroup = len(srcgroup._v_pathname)
if lenSrcGroup == 1:
lenSrcGroup = 0 # Case where srcgroup == "/"
if self.close:
# Close the destination file
self.h5file2.close()
# And open it again
self.h5file2 = open_file(self.file2, "r")
dstgroup = self.h5file2.get_node(self.dstnode)
# Check that the copy has been done correctly
lenDstGroup = len(dstgroup._v_pathname)
if lenDstGroup == 1:
lenDstGroup = 0 # Case where dstgroup == "/"
first = 1
nodelist1 = []
for node in srcgroup._f_walknodes():
if first:
# skip the first group
first = 0
continue
nodelist1.append(node._v_pathname[lenSrcGroup:])
first = 1
nodelist2 = []
for node in dstgroup._f_walknodes():
if first:
# skip the first group
first = 0
continue
nodelist2.append(node._v_pathname[lenDstGroup:])
if common.verbose:
print("The origin node list -->", nodelist1)
print("The copied node list -->", nodelist2)
self.assertEqual(nodelist1, nodelist2)
def test03_RecursiveFilters(self):
"Checking recursive copy of a Group (cheking Filters)"
if common.verbose:
print('\n', '-=' * 30)
print(("Running %s.test03_RecursiveFilters..." %
self.__class__.__name__))
# Create the destination node
group = self.h5file2.root
for groupname in self.dstnode.split("/"):
if groupname:
group = self.h5file2.create_group(group, groupname)
dstgroup = self.h5file2.get_node(self.dstnode)
# Copy a group non-recursively
srcgroup = self.h5file.get_node(self.srcnode)
srcgroup._f_copy_children(dstgroup,
recursive=True,
filters=self.filters)
lenSrcGroup = len(srcgroup._v_pathname)
if lenSrcGroup == 1:
lenSrcGroup = 0 # Case where srcgroup == "/"
if self.close:
# Close the destination file
self.h5file2.close()
# And open it again
self.h5file2 = open_file(self.file2, "r")
dstgroup = self.h5file2.get_node(self.dstnode)
# Check that the copy has been done correctly
lenDstGroup = len(dstgroup._v_pathname)
if lenDstGroup == 1:
lenDstGroup = 0 # Case where dstgroup == "/"
first = 1
nodelist1 = {}
for node in srcgroup._f_walknodes():
if first:
# skip the first group
first = 0
continue
nodelist1[node._v_name] = node._v_pathname[lenSrcGroup:]
first = 1
for node in dstgroup._f_walknodes():
if first:
# skip the first group
first = 0
continue
if isinstance(node, Group):
repr(node._v_filters) == repr(nodelist1[node._v_name])
else:
repr(node.filters) == repr(nodelist1[node._v_name])
class CopyGroupCase1(CopyGroupTestCase):
close = 0
filters = None
srcnode = '/group0/group1'
dstnode = '/'
class CopyGroupCase2(CopyGroupTestCase):
close = 1
filters = None
srcnode = '/group0/group1'
dstnode = '/'
class CopyGroupCase3(CopyGroupTestCase):
close = 0
filters = None
srcnode = '/group0'
dstnode = '/group2/group3'
class CopyGroupCase4(CopyGroupTestCase):
close = 1
filters = Filters(complevel=1)
srcnode = '/group0'
dstnode = '/group2/group3'
class CopyGroupCase5(CopyGroupTestCase):
close = 0
filters = Filters()
srcnode = '/'
dstnode = '/group2/group3'
class CopyGroupCase6(CopyGroupTestCase):
close = 1
filters = Filters(fletcher32=True)
srcnode = '/group0'
dstnode = '/group2/group3'
class CopyGroupCase7(CopyGroupTestCase):
close = 0
filters = Filters(complevel=1, shuffle=False)
srcnode = '/'
dstnode = '/'
class CopyGroupCase8(CopyGroupTestCase):
close = 1
filters = Filters(complevel=1, complib="lzo")
srcnode = '/'
dstnode = '/'
class CopyFileTestCase(unittest.TestCase):
title = "A title"
nrows = 10
def setUp(self):
# Create a temporary file
self.file = tempfile.mktemp(".h5")
self.file2 = tempfile.mktemp(".h5")
# Create the source file
self.h5file = open_file(self.file, "w")
self.populateFile()
def populateFile(self):
group = self.h5file.root
# Add some user attrs:
group._v_attrs.attr1 = "an string for root group"
group._v_attrs.attr2 = 124
# Create a tree
for j in range(5):
for i in range(2):
# Create a new group (brother of group)
group2 = self.h5file.create_group(group, 'bgroup' + str(i),
filters=None)
# Create a table
table = self.h5file.create_table(group2, 'table1', Record2,
title=self.title,
filters=None)
# Get the record object associated with the new table
d = table.row
# Fill the table
for i in xrange(self.nrows):
d['var1'] = '%04d' % (self.nrows - i)
d['var2'] = i
d['var3'] = i * 2
d.append() # This injects the Record values
# Flush the buffer for this table
table.flush()
# Add some user attrs:
table.attrs.attr1 = "an string"
table.attrs.attr2 = 234
# Create a couple of arrays in each group
var1List = [x['var1'] for x in table.iterrows()]
var3List = [x['var3'] for x in table.iterrows()]
self.h5file.create_array(group2, 'array1', var1List, "col 1")
self.h5file.create_array(group2, 'array2', var3List, "col 3")
# Create a couple of EArrays as well
ea1 = self.h5file.create_earray(group2, 'earray1',
StringAtom(itemsize=4), (0,),
"col 1")
ea2 = self.h5file.create_earray(group2, 'earray2',
Int16Atom(), (0,),
"col 3")
# Add some user attrs:
ea1.attrs.attr1 = "an string for earray"
ea2.attrs.attr2 = 123
# And fill them with some values
ea1.append(var1List)
ea2.append(var3List)
# Create a new group (descendant of group)
group3 = self.h5file.create_group(group, 'group' + str(j),
filters=None)
# Iterate over this new group (group3)
group = group3
# Add some user attrs:
group._v_attrs.attr1 = "an string for group"
group._v_attrs.attr2 = 124
def tearDown(self):
# Close the file
if self.h5file.isopen:
self.h5file.close()
if hasattr(self, 'h5file2') and self.h5file2.isopen:
self.h5file2.close()
os.remove(self.file)
if hasattr(self, 'file2') and os.path.exists(self.file2):
os.remove(self.file2)
common.cleanup(self)
#----------------------------------------
def test00_overwrite(self):
"Checking copy of a File (overwriting file)"
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test00_overwrite..." % self.__class__.__name__)
# Create a temporary file
file2h = open(self.file2, "w")
file2h.close()
# Copy the file to the destination
self.h5file.copy_file(self.file2, title=self.title,
overwrite=1,
copyuserattrs=0,
filters=None)
# Close the original file, if needed
if self.close:
self.h5file.close()
# re-open it
self.h5file = open_file(self.file, "r")
# ...and open the destination file
self.h5file2 = open_file(self.file2, "r")
# Check that the copy has been done correctly
srcgroup = self.h5file.root
dstgroup = self.h5file2.root
nodelist1 = srcgroup._v_children.keys()
nodelist2 = dstgroup._v_children.keys()
# Sort the lists
nodelist1.sort()
nodelist2.sort()
if common.verbose:
print("The origin node list -->", nodelist1)
print("The copied node list -->", nodelist2)
self.assertEqual(srcgroup._v_nchildren, dstgroup._v_nchildren)
self.assertEqual(nodelist1, nodelist2)
self.assertEqual(self.h5file2.title, self.title)
def test00a_srcdstequal(self):
"Checking copy of a File (srcfile == dstfile)"
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test00a_srcdstequal..." %
self.__class__.__name__)
# Copy the file to the destination
self.assertRaises(IOError, self.h5file.copy_file, self.h5file.filename)
def test00b_firstclass(self):
"Checking copy of a File (first-class function)"
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test00b_firstclass..." % self.__class__.__name__)
# Close the temporary file
self.h5file.close()
# Copy the file to the destination
copy_file(self.file, self.file2, title=self.title,
copyuserattrs=0, filters=None, overwrite=1)
# ...and open the source and destination file
self.h5file = open_file(self.file, "r")
self.h5file2 = open_file(self.file2, "r")
# Check that the copy has been done correctly
srcgroup = self.h5file.root
dstgroup = self.h5file2.root
nodelist1 = srcgroup._v_children.keys()
nodelist2 = dstgroup._v_children.keys()
# Sort the lists
nodelist1.sort()
nodelist2.sort()
if common.verbose:
print("The origin node list -->", nodelist1)
print("The copied node list -->", nodelist2)
self.assertEqual(srcgroup._v_nchildren, dstgroup._v_nchildren)
self.assertEqual(nodelist1, nodelist2)
self.assertEqual(self.h5file2.title, self.title)
def test01_copy(self):
"Checking copy of a File (attributes not copied)"
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test01_copy..." % self.__class__.__name__)
# Copy the file to the destination
self.h5file.copy_file(self.file2, title=self.title,
copyuserattrs=0,
filters=self.filters)
# Close the original file, if needed
if self.close:
self.h5file.close()
# re-open it
self.h5file = open_file(self.file, "r")
# ...and open the destination file
self.h5file2 = open_file(self.file2, "r")
# Check that the copy has been done correctly
srcgroup = self.h5file.root
dstgroup = self.h5file2.root
nodelist1 = srcgroup._v_children.keys()
nodelist2 = dstgroup._v_children.keys()
# Sort the lists
nodelist1.sort()
nodelist2.sort()
if common.verbose:
print("The origin node list -->", nodelist1)
print("The copied node list -->", nodelist2)
self.assertEqual(srcgroup._v_nchildren, dstgroup._v_nchildren)
self.assertEqual(nodelist1, nodelist2)
# print("_v_attrnames-->", self.h5file2.root._v_attrs._v_attrnames)
# print("--> <%s,%s>" % (self.h5file2.title, self.title))
self.assertEqual(self.h5file2.title, self.title)
# Check that user attributes has not been copied
for srcnode in srcgroup:
dstnode = getattr(dstgroup, srcnode._v_name)
srcattrs = srcnode._v_attrs
srcattrskeys = srcattrs._f_list("sys")
dstattrs = dstnode._v_attrs
dstattrskeys = dstattrs._f_list("all")
# Filters may differ, do not take into account
if self.filters is not None:
dstattrskeys.remove('FILTERS')
# These lists should already be ordered
if common.verbose:
print("srcattrskeys for node %s: %s" % (srcnode._v_name,
srcattrskeys))
print("dstattrskeys for node %s: %s" % (dstnode._v_name,
dstattrskeys))
self.assertEqual(srcattrskeys, dstattrskeys)
if common.verbose:
print("The attrs names has been copied correctly")
# Now, for the contents of attributes
for srcattrname in srcattrskeys:
srcattrvalue = str(getattr(srcattrs, srcattrname))
dstattrvalue = str(getattr(dstattrs, srcattrname))
self.assertEqual(srcattrvalue, dstattrvalue)
if self.filters is not None:
self.assertEqual(dstattrs.FILTERS, self.filters)
if common.verbose:
print("The attrs contents has been copied correctly")
def test02_Attrs(self):
"Checking copy of a File (attributes copied)"
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test02_Attrs..." % self.__class__.__name__)
# Copy the file to the destination
self.h5file.copy_file(self.file2, title=self.title,
copyuserattrs=1,
filters=self.filters)
# Close the original file, if needed
if self.close:
self.h5file.close()
# re-open it
self.h5file = open_file(self.file, "r")
# ...and open the destination file
self.h5file2 = open_file(self.file2, "r")
# Check that the copy has been done correctly
srcgroup = self.h5file.root
dstgroup = self.h5file2.root
for srcnode in srcgroup:
dstnode = getattr(dstgroup, srcnode._v_name)
srcattrs = srcnode._v_attrs
srcattrskeys = srcattrs._f_list("all")
dstattrs = dstnode._v_attrs
dstattrskeys = dstattrs._f_list("all")
# These lists should already be ordered
if common.verbose:
print("srcattrskeys for node %s: %s" % (srcnode._v_name,
srcattrskeys))
print("dstattrskeys for node %s: %s" % (dstnode._v_name,
dstattrskeys))
# Filters may differ, do not take into account
if self.filters is not None:
dstattrskeys.remove('FILTERS')
self.assertEqual(srcattrskeys, dstattrskeys)
if common.verbose:
print("The attrs names has been copied correctly")
# Now, for the contents of attributes
for srcattrname in srcattrskeys:
srcattrvalue = str(getattr(srcattrs, srcattrname))
dstattrvalue = str(getattr(dstattrs, srcattrname))
self.assertEqual(srcattrvalue, dstattrvalue)
if self.filters is not None:
self.assertEqual(dstattrs.FILTERS, self.filters)
if common.verbose:
print("The attrs contents has been copied correctly")
class CopyFileCase1(CopyFileTestCase):
close = 0
title = "A new title"
filters = None
class CopyFileCase2(CopyFileTestCase):
close = 1
title = "A new title"
filters = None
class CopyFileCase3(CopyFileTestCase):
close = 0
title = "A new title"
filters = Filters(complevel=1)
class CopyFileCase4(CopyFileTestCase):
close = 1
title = "A new title"
filters = Filters(complevel=1)
class CopyFileCase5(CopyFileTestCase):
close = 0
title = "A new title"
filters = Filters(fletcher32=True)
class CopyFileCase6(CopyFileTestCase):
close = 1
title = "A new title"
filters = Filters(fletcher32=True)
class CopyFileCase7(CopyFileTestCase):
close = 0
title = "A new title"
filters = Filters(complevel=1, complib="lzo")
class CopyFileCase8(CopyFileTestCase):
close = 1
title = "A new title"
filters = Filters(complevel=1, complib="lzo")
class CopyFileCase10(unittest.TestCase):
def test01_notoverwrite(self):
"Checking copy of a File (checking not overwriting)"
if common.verbose:
print('\n', '-=' * 30)
print("Running %s.test01_notoverwrite..." %
self.__class__.__name__)
# Create two empty files:
file = tempfile.mktemp(".h5")
fileh = open_file(file, "w")
file2 = tempfile.mktemp(".h5")
fileh2 = open_file(file2, "w")
fileh2.close() # close the second one
# Copy the first into the second
try:
fileh.copy_file(file2, overwrite=False)
except IOError:
if common.verbose:
(type, value, traceback) = sys.exc_info()
print("\nGreat!, the next IOError was catched!")
print(value)
else:
self.fail("expected a IOError")
# Delete files
fileh.close()
os.remove(file)
os.remove(file2)
class GroupFiltersTestCase(common.TempFileMixin, common.PyTablesTestCase):
filters = tables.Filters(complevel=4) # something non-default
def setUp(self):
super(GroupFiltersTestCase, self).setUp()
atom, shape = tables.IntAtom(), (1, 1)
create_group = self.h5file.create_group
create_carray = self.h5file.create_carray
create_group('/', 'implicit_no')
create_group('/implicit_no', 'implicit_no')
create_carray('/implicit_no/implicit_no', 'implicit_no',
atom=atom, shape=shape)
create_carray('/implicit_no/implicit_no', 'explicit_no',
atom=atom, shape=shape, filters=tables.Filters())
create_carray('/implicit_no/implicit_no', 'explicit_yes',
atom=atom, shape=shape, filters=self.filters)
create_group('/', 'explicit_yes', filters=self.filters)
create_group('/explicit_yes', 'implicit_yes')
create_carray('/explicit_yes/implicit_yes', 'implicit_yes',
atom=atom, shape=shape)
create_carray('/explicit_yes/implicit_yes', 'explicit_yes',
atom=atom, shape=shape, filters=self.filters)
create_carray('/explicit_yes/implicit_yes', 'explicit_no',
atom=atom, shape=shape, filters=tables.Filters())
def _check_filters(self, h5file, filters=None):
for node in h5file:
# Get node filters.
if hasattr(node, 'filters'):
node_filters = node.filters
else:
node_filters = node._v_filters
# Compare to given filters.
if filters is not None:
self.assertEqual(node_filters, filters)
return
# Guess filters to compare to by node name.
if node._v_name.endswith('_no'):
self.assertEqual(
node_filters, tables.Filters(),
"node ``%s`` should have no filters" % node._v_pathname)
elif node._v_name.endswith('_yes'):
self.assertEqual(
node_filters, self.filters,
"node ``%s`` should have filters" % node._v_pathname)
def test00_propagate(self):
"""Filters propagating to children."""
self._check_filters(self.h5file)
def _test_copyFile(self, filters=None):
copyfname = tempfile.mktemp(suffix='.h5')
try:
self.h5file.copy_file(copyfname, filters=filters)
try:
copyf = tables.open_file(copyfname)
self._check_filters(copyf, filters=filters)
finally:
copyf.close()
finally:
os.remove(copyfname)
def test01_copyFile(self):
"""Keeping filters when copying a file."""
self._test_copyFile()
def test02_copyFile_override(self):
"""Overriding filters when copying a file."""
self._test_copyFile(self.filters)
def _test_change(self, pathname, change_filters, new_filters):
group = self.h5file.get_node(pathname)
# Check expected current filters.
old_filters = tables.Filters()
if pathname.endswith('_yes'):
old_filters = self.filters
self.assertEqual(group._v_filters, old_filters)
# Change filters.
change_filters(group)
self.assertEqual(group._v_filters, new_filters)
# Get and check changed filters.
if self._reopen():
group = self.h5file.get_node(pathname)
self.assertEqual(group._v_filters, new_filters)
def test03_change(self):
"""Changing the filters of a group."""
def set_filters(group):
group._v_filters = self.filters
self._test_change('/', set_filters, self.filters)
def test04_delete(self):
"""Deleting the filters of a group."""
def del_filters(group):
del group._v_filters
self._test_change('/explicit_yes', del_filters, tables.Filters())
class SetBloscMaxThreadsTestCase(common.TempFileMixin,
common.PyTablesTestCase):
filters = tables.Filters(complevel=4, complib="blosc")
def test00(self):
"""Checking set_blosc_max_threads()"""
nthreads_old = tables.set_blosc_max_threads(4)
if common.verbose:
print("Previous max threads:", nthreads_old)
print("Should be:", self.h5file.params['MAX_BLOSC_THREADS'])
self.assertEqual(nthreads_old, self.h5file.params['MAX_BLOSC_THREADS'])
self.h5file.create_carray('/', 'some_array',
atom=tables.Int32Atom(), shape=(3, 3),
filters = self.filters)
nthreads_old = tables.set_blosc_max_threads(1)
if common.verbose:
print("Previous max threads:", nthreads_old)
print("Should be:", 4)
self.assertEqual(nthreads_old, 4)
def test01(self):
"""Checking set_blosc_max_threads() (re-open)"""
nthreads_old = tables.set_blosc_max_threads(4)
self.h5file.create_carray('/', 'some_array',
atom=tables.Int32Atom(), shape=(3, 3),
filters = self.filters)
self._reopen()
nthreads_old = tables.set_blosc_max_threads(4)
if common.verbose:
print("Previous max threads:", nthreads_old)
print("Should be:", self.h5file.params['MAX_BLOSC_THREADS'])
self.assertEqual(nthreads_old, self.h5file.params['MAX_BLOSC_THREADS'])
class FilterTestCase(common.PyTablesTestCase):
def test_filter_pack_type(self):
self.assertEqual(type(Filters()._pack()), numpy.int64)
@staticmethod
def _hexl(n):
if sys.version_info[0] > 2:
return hex(int(n))
else:
return hex(long(n)).rstrip('L')
def test_filter_pack_01(self):
filter_ = Filters()
self.assertEqual(self._hexl(filter_._pack()), '0x0')
def test_filter_pack_02(self):
filter_ = Filters(1, shuffle=False)
self.assertEqual(self._hexl(filter_._pack()), '0x101')
def test_filter_pack_03(self):
filter_ = Filters(9, 'zlib', shuffle=True, fletcher32=True)
self.assertEqual(self._hexl(filter_._pack()), '0x30109')
def test_filter_pack_04(self):
filter_ = Filters(1, shuffle=False, least_significant_digit=5)
self.assertEqual(self._hexl(filter_._pack()), '0x5040101')
def test_filter_unpack_01(self):
filter_ = Filters._unpack(numpy.int64(0x0))
self.assertFalse(filter_.shuffle)
self.assertFalse(filter_.fletcher32)
self.assertEqual(filter_.least_significant_digit, None)
self.assertEqual(filter_.complevel, 0)
self.assertEqual(filter_.complib, None)
def test_filter_unpack_02(self):
filter_ = Filters._unpack(numpy.int64(0x101))
self.assertFalse(filter_.shuffle)
self.assertFalse(filter_.fletcher32)
self.assertEqual(filter_.least_significant_digit, None)
self.assertEqual(filter_.complevel, 1)
self.assertEqual(filter_.complib, 'zlib')
def test_filter_unpack_03(self):
filter_ = Filters._unpack(numpy.int64(0x30109))
self.assertTrue(filter_.shuffle)
self.assertTrue(filter_.fletcher32)
self.assertEqual(filter_.least_significant_digit, None)
self.assertEqual(filter_.complevel, 9)
self.assertEqual(filter_.complib, 'zlib')
def test_filter_unpack_04(self):
filter_ = Filters._unpack(numpy.int64(0x5040101))
self.assertFalse(filter_.shuffle)
self.assertFalse(filter_.fletcher32)
self.assertEqual(filter_.least_significant_digit, 5)
self.assertEqual(filter_.complevel, 1)
self.assertEqual(filter_.complib, 'zlib')
class DefaultDriverTestCase(common.PyTablesTestCase):
DRIVER = None
DRIVER_PARAMS = {}
def setUp(self):
self.h5fname = tempfile.mktemp(suffix=".h5")
self.h5file = tables.open_file(self.h5fname, mode="w",
driver=self.DRIVER,
**self.DRIVER_PARAMS)
# Create an HDF5 file and contents
root = self.h5file.root
self.h5file.set_node_attr(root, "testattr", 41)
self.h5file.create_array(root, "array", [1, 2], title="array")
self.h5file.create_table(root, "table", {"var1": tables.IntCol()},
title="table")
def tearDown(self):
if self.h5file:
self.h5file.close()
self.h5file = None
if os.path.isfile(self.h5fname):
os.remove(self.h5fname)
def assertIsFile(self):
self.assertTrue(os.path.isfile(self.h5fname))
def test_newFile(self):
self.assertTrue(isinstance(self.h5file, tables.File))
self.assertIsFile()
def test_readFile(self):
self.h5file.close()
self.h5file = None
self.assertIsFile()
# Open an existing HDF5 file
self.h5file = tables.open_file(self.h5fname, mode="r",
driver=self.DRIVER,
**self.DRIVER_PARAMS)
# check contents
root = self.h5file.root
self.assertEqual(self.h5file.get_node_attr(root, "testattr"), 41)
self.assertTrue(isinstance(root.array, tables.Array))
self.assertEqual(root.array._v_title, "array")
self.assertTrue(isinstance(root.table, tables.Table))
self.assertEqual(root.table._v_title, "table")
self.assertTrue("var1" in root.table.colnames)
self.assertEqual(root.table.cols.var1.dtype, tables.IntCol().dtype)
def test_openFileA(self):
self.h5file.close()
self.h5file = None
self.assertIsFile()
# Open an existing HDF5 file in append mode
self.h5file = tables.open_file(self.h5fname, mode="a",
driver=self.DRIVER,
**self.DRIVER_PARAMS)
# check contents
root = self.h5file.root
self.assertEqual(self.h5file.get_node_attr(root, "testattr"), 41)
self.assertTrue(isinstance(root.array, tables.Array))
self.assertEqual(root.array._v_title, "array")
self.assertTrue(isinstance(root.table, tables.Table))
self.assertEqual(root.table._v_title, "table")
self.assertTrue("var1" in root.table.colnames)
self.assertEqual(root.table.cols.var1.dtype, tables.IntCol().dtype)
# write new data
root = self.h5file.root
self.h5file.set_node_attr(root, "testattr2", 42)
self.h5file.create_array(root, "array2", [1, 2], title="array2")
self.h5file.create_table(root, "table2", {"var2": tables.FloatCol()},
title="table2")
self.h5file.close()
# check contents
self.h5file = tables.open_file(self.h5fname, mode="a",
driver=self.DRIVER,
**self.DRIVER_PARAMS)
root = self.h5file.root
self.assertEqual(self.h5file.get_node_attr(root, "testattr"), 41)
self.assertEqual(self.h5file.get_node_attr(root, "testattr2"), 42)
self.assertTrue(isinstance(root.array, tables.Array))
self.assertEqual(root.array._v_title, "array")
self.assertTrue(isinstance(root.array2, tables.Array))
self.assertEqual(root.array2._v_title, "array2")
self.assertTrue(isinstance(root.table, tables.Table))
self.assertEqual(root.table._v_title, "table")
self.assertTrue("var1" in root.table.colnames)
self.assertEqual(root.table.cols.var1.dtype, tables.IntCol().dtype)
self.assertTrue(isinstance(root.table2, tables.Table))
self.assertEqual(root.table2._v_title, "table2")
self.assertTrue("var2" in root.table2.colnames)
self.assertEqual(root.table2.cols.var2.dtype, tables.FloatCol().dtype)
def test_openFileRW(self):
self.h5file.close()
self.h5file = None
self.assertIsFile()
# Open an existing HDF5 file in append mode
self.h5file = tables.open_file(self.h5fname, mode="r+",
driver=self.DRIVER,
**self.DRIVER_PARAMS)
# check contents
root = self.h5file.root
self.assertEqual(self.h5file.get_node_attr(root, "testattr"), 41)
self.assertTrue(isinstance(root.array, tables.Array))
self.assertEqual(root.array._v_title, "array")
self.assertTrue(isinstance(root.table, tables.Table))
self.assertEqual(root.table._v_title, "table")
self.assertTrue("var1" in root.table.colnames)
self.assertEqual(root.table.cols.var1.dtype, tables.IntCol().dtype)
# write new data
self.h5file.set_node_attr(root, "testattr2", 42)
self.h5file.create_array(root, "array2", [1, 2], title="array2")
self.h5file.create_table(root, "table2", {"var2": tables.FloatCol()},
title="table2")
self.h5file.close()
# check contents
self.h5file = tables.open_file(self.h5fname, mode="r+",
driver=self.DRIVER,
**self.DRIVER_PARAMS)
root = self.h5file.root
self.assertEqual(self.h5file.get_node_attr(root, "testattr"), 41)
self.assertEqual(self.h5file.get_node_attr(root, "testattr2"), 42)
self.assertTrue(isinstance(root.array, tables.Array))
self.assertEqual(root.array._v_title, "array")
self.assertTrue(isinstance(root.array2, tables.Array))
self.assertEqual(root.array2._v_title, "array2")
self.assertTrue(isinstance(root.table, tables.Table))
self.assertEqual(root.table._v_title, "table")
self.assertTrue("var1" in root.table.colnames)
self.assertEqual(root.table.cols.var1.dtype, tables.IntCol().dtype)
self.assertTrue(isinstance(root.table2, tables.Table))
self.assertEqual(root.table2._v_title, "table2")
self.assertTrue("var2" in root.table2.colnames)
self.assertEqual(root.table2.cols.var2.dtype, tables.FloatCol().dtype)
class Sec2DriverTestCase(DefaultDriverTestCase):
DRIVER = "H5FD_SEC2"
if hdf5_version >= "1.8.9":
def test_get_file_image(self):
image = self.h5file.get_file_image()
self.assertTrue(len(image) > 0)
if sys.version_info[0] < 3:
self.assertEqual([ord(i) for i in image[
:4]], [137, 72, 68, 70])
else:
self.assertEqual([i for i in image[:4]], [137, 72, 68, 70])
class StdioDriverTestCase(DefaultDriverTestCase):
DRIVER = "H5FD_STDIO"
if hdf5_version >= "1.8.9":
def test_get_file_image(self):
image = self.h5file.get_file_image()
self.assertTrue(len(image) > 0)
if sys.version_info[0] < 3:
self.assertEqual([ord(i) for i in image[
:4]], [137, 72, 68, 70])
else:
self.assertEqual([i for i in image[:4]], [137, 72, 68, 70])
class CoreDriverTestCase(DefaultDriverTestCase):
DRIVER = "H5FD_CORE"
if hdf5_version >= "1.8.9":
def test_get_file_image(self):
image = self.h5file.get_file_image()
self.assertTrue(len(image) > 0)
if sys.version_info[0] < 3:
self.assertEqual([ord(i) for i in image[
:4]], [137, 72, 68, 70])
else:
self.assertEqual([i for i in image[:4]], [137, 72, 68, 70])
class CoreDriverNoBackingStoreTestCase(common.PyTablesTestCase):
DRIVER = "H5FD_CORE"
def setUp(self):
self.h5fname = tempfile.mktemp(suffix=".h5")
self.h5file = None
def tearDown(self):
if self.h5file:
self.h5file.close()
elif self.h5fname in tables.file._open_files:
open_files = tables.file._open_files
for h5file in open_files.get_handlers_by_name(self.h5fname):
h5file.close()
self.h5file = None
if os.path.isfile(self.h5fname):
os.remove(self.h5fname)
def test_newFile(self):
"""Ensure that nothing is written to file."""
self.assertFalse(os.path.isfile(self.h5fname))
self.h5file = tables.open_file(self.h5fname, mode="w",
driver=self.DRIVER,
driver_core_backing_store=False)
# Create an HDF5 file and contents
root = self.h5file.root
self.h5file.set_node_attr(root, "testattr", 41)
self.h5file.create_array(root, "array", [1, 2], title="array")
self.h5file.create_table(root, "table", {"var1": tables.IntCol()},
title="table")
self.h5file.close() # flush
self.assertFalse(os.path.isfile(self.h5fname))
def test_readNewFileW(self):
self.assertFalse(os.path.isfile(self.h5fname))
# Create an HDF5 file and contents
self.h5file = tables.open_file(self.h5fname, mode="w",
driver=self.DRIVER,
driver_core_backing_store=False)
root = self.h5file.root
self.h5file.set_node_attr(root, "testattr", 41)
self.h5file.create_array(root, "array", [1, 2], title="array")
self.h5file.create_table(root, "table", {"var1": tables.IntCol()},
title="table")
self.assertEqual(self.h5file.get_node_attr(root, "testattr"), 41)
self.assertTrue(isinstance(root.array, tables.Array))
self.assertEqual(root.array._v_title, "array")
self.assertTrue(isinstance(root.table, tables.Table))
self.assertEqual(root.table._v_title, "table")
self.assertTrue("var1" in root.table.colnames)
self.assertEqual(root.table.cols.var1.dtype, tables.IntCol().dtype)
self.h5file.close() # flush
self.assertFalse(os.path.isfile(self.h5fname))
def test_readNewFileA(self):
self.assertFalse(os.path.isfile(self.h5fname))
# Create an HDF5 file and contents
self.h5file = tables.open_file(self.h5fname, mode="a",
driver=self.DRIVER,
driver_core_backing_store=False)
root = self.h5file.root
self.h5file.set_node_attr(root, "testattr", 41)
self.h5file.create_array(root, "array", [1, 2], title="array")
self.h5file.create_table(root, "table", {"var1": tables.IntCol()},
title="table")
self.assertEqual(self.h5file.get_node_attr(root, "testattr"), 41)
self.assertTrue(isinstance(root.array, tables.Array))
self.assertEqual(root.array._v_title, "array")
self.assertTrue(isinstance(root.table, tables.Table))
self.assertEqual(root.table._v_title, "table")
self.assertTrue("var1" in root.table.colnames)
self.assertEqual(root.table.cols.var1.dtype, tables.IntCol().dtype)
self.h5file.close() # flush
self.assertFalse(os.path.isfile(self.h5fname))
def test_openNewFileRW(self):
self.assertFalse(os.path.isfile(self.h5fname))
self.assertRaises(HDF5ExtError,
tables.open_file, self.h5fname, mode="r+",
driver=self.DRIVER, driver_core_backing_store=False)
def test_openNewFileR(self):
self.assertFalse(os.path.isfile(self.h5fname))
self.assertRaises(HDF5ExtError,
tables.open_file, self.h5fname, mode="r",
driver=self.DRIVER, driver_core_backing_store=False)
def _create_file(self, filename):
h5file = tables.open_file(filename, mode="w")
root = h5file.root
h5file.set_node_attr(root, "testattr", 41)
h5file.create_array(root, "array", [1, 2], title="array")
h5file.create_table(root, "table", {"var1": tables.IntCol()},
title="table")
h5file.close()
def test_readFile(self):
self._create_file(self.h5fname)
self.assertTrue(os.path.isfile(self.h5fname))
# Open an existing HDF5 file
self.h5file = tables.open_file(self.h5fname, mode="r",
driver=self.DRIVER,
driver_core_backing_store=False)
root = self.h5file.root
self.assertEqual(self.h5file.get_node_attr(root, "testattr"), 41)
self.assertTrue(isinstance(root.array, tables.Array))
self.assertEqual(root.array._v_title, "array")
self.assertTrue(isinstance(root.table, tables.Table))
self.assertEqual(root.table._v_title, "table")
self.assertTrue("var1" in root.table.colnames)
self.assertEqual(root.table.cols.var1.dtype, tables.IntCol().dtype)
def _get_digest(self, filename):
md5 = hashlib.md5()
fd = open(filename, 'rb')
for data in fd:
md5.update(data)
fd.close()
hexdigest = md5.hexdigest()
return hexdigest
def test_openFileA(self):
self._create_file(self.h5fname)
self.assertTrue(os.path.isfile(self.h5fname))
# compute the file hash
hexdigest = self._get_digest(self.h5fname)
# Open an existing HDF5 file in append mode
self.h5file = tables.open_file(self.h5fname, mode="a",
driver=self.DRIVER,
driver_core_backing_store=False)
# check contents
root = self.h5file.root
self.assertEqual(self.h5file.get_node_attr(root, "testattr"), 41)
self.assertTrue(isinstance(root.array, tables.Array))
self.assertEqual(root.array._v_title, "array")
self.assertTrue(isinstance(root.table, tables.Table))
self.assertEqual(root.table._v_title, "table")
self.assertTrue("var1" in root.table.colnames)
self.assertEqual(root.table.cols.var1.dtype, tables.IntCol().dtype)
# write new data
root = self.h5file.root
self.h5file.set_node_attr(root, "testattr2", 42)
self.h5file.create_array(root, "array2", [1, 2], title="array2")
self.h5file.create_table(root, "table2", {"var2": tables.FloatCol()},
title="table2")
self.h5file.close()
# ensure that there is no change on the file on disk
self.assertEqual(hexdigest, self._get_digest(self.h5fname))
def test_openFileRW(self):
self._create_file(self.h5fname)
self.assertTrue(os.path.isfile(self.h5fname))
# compute the file hash
hexdigest = self._get_digest(self.h5fname)
# Open an existing HDF5 file in append mode
self.h5file = tables.open_file(self.h5fname, mode="r+",
driver=self.DRIVER,
driver_core_backing_store=False)
# check contents
root = self.h5file.root
self.assertEqual(self.h5file.get_node_attr(root, "testattr"), 41)
self.assertTrue(isinstance(root.array, tables.Array))
self.assertEqual(root.array._v_title, "array")
self.assertTrue(isinstance(root.table, tables.Table))
self.assertEqual(root.table._v_title, "table")
self.assertTrue("var1" in root.table.colnames)
self.assertEqual(root.table.cols.var1.dtype, tables.IntCol().dtype)
# write new data
root = self.h5file.root
self.h5file.set_node_attr(root, "testattr2", 42)
self.h5file.create_array(root, "array2", [1, 2], title="array2")
self.h5file.create_table(root, "table2", {"var2": tables.FloatCol()},
title="table2")
self.h5file.close()
# ensure that there is no change on the file on disk
self.assertEqual(hexdigest, self._get_digest(self.h5fname))
if hdf5_version >= "1.8.9":
def test_get_file_image(self):
self.h5file = tables.open_file(self.h5fname, mode="w",
driver=self.DRIVER,
driver_core_backing_store=False)
root = self.h5file.root
self.h5file.set_node_attr(root, "testattr", 41)
self.h5file.create_array(root, "array", [1, 2], title="array")
self.h5file.create_table(root, "table", {"var1": tables.IntCol()},
title="table")
image = self.h5file.get_file_image()
self.assertTrue(len(image) > 0)
if sys.version_info[0] < 3:
self.assertEqual([ord(i) for i in image[
:4]], [137, 72, 68, 70])
else:
self.assertEqual([i for i in image[:4]], [137, 72, 68, 70])
class SplitDriverTestCase(DefaultDriverTestCase):
DRIVER = "H5FD_SPLIT"
DRIVER_PARAMS = {
"driver_split_meta_ext": "-xm.h5",
"driver_split_raw_ext": "-xr.h5",
}
def setUp(self):
self.h5fname = tempfile.mktemp()
self.h5fnames = [self.h5fname + self.DRIVER_PARAMS[k] for k in
("driver_split_meta_ext", "driver_split_raw_ext")]
self.h5file = tables.open_file(self.h5fname, mode="w",
driver=self.DRIVER,
**self.DRIVER_PARAMS)
root = self.h5file.root
self.h5file.set_node_attr(root, "testattr", 41)
self.h5file.create_array(root, "array", [1, 2], title="array")
self.h5file.create_table(root, "table", {"var1": tables.IntCol()},
title="table")
def tearDown(self):
if self.h5file:
self.h5file.close()
self.h5file = None
for fname in self.h5fnames:
if os.path.isfile(fname):
os.remove(fname)
def assertIsFile(self):
for fname in self.h5fnames:
self.assertTrue(os.path.isfile(fname))
class NotSpportedDriverTestCase(common.PyTablesTestCase):
DRIVER = None
DRIVER_PARAMS = {}
EXCEPTION = ValueError
def setUp(self):
self.h5fname = tempfile.mktemp(suffix=".h5")
def tearDown(self):
open_files = tables.file._open_files
if self.h5fname in open_files:
for h5file in open_files.get_handlers_by_name(self.h5fname):
h5file.close()
if os.path.exists(self.h5fname):
os.remove(self.h5fname)
def test_newFile(self):
self.assertRaises(self.EXCEPTION, tables.open_file, self.h5fname,
mode="w", driver=self.DRIVER, **self.DRIVER_PARAMS)
self.assertFalse(os.path.isfile(self.h5fname))
if "H5FD_LOG" in tables.hdf5extension._supported_drivers:
BaseLogDriverTestCase = DefaultDriverTestCase
else:
BaseLogDriverTestCase = NotSpportedDriverTestCase
class LogDriverTestCase(BaseLogDriverTestCase):
DRIVER = "H5FD_LOG"
def setUp(self):
# local binding
self.DRIVER_PARAMS = {
"driver_log_file": tempfile.mktemp(suffix=".log")
}
super(LogDriverTestCase, self).setUp()
def tearDown(self):
super(LogDriverTestCase, self).tearDown()
if os.path.exists(self.DRIVER_PARAMS["driver_log_file"]):
os.remove(self.DRIVER_PARAMS["driver_log_file"])
if HAVE_DIRECT_DRIVER:
class DirectDriverTestCase(DefaultDriverTestCase):
DRIVER = "H5FD_DIRECT"
else:
class DirectDriverTestCase(NotSpportedDriverTestCase):
DRIVER = "H5FD_DIRECT"
EXCEPTION = RuntimeError
if HAVE_WINDOWS_DRIVER:
class WindowsDriverTestCase(DefaultDriverTestCase):
DRIVER = "H5FD_WINDOWS"
else:
class WindowsDriverTestCase(NotSpportedDriverTestCase):
DRIVER = "H5FD_WINDOWS"
EXCEPTION = RuntimeError
class FamilyDriverTestCase(NotSpportedDriverTestCase):
DRIVER = "H5FD_FAMILY"
class MultiDriverTestCase(NotSpportedDriverTestCase):
DRIVER = "H5FD_MULTI"
class MpioDriverTestCase(NotSpportedDriverTestCase):
DRIVER = "H5FD_MPIO"
class MpiPosixDriverTestCase(NotSpportedDriverTestCase):
DRIVER = "H5FD_MPIPOSIX"
class StreamDriverTestCase(NotSpportedDriverTestCase):
DRIVER = "H5FD_STREAM"
class InMemoryCoreDriverTestCase(common.PyTablesTestCase):
DRIVER = "H5FD_CORE"
def setUp(self):
self.h5fname = tempfile.mktemp(".h5")
self.h5file = None
def tearDown(self):
if self.h5file:
self.h5file.close()
self.h5file = None
if os.path.isfile(self.h5fname):
os.remove(self.h5fname)
def _create_image(self, filename="in-memory", title="Title", mode='w'):
fileh = open_file(filename, mode=mode, title=title,
driver=self.DRIVER, driver_core_backing_store=0)
try:
fileh.create_array(fileh.root, 'array', [1, 2], title="Array")
fileh.create_table(fileh.root, 'table', {
'var1': IntCol()}, "Table")
fileh.root._v_attrs.testattr = 41
image = fileh.get_file_image()
finally:
fileh.close()
return image
def test_newFileW(self):
image = self._create_image(self.h5fname, mode='w')
self.assertTrue(len(image) > 0)
if sys.version_info[0] < 3:
self.assertEqual([ord(i) for i in image[:4]], [137, 72, 68, 70])
else:
self.assertEqual([i for i in image[:4]], [137, 72, 68, 70])
self.assertFalse(os.path.exists(self.h5fname))
def test_newFileA(self):
image = self._create_image(self.h5fname, mode='a')
self.assertTrue(len(image) > 0)
if sys.version_info[0] < 3:
self.assertEqual([ord(i) for i in image[:4]], [137, 72, 68, 70])
else:
self.assertEqual([i for i in image[:4]], [137, 72, 68, 70])
self.assertFalse(os.path.exists(self.h5fname))
def test_openFileR(self):
image = self._create_image(self.h5fname)
self.assertFalse(os.path.exists(self.h5fname))
# Open an existing file
self.h5file = open_file(self.h5fname, mode="r",
driver=self.DRIVER,
driver_core_image=image,
driver_core_backing_store=0)
# Get the CLASS attribute of the arr object
self.assertTrue(hasattr(self.h5file.root._v_attrs, "TITLE"))
self.assertEqual(self.h5file.get_node_attr("/", "TITLE"), "Title")
self.assertTrue(hasattr(self.h5file.root._v_attrs, "testattr"))
self.assertEqual(self.h5file.get_node_attr("/", "testattr"), 41)
self.assertTrue(hasattr(self.h5file.root, "array"))
self.assertEqual(self.h5file.get_node_attr("/array", "TITLE"), "Array")
self.assertTrue(hasattr(self.h5file.root, "table"))
self.assertEqual(self.h5file.get_node_attr("/table", "TITLE"), "Table")
self.assertEqual(self.h5file.root.array.read(), [1, 2])
def test_openFileRW(self):
image = self._create_image(self.h5fname)
self.assertFalse(os.path.exists(self.h5fname))
# Open an existing file
self.h5file = open_file(self.h5fname, mode="r+",
driver=self.DRIVER,
driver_core_image=image,
driver_core_backing_store=0)
# Get the CLASS attribute of the arr object
self.assertTrue(hasattr(self.h5file.root._v_attrs, "TITLE"))
self.assertEqual(self.h5file.get_node_attr("/", "TITLE"), "Title")
self.assertTrue(hasattr(self.h5file.root._v_attrs, "testattr"))
self.assertEqual(self.h5file.get_node_attr("/", "testattr"), 41)
self.assertTrue(hasattr(self.h5file.root, "array"))
self.assertEqual(self.h5file.get_node_attr("/array", "TITLE"), "Array")
self.assertTrue(hasattr(self.h5file.root, "table"))
self.assertEqual(self.h5file.get_node_attr("/table", "TITLE"), "Table")
self.assertEqual(self.h5file.root.array.read(), [1, 2])
self.h5file.create_array(self.h5file.root, 'array2', range(10000),
title="Array2")
self.h5file.root._v_attrs.testattr2 = 42
self.h5file.close()
self.assertFalse(os.path.exists(self.h5fname))
def test_openFileRW_update(self):
filename = tempfile.mktemp(".h5")
image1 = self._create_image(filename)
self.assertFalse(os.path.exists(self.h5fname))
# Open an existing file
self.h5file = open_file(self.h5fname, mode="r+",
driver=self.DRIVER,
driver_core_image=image1,
driver_core_backing_store=0)
# Get the CLASS attribute of the arr object
self.assertTrue(hasattr(self.h5file.root._v_attrs, "TITLE"))
self.assertEqual(self.h5file.get_node_attr("/", "TITLE"), "Title")
self.assertTrue(hasattr(self.h5file.root._v_attrs, "testattr"))
self.assertEqual(self.h5file.get_node_attr("/", "testattr"), 41)
self.assertTrue(hasattr(self.h5file.root, "array"))
self.assertEqual(self.h5file.get_node_attr("/array", "TITLE"), "Array")
self.assertTrue(hasattr(self.h5file.root, "table"))
self.assertEqual(self.h5file.get_node_attr("/table", "TITLE"), "Table")
self.assertEqual(self.h5file.root.array.read(), [1, 2])
data = range(2 * tables.parameters.DRIVER_CORE_INCREMENT)
self.h5file.create_array(self.h5file.root, 'array2', data,
title="Array2")
self.h5file.root._v_attrs.testattr2 = 42
image2 = self.h5file.get_file_image()
self.h5file.close()
self.assertFalse(os.path.exists(self.h5fname))
self.assertNotEqual(len(image1), len(image2))
self.assertNotEqual(image1, image2)
# Open an existing file
self.h5file = open_file(self.h5fname, mode="r",
driver=self.DRIVER,
driver_core_image=image2,
driver_core_backing_store=0)
# Get the CLASS attribute of the arr object
self.assertTrue(hasattr(self.h5file.root._v_attrs, "TITLE"))
self.assertEqual(self.h5file.get_node_attr("/", "TITLE"), "Title")
self.assertTrue(hasattr(self.h5file.root._v_attrs, "testattr"))
self.assertEqual(self.h5file.get_node_attr("/", "testattr"), 41)
self.assertTrue(hasattr(self.h5file.root, "array"))
self.assertEqual(self.h5file.get_node_attr("/array", "TITLE"), "Array")
self.assertTrue(hasattr(self.h5file.root, "table"))
self.assertEqual(self.h5file.get_node_attr("/table", "TITLE"), "Table")
self.assertEqual(self.h5file.root.array.read(), [1, 2])
self.assertTrue(hasattr(self.h5file.root._v_attrs, "testattr2"))
self.assertEqual(self.h5file.get_node_attr("/", "testattr2"), 42)
self.assertTrue(hasattr(self.h5file.root, "array2"))
self.assertEqual(self.h5file.get_node_attr(
"/array2", "TITLE"), "Array2")
self.assertEqual(self.h5file.root.array2.read(), data)
self.h5file.close()
self.assertFalse(os.path.exists(self.h5fname))
def test_openFileA(self):
image = self._create_image(self.h5fname)
self.assertFalse(os.path.exists(self.h5fname))
# Open an existing file
self.h5file = open_file(self.h5fname, mode="a",
driver=self.DRIVER,
driver_core_image=image,
driver_core_backing_store=0)
# Get the CLASS attribute of the arr object
self.assertTrue(hasattr(self.h5file.root._v_attrs, "TITLE"))
self.assertEqual(self.h5file.get_node_attr("/", "TITLE"), "Title")
self.assertTrue(hasattr(self.h5file.root._v_attrs, "testattr"))
self.assertEqual(self.h5file.get_node_attr("/", "testattr"), 41)
self.assertTrue(hasattr(self.h5file.root, "array"))
self.assertEqual(self.h5file.get_node_attr("/array", "TITLE"), "Array")
self.assertTrue(hasattr(self.h5file.root, "table"))
self.assertEqual(self.h5file.get_node_attr("/table", "TITLE"), "Table")
self.assertEqual(self.h5file.root.array.read(), [1, 2])
self.h5file.close()
self.assertFalse(os.path.exists(self.h5fname))
def test_openFileA_update(self):
filename = tempfile.mktemp(".h5")
image1 = self._create_image(filename)
self.assertFalse(os.path.exists(self.h5fname))
# Open an existing file
self.h5file = open_file(self.h5fname, mode="a",
driver=self.DRIVER,
driver_core_image=image1,
driver_core_backing_store=0)
# Get the CLASS attribute of the arr object
self.assertTrue(hasattr(self.h5file.root._v_attrs, "TITLE"))
self.assertEqual(self.h5file.get_node_attr("/", "TITLE"), "Title")
self.assertTrue(hasattr(self.h5file.root._v_attrs, "testattr"))
self.assertEqual(self.h5file.get_node_attr("/", "testattr"), 41)
self.assertTrue(hasattr(self.h5file.root, "array"))
self.assertEqual(self.h5file.get_node_attr("/array", "TITLE"), "Array")
self.assertTrue(hasattr(self.h5file.root, "table"))
self.assertEqual(self.h5file.get_node_attr("/table", "TITLE"), "Table")
self.assertEqual(self.h5file.root.array.read(), [1, 2])
data = range(2 * tables.parameters.DRIVER_CORE_INCREMENT)
self.h5file.create_array(self.h5file.root, 'array2', data,
title="Array2")
self.h5file.root._v_attrs.testattr2 = 42
image2 = self.h5file.get_file_image()
self.h5file.close()
self.assertFalse(os.path.exists(self.h5fname))
self.assertNotEqual(len(image1), len(image2))
self.assertNotEqual(image1, image2)
# Open an existing file
self.h5file = open_file(self.h5fname, mode="r",
driver=self.DRIVER,
driver_core_image=image2,
driver_core_backing_store=0)
# Get the CLASS attribute of the arr object
self.assertTrue(hasattr(self.h5file.root._v_attrs, "TITLE"))
self.assertEqual(self.h5file.get_node_attr("/", "TITLE"), "Title")
self.assertTrue(hasattr(self.h5file.root._v_attrs, "testattr"))
self.assertEqual(self.h5file.get_node_attr("/", "testattr"), 41)
self.assertTrue(hasattr(self.h5file.root, "array"))
self.assertEqual(self.h5file.get_node_attr("/array", "TITLE"), "Array")
self.assertTrue(hasattr(self.h5file.root, "table"))
self.assertEqual(self.h5file.get_node_attr("/table", "TITLE"), "Table")
self.assertEqual(self.h5file.root.array.read(), [1, 2])
self.assertTrue(hasattr(self.h5file.root._v_attrs, "testattr2"))
self.assertEqual(self.h5file.get_node_attr("/", "testattr2"), 42)
self.assertTrue(hasattr(self.h5file.root, "array2"))
self.assertEqual(self.h5file.get_node_attr(
"/array2", "TITLE"), "Array2")
self.assertEqual(self.h5file.root.array2.read(), data)
self.h5file.close()
self.assertFalse(os.path.exists(self.h5fname))
def test_str(self):
self.h5file = open_file(self.h5fname, mode="w", title="Title",
driver=self.DRIVER,
driver_core_backing_store=0)
self.h5file.create_array(self.h5file.root, 'array', [1, 2],
title="Array")
self.h5file.create_table(self.h5file.root, 'table', {'var1': IntCol()},
"Table")
self.h5file.root._v_attrs.testattr = 41
# ensure that the __str__ method works even if there is no phisical
# file on disk (in which case the os.stat operation for date retrieval
# fails)
self.assertTrue(str(self.h5file) is not None)
self.h5file.close()
self.assertFalse(os.path.exists(self.h5fname))
class QuantizeTestCase(unittest.TestCase):
mode = "w"
title = "This is the table title"
expectedrows = 10
appendrows = 5
def setUp(self):
self.data = numpy.linspace(-5., 5., 41)
self.randomdata = numpy.random.random_sample(1000000)
self.randomints = numpy.random.random_integers(
-1000000, 1000000, 1000000).astype('int64')
# Create a temporary file
self.file = tempfile.mktemp(".h5")
# Create an instance of HDF5 Table
self.h5file = open_file(self.file, self.mode, self.title)
self.populateFile()
self.h5file.close()
self.quantizeddata_0 = numpy.asarray(
[-5.] * 2 + [-4.] * 5 + [-3.] * 3 + [-2.] * 5 + [-1.] * 3 +
[0.] * 5 + [1.] * 3 + [2.] * 5 + [3.] * 3 + [4.] * 5 + [5.] * 2)
self.quantizeddata_m1 = numpy.asarray(
[-8.] * 4 + [0.] * 33 + [8.] * 4)
def populateFile(self):
root = self.h5file.root
filters = Filters(complevel=1, complib="blosc",
least_significant_digit=1)
ints = self.h5file.create_carray(root, "integers", Int64Atom(),
(1000000,), filters=filters)
ints[:] = self.randomints
floats = self.h5file.create_carray(root, "floats", Float32Atom(),
(1000000,), filters=filters)
floats[:] = self.randomdata
data1 = self.h5file.create_carray(root, "data1", Float64Atom(),
(41,), filters=filters)
data1[:] = self.data
filters = Filters(complevel=1, complib="blosc",
least_significant_digit=0)
data0 = self.h5file.create_carray(root, "data0", Float64Atom(),
(41,), filters=filters)
data0[:] = self.data
filters = Filters(complevel=1, complib="blosc",
least_significant_digit=2)
data2 = self.h5file.create_carray(root, "data2", Float64Atom(),
(41,), filters=filters)
data2[:] = self.data
filters = Filters(complevel=1, complib="blosc",
least_significant_digit=-1)
datam1 = self.h5file.create_carray(root, "datam1", Float64Atom(),
(41,), filters=filters)
datam1[:] = self.data
def tearDown(self):
# Close the file
if self.h5file.isopen:
self.h5file.close()
os.remove(self.file)
common.cleanup(self)
#----------------------------------------
def test00_quantizeData(self):
"""Checking the quantize() function."""
quantized_0 = quantize(self.data, 0)
quantized_1 = quantize(self.data, 1)
quantized_2 = quantize(self.data, 2)
quantized_m1 = quantize(self.data, -1)
numpy.testing.assert_array_equal(quantized_0, self.quantizeddata_0)
numpy.testing.assert_array_equal(quantized_1, self.data)
numpy.testing.assert_array_equal(quantized_2, self.data)
numpy.testing.assert_array_equal(quantized_m1, self.quantizeddata_m1)
def test01_quantizeDataMaxError(self):
"""Checking the maximum error introduced by the quantize() function."""
quantized_0 = quantize(self.randomdata, 0)
quantized_1 = quantize(self.randomdata, 1)
quantized_2 = quantize(self.randomdata, 2)
quantized_m1 = quantize(self.randomdata, -1)
# assertLess is new in Python 2.7
#self.assertLess(numpy.abs(quantized_0 - self.randomdata).max(), 0.5)
#self.assertLess(numpy.abs(quantized_1 - self.randomdata).max(), 0.05)
#self.assertLess(numpy.abs(quantized_2 - self.randomdata).max(), 0.005)
#self.assertLess(numpy.abs(quantized_m1 - self.randomdata).max(), 1.)
self.assertTrue(numpy.abs(quantized_0 - self.randomdata).max() < 0.5)
self.assertTrue(numpy.abs(quantized_1 - self.randomdata).max() < 0.05)
self.assertTrue(numpy.abs(quantized_2 - self.randomdata).max() < 0.005)
self.assertTrue(numpy.abs(quantized_m1 - self.randomdata).max() < 1.)
def test02_array(self):
"""Checking quantized data as written to disk."""
self.h5file = open_file(self.file, "r")
numpy.testing.assert_array_equal(self.h5file.root.data1[:], self.data)
numpy.testing.assert_array_equal(self.h5file.root.data2[:], self.data)
numpy.testing.assert_array_equal(self.h5file.root.data0[:],
self.quantizeddata_0)
numpy.testing.assert_array_equal(self.h5file.root.datam1[:],
self.quantizeddata_m1)
numpy.testing.assert_array_equal(self.h5file.root.integers[:],
self.randomints)
self.assertEqual(self.h5file.root.integers[:].dtype,
self.randomints.dtype)
# assertLess is new in Python 2.7
#self.assertLess(
# numpy.abs(self.h5file.root.floats[:] - self.randomdata).max(),
# 0.05
#)
self.assertTrue(
numpy.abs(self.h5file.root.floats[:] - self.randomdata).max() <
0.05
)
#----------------------------------------------------------------------
def suite():
import doctest
theSuite = unittest.TestSuite()
niter = 1
# common.heavy = 1 # Uncomment this only for testing purposes!
for i in range(niter):
theSuite.addTest(unittest.makeSuite(FiltersCase1))
theSuite.addTest(unittest.makeSuite(FiltersCase2))
theSuite.addTest(unittest.makeSuite(FiltersCase10))
theSuite.addTest(unittest.makeSuite(FiltersCaseBloscBloscLZ))
if 'lz4' in tables.blosc_compressor_list():
theSuite.addTest(unittest.makeSuite(FiltersCaseBloscLZ4))
theSuite.addTest(unittest.makeSuite(FiltersCaseBloscLZ4HC))
if 'snappy' in tables.blosc_compressor_list():
theSuite.addTest(unittest.makeSuite(FiltersCaseBloscSnappy))
if 'zlib' in tables.blosc_compressor_list():
theSuite.addTest(unittest.makeSuite(FiltersCaseBloscZlib))
theSuite.addTest(unittest.makeSuite(CopyGroupCase1))
theSuite.addTest(unittest.makeSuite(CopyGroupCase2))
theSuite.addTest(unittest.makeSuite(CopyFileCase1))
theSuite.addTest(unittest.makeSuite(CopyFileCase2))
theSuite.addTest(unittest.makeSuite(GroupFiltersTestCase))
theSuite.addTest(unittest.makeSuite(SetBloscMaxThreadsTestCase))
theSuite.addTest(unittest.makeSuite(FilterTestCase))
theSuite.addTest(doctest.DocTestSuite(tables.filters))
theSuite.addTest(unittest.makeSuite(DefaultDriverTestCase))
theSuite.addTest(unittest.makeSuite(Sec2DriverTestCase))
theSuite.addTest(unittest.makeSuite(StdioDriverTestCase))
theSuite.addTest(unittest.makeSuite(CoreDriverTestCase))
theSuite.addTest(unittest.makeSuite(CoreDriverNoBackingStoreTestCase))
theSuite.addTest(unittest.makeSuite(SplitDriverTestCase))
theSuite.addTest(unittest.makeSuite(LogDriverTestCase))
theSuite.addTest(unittest.makeSuite(DirectDriverTestCase))
theSuite.addTest(unittest.makeSuite(WindowsDriverTestCase))
theSuite.addTest(unittest.makeSuite(FamilyDriverTestCase))
theSuite.addTest(unittest.makeSuite(MultiDriverTestCase))
theSuite.addTest(unittest.makeSuite(MpioDriverTestCase))
theSuite.addTest(unittest.makeSuite(MpiPosixDriverTestCase))
theSuite.addTest(unittest.makeSuite(StreamDriverTestCase))
if hdf5_version >= "1.8.9":
theSuite.addTest(unittest.makeSuite(InMemoryCoreDriverTestCase))
theSuite.addTest(unittest.makeSuite(QuantizeTestCase))
if common.heavy:
theSuite.addTest(unittest.makeSuite(createTestCase))
theSuite.addTest(unittest.makeSuite(FiltersCase3))
theSuite.addTest(unittest.makeSuite(FiltersCase4))
theSuite.addTest(unittest.makeSuite(FiltersCase5))
theSuite.addTest(unittest.makeSuite(FiltersCase6))
theSuite.addTest(unittest.makeSuite(FiltersCase7))
theSuite.addTest(unittest.makeSuite(FiltersCase8))
theSuite.addTest(unittest.makeSuite(FiltersCase9))
theSuite.addTest(unittest.makeSuite(CopyFileCase3))
theSuite.addTest(unittest.makeSuite(CopyFileCase4))
theSuite.addTest(unittest.makeSuite(CopyFileCase5))
theSuite.addTest(unittest.makeSuite(CopyFileCase6))
theSuite.addTest(unittest.makeSuite(CopyFileCase7))
theSuite.addTest(unittest.makeSuite(CopyFileCase8))
theSuite.addTest(unittest.makeSuite(CopyFileCase10))
theSuite.addTest(unittest.makeSuite(CopyGroupCase3))
theSuite.addTest(unittest.makeSuite(CopyGroupCase4))
theSuite.addTest(unittest.makeSuite(CopyGroupCase5))
theSuite.addTest(unittest.makeSuite(CopyGroupCase6))
theSuite.addTest(unittest.makeSuite(CopyGroupCase7))
theSuite.addTest(unittest.makeSuite(CopyGroupCase8))
return theSuite
if __name__ == '__main__':
unittest.main(defaultTest='suite')
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