class TestSuite(unittest.TestCase):
# @see
# http://www.saltycrane.com/blog/2012/07/how-prevent-nose-unittest-using-docstring-when-verbosity-2/
def setUp(self):
self.cs = CheckSuite()
self.cs.load_all_available_checkers()
def shortDescription(self):
return None
# override __str__ and __repr__ behavior to show a copy-pastable nosetest name for ion tests
# ion.module:TestClassName.test_function_name
def __repr__(self):
name = self.id()
name = name.split('.')
if name[0] not in ["ion", "pyon"]:
return "%s (%s)" % (name[-1], '.'.join(name[:-1]))
else:
return "%s ( %s )" % (name[-1], '.'.join(name[:-2]) + ":" +
'.'.join(name[-2:]))
__str__ = __repr__
def test_suite(self):
# BWA: what's the purpose of this test? Just to see if the suite
# runs without errors?
ds = self.cs.load_dataset(static_files['2dim'])
self.cs.run(ds, 'acdd')
def test_unicode_formatting(self):
ds = self.cs.load_dataset(static_files['bad_region'])
score_groups = self.cs.run(ds, 'cf')
limit = 2
for checker, rpair in score_groups.items():
groups, errors = rpair
score_list, points, out_of = self.cs.standard_output(ds.filepath(),
limit, checker,
groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, points, out_of, checker)
def test_skip_checks(self):
"""Tests that checks are properly skipped when specified"""
ds = self.cs.load_dataset(static_files['2dim'])
# exclude title from the check attributes
score_groups = self.cs.run(ds, ['check_high'], 'acdd')
assert all(sg.name not in {'Conventions', 'title', 'keywords',
'summary'} for sg in score_groups['acdd'][0])
def test_group_func(self):
# This is checking for issue #183, where group_func results in
# IndexError: list index out of range
ds = self.cs.load_dataset(static_files['bad_data_type'])
score_groups = self.cs.run(ds, 'cf')
limit = 2
for checker, rpair in score_groups.items():
groups, errors = rpair
score_list, points, out_of = self.cs.standard_output(ds.filepath(),
limit, checker,
groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, points, out_of, checker)
def test_score_grouping(self):
# Testing the grouping of results for output, which can fail
# if some assumptions are not met, e.g. if a Result object has
# a value attribute of unexpected type
res = [
Result(BaseCheck.MEDIUM, True, 'one'),
Result(BaseCheck.MEDIUM, (1, 3), 'one'),
Result(BaseCheck.MEDIUM, None, 'one'),
Result(BaseCheck.MEDIUM, True, 'two'),
Result(BaseCheck.MEDIUM, np.isnan(1), 'two') # value is type numpy.bool_
]
score = self.cs.scores(res)
self.assertEqual(score[0].name, 'one')
self.assertEqual(score[0].value, (2, 4))
self.assertEqual(score[1].name, 'two')
self.assertEqual(score[1].value, (1, 2))
def test_cdl_file(self):
# Testing whether you can run compliance checker on a .cdl file
# Load the cdl file
ds = self.cs.load_dataset(static_files['test_cdl'])
vals = self.cs.run(ds, 'cf')
limit = 2
for checker, rpair in vals.items():
groups, errors = rpair
score_list, cdl_points, cdl_out_of = self.cs.standard_output(ds.filepath(),
limit,
checker,
groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, cdl_points, cdl_out_of, checker)
ds.close()
# Ok now load the nc file that it came from
ds = self.cs.load_dataset(static_files['test_cdl_nc'])
vals = self.cs.run(ds, 'cf')
limit = 2
for checker, rpair in vals.items():
groups, errors = rpair
score_list, nc_points, nc_out_of = self.cs.standard_output(ds.filepath(),
limit,
checker,
groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, nc_points, nc_out_of, checker)
ds.close()
nc_file_path = static_files['test_cdl'].replace('.cdl', '.nc')
self.addCleanup(os.remove, nc_file_path)
# Ok the scores should be equal!
self.assertEqual(nc_points, cdl_points)
self.assertEqual(nc_out_of, cdl_out_of)
def test_load_local_dataset_GenericFile(self):
resp = self.cs.load_local_dataset(static_files['empty'])
assert isinstance(resp, GenericFile) == True
def test_standard_output_score_header(self):
"""
Check that the output score header only checks the number of
of potential issues, rather than the weighted score
"""
ds = self.cs.load_dataset(static_files['bad_region'])
score_groups = self.cs.run(ds, [], 'cf')
limit = 2
groups, errors = score_groups['cf']
score_list, all_passed, out_of = self.cs.standard_output(
ds.filepath(),
limit, 'cf',
groups)
self.assertEqual((all_passed, out_of), (30, 47))
class TestSuite(unittest.TestCase):
# @see
# http://www.saltycrane.com/blog/2012/07/how-prevent-nose-unittest-using-docstring-when-verbosity-2/
def setUp(self):
self.cs = CheckSuite()
self.cs.load_all_available_checkers()
def shortDescription(self):
return None
# override __str__ and __repr__ behavior to show a copy-pastable nosetest name for ion tests
# ion.module:TestClassName.test_function_name
def __repr__(self):
name = self.id()
name = name.split(".")
if name[0] not in ["ion", "pyon"]:
return "%s (%s)" % (name[-1], ".".join(name[:-1]))
else:
return "%s ( %s )" % (
name[-1],
".".join(name[:-2]) + ":" + ".".join(name[-2:]),
)
__str__ = __repr__
def test_suite(self):
# BWA: what's the purpose of this test? Just to see if the suite
# runs without errors?
ds = self.cs.load_dataset(static_files["2dim"])
self.cs.run(ds, "acdd")
def test_unicode_formatting(self):
ds = self.cs.load_dataset(static_files["bad_region"])
score_groups = self.cs.run(ds, "cf")
limit = 2
for checker, rpair in score_groups.items():
groups, errors = rpair
score_list, points, out_of = self.cs.standard_output(
ds.filepath(), limit, checker, groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, points, out_of,
checker)
def test_generate_dataset_netCDF4(self):
"""
Tests that suite.generate_dataset works with cdl file with netCDF4
features.
"""
# create netCDF4 file
ds_name = self.cs.generate_dataset(static_files["netCDF4"])
# check if correct name is return
assert ds_name == static_files["netCDF4"].replace(".cdl", ".nc")
# check if netCDF4 file was created
assert os.path.isfile(static_files["netCDF4"].replace(".cdl", ".nc"))
def test_skip_checks(self):
"""Tests that checks are properly skipped when specified"""
ds = self.cs.load_dataset(static_files["2dim"])
# exclude title from the check attributes
score_groups = self.cs.run(ds, ["check_high"], "acdd")
assert all(
sg.name not in {"Conventions", "title", "keywords", "summary"}
for sg in score_groups["acdd"][0])
def test_skip_check_level(self):
"""Checks level limited skip checks"""
ds = self.cs.load_dataset(static_files["ru07"])
score_groups = self.cs.run(
ds,
[
"check_flags:A",
"check_convention_possibly_var_attrs:M",
"check_standard_name:L",
],
"cf",
)
name_set = {sg.name for sg in score_groups["cf"][0]}
# flattened set of messages
msg_set = {msg for sg in score_groups["cf"][0] for msg in sg.msgs}
expected_excluded_names = {
u"§3.5 flag_meanings for lat",
u"§3.5 flag_meanings for lon",
u"§3.5 lat is a valid flags variable",
u"§3.5 lat is a valid flags variable",
u"§3.5 lon is a valid flags variable",
}
self.assertTrue(len(expected_excluded_names & name_set) == 0)
# should skip references
ref_msg = u"references global attribute should be a non-empty string"
self.assertTrue(ref_msg not in msg_set)
# check_standard_name is high priority, but we requested only low,
# so the standard_name check should still exist
standard_name_hdr = u"§3.3 Standard Name"
self.assertTrue(standard_name_hdr in name_set)
def test_group_func(self):
# This is checking for issue #183, where group_func results in
# IndexError: list index out of range
ds = self.cs.load_dataset(static_files["bad_data_type"])
score_groups = self.cs.run(ds, "cf")
limit = 2
for checker, rpair in score_groups.items():
groups, errors = rpair
score_list, points, out_of = self.cs.standard_output(
ds.filepath(), limit, checker, groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, points, out_of,
checker)
def test_score_grouping(self):
# Testing the grouping of results for output, which can fail
# if some assumptions are not met, e.g. if a Result object has
# a value attribute of unexpected type
res = [
Result(BaseCheck.MEDIUM, True, "one"),
Result(BaseCheck.MEDIUM, (1, 3), "one"),
Result(BaseCheck.MEDIUM, None, "one"),
Result(BaseCheck.MEDIUM, True, "two"),
Result(BaseCheck.MEDIUM, np.isnan(1),
"two"), # value is type numpy.bool_
]
score = self.cs.scores(res)
self.assertEqual(score[0].name, "one")
self.assertEqual(score[0].value, (2, 4))
self.assertEqual(score[1].name, "two")
self.assertEqual(score[1].value, (1, 2))
def test_cdl_file(self):
# Testing whether you can run compliance checker on a .cdl file
# Load the cdl file
ds = self.cs.load_dataset(static_files["test_cdl"])
vals = self.cs.run(ds, "cf")
limit = 2
for checker, rpair in vals.items():
groups, errors = rpair
score_list, cdl_points, cdl_out_of = self.cs.standard_output(
ds.filepath(), limit, checker, groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, cdl_points,
cdl_out_of, checker)
ds.close()
# Ok now load the nc file that it came from
ds = self.cs.load_dataset(static_files["test_cdl_nc"])
vals = self.cs.run(ds, "cf")
limit = 2
for checker, rpair in vals.items():
groups, errors = rpair
score_list, nc_points, nc_out_of = self.cs.standard_output(
ds.filepath(), limit, checker, groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, nc_points,
nc_out_of, checker)
ds.close()
nc_file_path = static_files["test_cdl"].replace(".cdl", ".nc")
self.addCleanup(os.remove, nc_file_path)
# Ok the scores should be equal!
self.assertEqual(nc_points, cdl_points)
self.assertEqual(nc_out_of, cdl_out_of)
def test_load_local_dataset_GenericFile(self):
resp = self.cs.load_local_dataset(static_files["empty"])
assert isinstance(resp, GenericFile) == True
def test_standard_output_score_header(self):
"""
Check that the output score header only checks the number of
of potential issues, rather than the weighted score
"""
ds = self.cs.load_dataset(static_files["bad_region"])
score_groups = self.cs.run(ds, [], "cf")
limit = 2
groups, errors = score_groups["cf"]
score_list, all_passed, out_of = self.cs.standard_output(
ds.filepath(), limit, "cf", groups)
assert all_passed < out_of
def test_netCDF4_features(self):
"""
Check if a proper netCDF4 file with netCDF4-datatypes is created.
"""
# create and open dataset
ds = self.cs.load_dataset(static_files["netCDF4"])
# check if netCDF type of global attributes is correct
assert isinstance(ds.global_att_of_type_int, np.int32)
# check if netCDF4 type of global attributes is correct
assert isinstance(ds.global_att_of_type_int64, np.int64)
# check if netCDF type of variable is correct
assert ds["tas"].dtype is np.dtype("float32")
# check if netCDF4 type of variable is correct
assert ds["mask"].dtype is np.dtype("int64")
def test_load_local_dataset_GenericFile(self):
cs = CheckSuite()
resp = cs.load_local_dataset(static_files['empty'])
assert isinstance(resp, GenericFile) == True
class TestSuite(unittest.TestCase):
# @see
# http://www.saltycrane.com/blog/2012/07/how-prevent-nose-unittest-using-docstring-when-verbosity-2/
def setUp(self):
self.cs = CheckSuite()
self.cs.load_all_available_checkers()
def shortDescription(self):
return None
# override __str__ and __repr__ behavior to show a copy-pastable nosetest name for ion tests
# ion.module:TestClassName.test_function_name
def __repr__(self):
name = self.id()
name = name.split('.')
if name[0] not in ["ion", "pyon"]:
return "%s (%s)" % (name[-1], '.'.join(name[:-1]))
else:
return "%s ( %s )" % (name[-1], '.'.join(name[:-2]) + ":" +
'.'.join(name[-2:]))
__str__ = __repr__
def test_suite(self):
# BWA: what's the purpose of this test? Just to see if the suite
# runs without errors?
ds = self.cs.load_dataset(static_files['2dim'])
self.cs.run(ds, 'acdd')
def test_unicode_formatting(self):
ds = self.cs.load_dataset(static_files['bad_region'])
score_groups = self.cs.run(ds, 'cf')
limit = 2
for checker, rpair in score_groups.items():
groups, errors = rpair
score_list, points, out_of = self.cs.standard_output(ds.filepath(),
limit, checker,
groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, points, out_of, checker)
def test_skip_checks(self):
"""Tests that checks are properly skipped when specified"""
ds = self.cs.load_dataset(static_files['2dim'])
# exclude title from the check attributes
score_groups = self.cs.run(ds, ['check_high'], 'acdd')
assert all(sg.name not in {'Conventions', 'title', 'keywords',
'summary'} for sg in score_groups['acdd'][0])
def test_skip_check_level(self):
"""Checks level limited skip checks"""
ds = self.cs.load_dataset(static_files['ru07'])
score_groups = self.cs.run(ds, ['check_flags:A',
'check_convention_possibly_var_attrs:M',
'check_standard_name:L'], 'cf')
name_set = {sg.name for sg in score_groups['cf'][0]}
# flattened set of messages
msg_set = {msg for sg in score_groups['cf'][0] for msg in sg.msgs}
expected_excluded_names = {u'§3.5 flag_meanings for lat',
u'§3.5 flag_meanings for lon',
u'§3.5 lat is a valid flags variable',
u'§3.5 lat is a valid flags variable',
u'§3.5 lon is a valid flags variable'}
self.assertTrue(len(expected_excluded_names & name_set) == 0)
# should skip references
ref_msg = u'references global attribute should be a non-empty string'
self.assertTrue(ref_msg not in msg_set)
# check_standard_name is high priority, but we requested only low,
# so the standard_name check should still exist
standard_name_hdr = u'§3.3 Standard Name'
self.assertTrue(standard_name_hdr in name_set)
def test_group_func(self):
# This is checking for issue #183, where group_func results in
# IndexError: list index out of range
ds = self.cs.load_dataset(static_files['bad_data_type'])
score_groups = self.cs.run(ds, 'cf')
limit = 2
for checker, rpair in score_groups.items():
groups, errors = rpair
score_list, points, out_of = self.cs.standard_output(ds.filepath(),
limit, checker,
groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, points, out_of, checker)
def test_score_grouping(self):
# Testing the grouping of results for output, which can fail
# if some assumptions are not met, e.g. if a Result object has
# a value attribute of unexpected type
res = [
Result(BaseCheck.MEDIUM, True, 'one'),
Result(BaseCheck.MEDIUM, (1, 3), 'one'),
Result(BaseCheck.MEDIUM, None, 'one'),
Result(BaseCheck.MEDIUM, True, 'two'),
Result(BaseCheck.MEDIUM, np.isnan(1), 'two') # value is type numpy.bool_
]
score = self.cs.scores(res)
self.assertEqual(score[0].name, 'one')
self.assertEqual(score[0].value, (2, 4))
self.assertEqual(score[1].name, 'two')
self.assertEqual(score[1].value, (1, 2))
def test_cdl_file(self):
# Testing whether you can run compliance checker on a .cdl file
# Load the cdl file
ds = self.cs.load_dataset(static_files['test_cdl'])
vals = self.cs.run(ds, 'cf')
limit = 2
for checker, rpair in vals.items():
groups, errors = rpair
score_list, cdl_points, cdl_out_of = self.cs.standard_output(ds.filepath(),
limit,
checker,
groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, cdl_points, cdl_out_of, checker)
ds.close()
# Ok now load the nc file that it came from
ds = self.cs.load_dataset(static_files['test_cdl_nc'])
vals = self.cs.run(ds, 'cf')
limit = 2
for checker, rpair in vals.items():
groups, errors = rpair
score_list, nc_points, nc_out_of = self.cs.standard_output(ds.filepath(),
limit,
checker,
groups)
# This asserts that print is able to generate all of the unicode output
self.cs.standard_output_generation(groups, limit, nc_points, nc_out_of, checker)
ds.close()
nc_file_path = static_files['test_cdl'].replace('.cdl', '.nc')
self.addCleanup(os.remove, nc_file_path)
# Ok the scores should be equal!
self.assertEqual(nc_points, cdl_points)
self.assertEqual(nc_out_of, cdl_out_of)
def test_load_local_dataset_GenericFile(self):
resp = self.cs.load_local_dataset(static_files['empty'])
assert isinstance(resp, GenericFile) == True
def test_standard_output_score_header(self):
"""
Check that the output score header only checks the number of
of potential issues, rather than the weighted score
"""
ds = self.cs.load_dataset(static_files['bad_region'])
score_groups = self.cs.run(ds, [], 'cf')
limit = 2
groups, errors = score_groups['cf']
score_list, all_passed, out_of = self.cs.standard_output(
ds.filepath(),
limit, 'cf',
groups)
assert all_passed < out_of
