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#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2011-2017, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# -----------------------------------------------------------------------------
from unittest import TestCase, main
from copy import deepcopy
from biom import example_table, Table
from biom.exception import TableException
from biom.err import (_test_empty, _test_obssize, _test_sampsize, _test_obsdup,
_test_sampdup, _test_obsmdsize, _test_sampmdsize,
errstate, geterr, seterr, geterrcall, seterrcall,
errcheck, __errprof)
runtime_ep = __errprof
runtime_ep_profile = deepcopy(runtime_ep._profile)
runtime_ep_state = runtime_ep._state.copy()
runtime_ep_test = runtime_ep._test.copy()
class ErrModeTests(TestCase):
def setUp(self):
self.ex_table = example_table.copy()
def test_test_empty(self):
self.assertTrue(_test_empty(Table([], [], [])))
self.assertFalse(_test_empty(self.ex_table))
def test_test_obssize(self):
self.assertFalse(_test_obssize(self.ex_table))
self.ex_table._observation_ids = self.ex_table._observation_ids[:-1]
self.assertTrue(_test_obssize(self.ex_table))
def test_test_sampsize(self):
self.assertFalse(_test_sampsize(self.ex_table))
self.ex_table._sample_ids = self.ex_table._sample_ids[:-1]
self.assertTrue(_test_sampsize(self.ex_table))
def test_test_obsdup(self):
self.assertFalse(_test_obsdup(self.ex_table))
self.ex_table._observation_ids[0] = self.ex_table._observation_ids[1]
self.assertTrue(_test_obsdup(self.ex_table))
def test_test_sampdup(self):
self.assertFalse(_test_sampdup(self.ex_table))
self.ex_table._sample_ids[0] = self.ex_table._sample_ids[1]
self.assertTrue(_test_sampdup(self.ex_table))
def test_test_obsmdsize(self):
self.assertFalse(_test_obsdup(self.ex_table))
self.ex_table._observation_metadata = \
self.ex_table._observation_metadata[:-1]
self.assertTrue(_test_obsmdsize(self.ex_table))
def test_test_sampmdsize(self):
self.assertFalse(_test_sampdup(self.ex_table))
self.ex_table._sample_metadata = \
self.ex_table._sample_metadata[:-1]
self.assertTrue(_test_sampmdsize(self.ex_table))
class ErrorProfileTests(TestCase):
def setUp(self):
self.ex_table = example_table.copy()
self.ep = runtime_ep
self.ep.state = {'all': 'raise'}
def tearDown(self):
self.ep._profile = deepcopy(runtime_ep_profile.copy())
self.ep._state = runtime_ep_state.copy()
self.ep._test = runtime_ep_test.copy()
def test_test(self):
self.ep.test(self.ex_table)
self.ep.test(self.ex_table, 'empty')
self.ep.test(self.ex_table, 'empty', 'obssize')
self.ex_table._observation_ids = self.ex_table._observation_ids[:-1]
self.ep.test(self.ex_table, 'empty')
self.assertTrue(isinstance(self.ep.test(self.ex_table, 'obssize'),
TableException))
def test_state(self):
self.ep.state = {'all': 'ignore'}
self.assertEqual(set(self.ep._state.values()), set(['ignore']))
self.ep.state = {'empty': 'call'}
self.assertEqual(set(self.ep._state.values()), set(['ignore', 'call']))
self.assertEqual(self.ep.state['empty'], 'call')
with self.assertRaises(KeyError):
self.ep.state = {'empty': 'missing'}
with self.assertRaises(KeyError):
self.ep.state = {'emptyasdasd': 'ignore'}
def test_contains(self):
self.assertTrue('empty' in self.ep)
self.assertFalse('emptyfoo' in self.ep)
def test_handle_error(self):
def callback(foo):
return 10
self.ep.setcall('empty', callback)
self.assertTrue(isinstance(self.ep._handle_error('empty', None),
TableException))
self.ep.state = {'empty': 'call'}
self.assertEqual(self.ep._handle_error('empty', None), 10)
def test_setcall(self):
def callback(foo):
return 10
self.assertEqual(self.ep._profile['empty']['call'](None), None)
self.ep.setcall('empty', callback)
self.assertEqual(self.ep._profile['empty']['call'](None), 10)
with self.assertRaises(KeyError):
self.ep.setcall('emptyfoo', callback)
def test_getcall(self):
def callback(foo):
return 10
self.ep.setcall('empty', callback)
self.assertEqual(self.ep.getcall('empty'), callback)
with self.assertRaises(KeyError):
self.ep.getcall('emptyfoo')
def test_register_unregister(self):
def cb(x):
return 123
def test(x):
return x == 5
self.ep.register('foo', 'bar', 'ignore', test, callback=cb)
self.assertTrue('foo' in self.ep)
self.ep.state = {'foo': 'call'}
self.assertEqual(self.ep._handle_error('foo', None), 123)
foo_prof = self.ep._profile['foo'].copy()
prof, func, state = self.ep.unregister('foo')
self.assertEqual(func, test)
self.assertEqual(state, 'call')
self.assertEqual(prof, foo_prof)
with self.assertRaises(KeyError):
self.ep.register('empty', 1, 2, lambda: None)
with self.assertRaises(KeyError):
self.ep.register('foo', 'missing', 2, lambda: None)
with self.assertRaises(KeyError):
self.ep.unregister('non_existant')
class SupportTests(TestCase):
def setUp(self):
self.ex_table = example_table.copy()
def test_geterr(self):
state = geterr()
self.assertEqual(state, runtime_ep._state)
old = seterr(all='call')
self.assertNotEqual(geterr(), state)
seterr(**old)
def test_seterr(self):
existing = seterr(empty='warn')
self.assertEqual(runtime_ep._state['empty'], 'warn')
self.assertNotEqual(runtime_ep._state['empty'], existing)
seterr(empty=existing['empty'])
self.assertNotEqual(runtime_ep._state['empty'], 'warn')
self.assertEqual(runtime_ep._state, existing)
def test_geterrcall(self):
exp = runtime_ep._profile['sampsize']['call']
obs = geterrcall('sampsize')
self.assertEqual(obs, exp)
with self.assertRaises(KeyError):
geterrcall('asdasd')
def test_seterrcall(self):
def foo(x):
return 10
seterrcall('sampmdsize', foo)
obs = geterrcall('sampmdsize')
self.assertEqual(obs, foo)
def test_errcheck(self):
self.assertEqual(errcheck(self.ex_table), None)
self.ex_table._sample_ids = self.ex_table._sample_ids[:-1]
with self.assertRaises(TableException):
errcheck(self.ex_table)
def test_errstate(self):
def foo(item):
return "the callback called"
table = Table([], [], [])
seterrcall('empty', foo)
self.assertNotEqual(geterr()['empty'], 'call')
with errstate(empty='call'):
result = errcheck(table)
self.assertEqual(result, "the callback called")
self.assertNotEqual(geterr()['empty'], 'call')
if __name__ == '__main__':
main()
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