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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# ----------------------------------------------------------------------------
from collections import defaultdict
from skbio.workflow import (Exists, NotExecuted, NotNone, Workflow, not_none,
requires, method)
from unittest import TestCase, main
def construct_iterator(**kwargs):
"""make an iterator for testing purposes"""
to_gen = []
for k in sorted(kwargs):
if k.startswith('iter'):
to_gen.append(kwargs[k])
if len(to_gen) == 1:
return (x for x in to_gen[0])
else:
return zip(*to_gen)
class MockWorkflow(Workflow):
def initialize_state(self, item):
self.state[0] = None
self.state[1] = item
@method(priority=90)
@requires(option='A', values=True)
def wf_groupA(self):
self.methodA1()
self.methodA2()
@method()
@requires(option='B', values=True)
def wf_groupB(self):
self.methodB1()
self.methodB2()
@method(priority=10)
@requires(option='C', values=True)
def wf_groupC(self):
self.methodC1()
self.methodC2()
def methodA1(self):
name = 'A1'
self.stats[name] += 1
if self.state[-1] == 'fail %s' % name:
self.failed = True
self.state = [name, self.state[-1]]
def methodA2(self):
name = 'A2'
self.stats[name] += 1
if self.state[-1] == 'fail %s' % name:
self.failed = True
self.state = [name, self.state[-1]]
def methodB1(self):
name = 'B1'
self.stats[name] += 1
if self.state[-1] == 'fail %s' % name:
self.failed = True
self.state = 'failed'
else:
self.state = [name, self.state[-1]]
@requires(option='foo', values=[1, 2, 3])
def methodB2(self):
name = 'B2'
self.stats[name] += 1
if self.state[-1] == 'fail %s' % name:
self.failed = True
self.state = 'failed'
else:
self.state = [name, self.state[-1]]
def methodC1(self):
name = 'C1'
self.stats[name] += 1
if self.state[-1] == 'fail %s' % name:
self.failed = True
self.state = [name, self.state[-1]]
@requires(option='C2', values=[1, 2, 3])
def methodC2(self):
name = 'C2'
self.stats[name] += 1
if self.state[-1] == 'fail %s' % name:
self.failed = True
self.state = [name, self.state[-1]]
class WorkflowTests(TestCase):
def setUp(self):
opts = {'A': True, 'C': True}
self.obj_short = MockWorkflow([None, None], options=opts,
stats=defaultdict(int))
self.obj_debug = MockWorkflow([None, None], debug=True, options=opts,
stats=defaultdict(int))
self.obj_noshort = MockWorkflow([None, None], short_circuit=False,
options=opts,
stats=defaultdict(int))
def test_debug_trace(self):
gen = construct_iterator(**{'iter_x': [1, 2, 3, 4, 5]})
obj = self.obj_debug(gen)
exp = ['C1', 1]
obs = next(obj)
self.assertEqual(obs, exp)
exp_trace = set([('wf_groupA', 0),
('methodA1', 1),
('methodA2', 2),
('wf_groupC', 3),
('methodC1', 4)])
exp_pre_state = {('wf_groupA', 0): [None, 1],
('methodA1', 1): [None, 1],
('methodA2', 2): ['A1', 1],
('wf_groupC', 3): ['A2', 1],
('methodC1', 4): ['A2', 1]}
exp_post_state = {('wf_groupA', 0): ['A2', 1],
('methodA1', 1): ['A1', 1],
('methodA2', 2): ['A2', 1],
('wf_groupC', 3): ['C1', 1],
('methodC1', 4): ['C1', 1]}
obs_trace = self.obj_debug.debug_trace
obs_pre_state = self.obj_debug.debug_pre_state
obs_post_state = self.obj_debug.debug_post_state
self.assertEqual(obs_trace, exp_trace)
self.assertEqual(obs_pre_state, exp_pre_state)
self.assertEqual(obs_post_state, exp_post_state)
def test_init(self):
self.assertEqual(self.obj_short.options, {'A': True, 'C': True})
self.assertEqual(self.obj_short.stats, {})
self.assertTrue(self.obj_short.short_circuit)
self.assertEqual(self.obj_noshort.options, {'A': True, 'C': True})
self.assertEqual(self.obj_noshort.stats, {})
self.assertFalse(self.obj_noshort.short_circuit)
def test_init_reserved_attributes(self):
with self.assertRaises(AttributeError):
Workflow('foo', failed=True)
def test_all_wf_methods(self):
# note on priority: groupA:90, groupC:10, groupB:0 (default)
exp = [self.obj_short.wf_groupA, self.obj_short.wf_groupC,
self.obj_short.wf_groupB]
obs = self.obj_short._all_wf_methods()
self.assertEqual(obs, exp)
def test_call_AC_no_fail(self):
iter_ = construct_iterator(**{'iter_x': [1, 2, 3, 4, 5]})
# success function
def sf(x):
return x.state[:]
exp_stats = {'A1': 5, 'A2': 5, 'C1': 5}
# C2 isn't executed as its requirements aren't met in the options
exp_result = [['C1', 1], ['C1', 2], ['C1', 3], ['C1', 4], ['C1', 5]]
obs_result = list(self.obj_short(iter_, sf, None))
self.assertEqual(obs_result, exp_result)
self.assertEqual(self.obj_short.stats, exp_stats)
def test_call_AC_fail(self):
iter_ = construct_iterator(**{'iter_x': [1, 2, 'fail A2', 4, 5]})
# success function
def sf(x):
return x.state[:]
ff = sf # failed function
exp_stats = {'A1': 5, 'A2': 5, 'C1': 4, 'C2': 4}
self.obj_short.options['C2'] = 1
# pass in a failed callback to capture the result, and pause execution
gen = self.obj_short(iter_, sf, ff)
r1 = next(gen)
self.assertEqual(r1, ['C2', 1])
self.assertFalse(self.obj_short.failed)
r2 = next(gen)
self.assertEqual(r2, ['C2', 2])
self.assertFalse(self.obj_short.failed)
r3 = next(gen)
self.assertEqual(self.obj_short.state, ['A2', 'fail A2'])
self.assertTrue(self.obj_short.failed)
self.assertEqual(r3, ['A2', 'fail A2'])
r4 = next(gen)
self.assertEqual(r4, ['C2', 4])
self.assertFalse(self.obj_short.failed)
r5 = next(gen)
self.assertEqual(r5, ['C2', 5])
self.assertFalse(self.obj_short.failed)
self.assertEqual(self.obj_short.stats, exp_stats)
def test_call_AC_fail_noshort(self):
iter_ = construct_iterator(**{'iter_x': [1, 2, 'fail A2', 4, 5]})
# success function
def sf(x):
return x.state[:]
ff = sf # failed function
exp_stats = {'A1': 5, 'A2': 5, 'C1': 5}
# pass in a failed callback to capture the result, and pause execution
gen = self.obj_noshort(iter_, sf, ff)
r1 = next(gen)
self.assertEqual(r1, ['C1', 1])
self.assertFalse(self.obj_noshort.failed)
r2 = next(gen)
self.assertEqual(r2, ['C1', 2])
self.assertFalse(self.obj_noshort.failed)
next(gen)
self.assertEqual(self.obj_noshort.state, ['C1', 'fail A2'])
self.assertTrue(self.obj_noshort.failed)
r4 = next(gen)
self.assertEqual(r4, ['C1', 4])
self.assertFalse(self.obj_noshort.failed)
r5 = next(gen)
self.assertEqual(r5, ['C1', 5])
self.assertFalse(self.obj_noshort.failed)
self.assertEqual(self.obj_noshort.stats, exp_stats)
class MockWorkflowReqTest(Workflow):
def _allocate_state(self):
self.state = None
def initialize_state(self, item):
self.state = [None, item]
@method(priority=5)
@requires(state=lambda x: x[-1] < 3)
def wf_needs_data(self):
name = 'needs_data'
self.stats[name] += 1
if self.state[-1] == 'fail %s' % name:
self.failed = True
self.state = [name, self.state[-1]]
@method(priority=10)
def wf_always_run(self):
name = 'always_run'
self.stats[name] += 1
if self.state[-1] == 'fail %s' % name:
self.failed = True
self.state = [name, self.state[-1]]
@method(priority=20)
@requires(option='cannot_be_none', values=not_none)
def wf_run_if_not_none(self):
name = 'run_if_not_none'
self.stats[name] += 1
if self.state[-1] == 'fail %s' % name:
self.failed = True
self.state = [name, self.state[-1]]
class RequiresTests(TestCase):
def test_validdata(self):
obj = MockWorkflowReqTest([None, None], stats=defaultdict(int))
single_iter = construct_iterator(**{'iter_x': [1, 2, 3, 4, 5]})
exp_stats = {'needs_data': 2, 'always_run': 5}
exp_result = [['needs_data', 1], ['needs_data', 2], ['always_run', 3],
['always_run', 4], ['always_run', 5]]
obs_result = list(obj(single_iter))
self.assertEqual(obs_result, exp_result)
self.assertEqual(obj.stats, exp_stats)
def test_not_none_avoid(self):
obj = MockWorkflowReqTest([None, None], {'cannot_be_none': None},
stats=defaultdict(int))
single_iter = construct_iterator(**{'iter_x': [1, 2, 3, 4, 5]})
exp_stats = {'needs_data': 2, 'always_run': 5}
exp_result = [['needs_data', 1], ['needs_data', 2], ['always_run', 3],
['always_run', 4], ['always_run', 5]]
obs_result = list(obj(single_iter))
self.assertEqual(obs_result, exp_result)
self.assertEqual(obj.stats, exp_stats)
def test_not_none_execute(self):
obj = MockWorkflowReqTest([None, None],
options={'cannot_be_none': True}, debug=True,
stats=defaultdict(int))
single_iter = construct_iterator(**{'iter_x': [1, 2, 3, 4, 5]})
exp_stats = {'needs_data': 2, 'always_run': 5, 'run_if_not_none': 5}
exp_result = [['needs_data', 1], ['needs_data', 2], ['always_run', 3],
['always_run', 4], ['always_run', 5]]
obs_result = list(obj(single_iter))
self.assertEqual(obs_result, exp_result)
self.assertEqual(obj.stats, exp_stats)
def test_methodb1(self):
obj = MockWorkflow([None, None], stats=defaultdict(int))
obj.initialize_state('test')
obj.methodB1()
self.assertEqual(obj.state, ['B1', 'test'])
self.assertFalse(obj.failed)
# methodb1 executes regardless of if self.failed
obj.failed = True
obj.initialize_state('test 2')
obj.methodB1()
self.assertEqual(obj.state, ['B1', 'test 2'])
obj.failed = False
obj.state = [None, 'fail B1']
obj.methodB1()
self.assertEqual(obj.state, 'failed')
self.assertEqual(obj.stats, {'B1': 3})
def test_methodb2_accept(self):
# methodb2 is setup to be valid when foo is in [1,2,3], make sure we
# can execute
obj = MockWorkflow([None, None], options={'foo': 1},
stats=defaultdict(int))
obj.initialize_state('test')
obj.methodB2()
self.assertEqual(obj.state, ['B2', 'test'])
self.assertEqual(obj.stats, {'B2': 1})
def test_methodb2_ignore(self):
# methodb2 is setup to be valid when foo is in [1, 2, 3], make sure
# we do not execute
obj = MockWorkflow([None, None], options={'foo': 'bar'},
stats=defaultdict(int))
obj.methodB2()
self.assertEqual(obj.state, [None, None])
self.assertEqual(obj.stats, {})
class PriorityTests(TestCase):
def test_dec(self):
@method(priority=10)
def foo(x, y, z):
"""doc check"""
return x + y + z
self.assertEqual(foo.priority, 10)
self.assertEqual(foo.__name__, 'foo')
self.assertEqual(foo.__doc__, 'doc check')
class NotExecutedTests(TestCase):
def test_call(self):
ne = NotExecuted()
obs = ne('foo')
self.assertTrue(obs is ne)
self.assertEqual(obs.msg, 'foo')
class ExistsTests(TestCase):
def test_contains(self):
e = Exists()
self.assertTrue('foo' in e)
self.assertTrue(None in e)
class NotNoneTests(TestCase):
def test_contains(self):
nn = NotNone()
self.assertTrue('foo' in nn)
self.assertFalse(None in nn)
if __name__ == '__main__':
main()
|
