def test_format_object(self):
param_name = 'FORMAT_OBJECT'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, 'Alignment')
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 'xyz',
[_INVALID_ERROR.format('format_object')])
self._test_negative(params, param_name, '',
[_INVALID_ERROR.format('format_object')])
def test_descriptions(self):
param_name = 'DESCRIPTIONS'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, 1)
self._test_positive(params, param_name, 32)
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 0, [_INVALID_ERROR.format('descriptions')])
self._test_negative(params, param_name, -1, [_INVALID_ERROR.format('descriptions')])
self._test_negative(params, param_name, -478, [_INVALID_ERROR.format('descriptions')])
def test_hitlist_size(self):
param_name = 'HITLIST_SIZE'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, 1)
self._test_positive(params, param_name, 265)
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 0, [_INVALID_ERROR.format('hitlist_size')])
self._test_negative(params, param_name, -1, [_INVALID_ERROR.format('hitlist_size')])
self._test_negative(params, param_name, -46, [_INVALID_ERROR.format('hitlist_size')])
def test_alignments(self):
param_name = 'ALIGNMENTS'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, 1)
self._test_positive(params, param_name, 45)
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 0, [_INVALID_ERROR.format('alignments')])
self._test_negative(params, param_name, -1, [_INVALID_ERROR.format('alignments')])
self._test_negative(params, param_name, -8, [_INVALID_ERROR.format('alignments')])
def test_composition_based_statistics(self):
param_name = 'COMPOSITION_BASED_STATISTICS'
params = dict(self.valid_required_params)
for allowed_value in range(4):
self._test_positive(params, param_name, allowed_value)
self._test_negative(params, param_name, 4, [_INVALID_ERROR.format('composition_based_statistics')])
self._test_negative(params, param_name, 154, [_INVALID_ERROR.format('composition_based_statistics')])
self._test_negative(params, param_name, -1, [_INVALID_ERROR.format('composition_based_statistics')])
self._test_negative(params, param_name, -6481, [_INVALID_ERROR.format('composition_based_statistics')])
def test_nucl_penalty(self):
param_name = 'NUCL_PENALTY'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, -1)
self._test_positive(params, param_name, -127)
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 0, [_INVALID_ERROR.format('nucl_penalty')])
self._test_negative(params, param_name, 1, [_INVALID_ERROR.format('nucl_penalty')])
self._test_negative(params, param_name, 53, [_INVALID_ERROR.format('nucl_penalty')])
def test_expect(self):
param_name = 'EXPECT'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, 1)
self._test_positive(params, param_name, 127)
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 0, [_INVALID_ERROR.format('expect')])
self._test_negative(params, param_name, -1, [_INVALID_ERROR.format('expect')])
self._test_negative(params, param_name, -53, [_INVALID_ERROR.format('expect')])
def test_nucl_reward(self):
param_name = 'NUCL_REWARD'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, 1)
self._test_positive(params, param_name, 127)
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 0, [_INVALID_ERROR.format('nucl_reward')])
self._test_negative(params, param_name, -1, [_INVALID_ERROR.format('nucl_reward')])
self._test_negative(params, param_name, -53, [_INVALID_ERROR.format('nucl_reward')])
def test_num_threads(self):
param_name = 'NUM_THREADS'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, 1)
self._test_positive(params, param_name, 777)
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 0, [_INVALID_ERROR.format('num_threads')])
self._test_negative(params, param_name, -1, [_INVALID_ERROR.format('num_threads')])
self._test_negative(params, param_name, -5987, [_INVALID_ERROR.format('num_threads')])
def test_word_size(self):
param_name = 'WORD_SIZE'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, 1)
self._test_positive(params, param_name, 234)
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 0, [_INVALID_ERROR.format('word_size')])
self._test_negative(params, param_name, -1, [_INVALID_ERROR.format('word_size')])
self._test_negative(params, param_name, -2, [_INVALID_ERROR.format('word_size')])
def test_threshold(self):
param_name = 'THRESHOLD'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, 1)
self._test_positive(params, param_name, 62487)
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 0, [_INVALID_ERROR.format('threshold')])
self._test_negative(params, param_name, -1, [_INVALID_ERROR.format('threshold')])
self._test_negative(params, param_name, -6547, [_INVALID_ERROR.format('threshold')])
def test_format_type(self):
allowed_values = ['HTML', 'Text', 'XML', 'XML2', 'JSON2', 'Tabular']
param_name = 'FORMAT_TYPE'
params = dict(self.valid_required_params)
for allowed_value in allowed_values:
self._test_positive(params, param_name, allowed_value)
self._test_positive(params, param_name, None)
self._test_positive(params, param_name, '')
self._test_negative(params, param_name, 'X', [_INVALID_ERROR.format('format_type')])
self._test_negative(params, param_name, 'Text2', [_INVALID_ERROR.format('format_type')])
def test_filter(self):
allowed_values = ['F', 'T', 'L', 'mT', 'mL']
param_name = 'FILTER'
params = dict(self.valid_required_params)
for allowed_value in allowed_values:
self._test_positive(params, param_name, allowed_value)
self._test_positive(params, param_name, '')
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 'X', [_INVALID_ERROR.format('filter')])
self._test_negative(params, param_name, 'test123', [_INVALID_ERROR.format('filter')])
def test_ncbi_gi(self):
param_name = 'NCBI_GI'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, 'T')
self._test_positive(params, param_name, 'F')
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, '', [_INVALID_ERROR.format('ncbi_gi')])
self._test_negative(params, param_name, 'X', [_INVALID_ERROR.format('ncbi_gi')])
self._test_negative(params, param_name, 'True', [_INVALID_ERROR.format('ncbi_gi')])
self._test_negative(params, param_name, 'False', [_INVALID_ERROR.format('ncbi_gi')])
self._test_negative(params, param_name, 'test123', [_INVALID_ERROR.format('ncbi_gi')])
def test_matrix(self):
param_name = 'MATRIX'
params = dict(self.valid_required_params)
allowed_values = ['BLOSUM45', 'BLOSUM50', 'BLOSUM62', 'BLOSUM80', 'BLOSUM90', 'PAM250', 'PAM30', 'PAM70']
for allowed_value in allowed_values:
self._test_positive(params, param_name, allowed_value)
self._test_positive(params, param_name, None)
self._test_negative(params, param_name, 'test', [_INVALID_ERROR.format('matrix')])
def test_gap_costs(self):
param_name = 'GAPCOSTS'
params = dict(self.valid_required_params)
self._test_positive(params, param_name, '11 1')
self._test_positive(params, param_name, '1 1')
self._test_positive(params, param_name, '256 84713')
self._test_negative(params, param_name, '-1 15', [_INVALID_ERROR.format('gapcosts')])
self._test_negative(params, param_name, '0 15', [_INVALID_ERROR.format('gapcosts')])
self._test_negative(params, param_name, '84 -5612', [_INVALID_ERROR.format('gapcosts')])
self._test_negative(params, param_name, '84 8 5', [_INVALID_ERROR.format('gapcosts')])
self._test_negative(params, param_name, '-621 -223487', [_INVALID_ERROR.format('gapcosts')])
self._test_negative(params, param_name, '0 0', [_INVALID_ERROR.format('gapcosts')])
def test_required_params(self):
params = {'QUERY': 'test', 'DATABASE': 'test_db'}
for program in _PROGRAMS:
self._test_positive(params, 'PROGRAM', program)
errors = self.validator.validate_params({'DATABASE': '', 'PROGRAM': _PROGRAMS[0]})
self.assertEqual(len(errors), 2)
self.assertIn(_NOT_EMPTY_ERROR.format('database'), errors)
self.assertIn(_NOT_NONE_ERROR.format('query'), errors)
errors = self.validator.validate_params({'QUERY': '', 'PROGRAM': _PROGRAMS[0]})
self.assertEqual(len(errors), 2)
self.assertIn(_NOT_EMPTY_ERROR.format('query'), errors)
self.assertIn(_NOT_NONE_ERROR.format('database'), errors)
errors = self.validator.validate_params({'QUERY': '', 'PROGRAM': 'xyz'})
self.assertEqual(len(errors), 3)
self.assertIn(_NOT_EMPTY_ERROR.format('query'), errors)
self.assertIn(_NOT_NONE_ERROR.format('database'), errors)
self.assertIn(_INVALID_ERROR.format('program'), errors)