def test_handles_cwltool_failures(self, mock_cwl_main):
p = PredictionRunner(self.sequence, self.model, self.config,
self.models_dir, self.output_dir)
def side_effect(args, stdout, stderr):
print >> stderr, 'error in cwl_main'
return 1
mock_cwl_main.side_effect = side_effect
with self.assertRaises(RunnerException):
p.run()
self.assertTrue(mock_cwl_main.called)
def test_runs_cwltool_gets_output(self, mock_cwl_main):
p = PredictionRunner(self.sequence, self.model, self.config,
self.models_dir, self.output_dir)
def side_effect(args, stdout, stderr):
print >> stdout, '{"predictions":{"path": "/preds.bed","class": "File","size": 124}}'
return 0
mock_cwl_main.side_effect = side_effect
result = p.run()
self.assertTrue(mock_cwl_main.called)
self.assertEqual(result['path'], '/preds.bed')
def run(self, sequence_file, model_identifier):
if '_vs_' in model_identifier:
strategy = PredictionRunner.strategy_preference
config_file = self.config.preferences_config_file
else:
strategy = PredictionRunner.strategy_predict
config_file = self.config.predictions_config_file
runner = PredictionRunner(sequence_file,
model_identifier,
config_file,
self.config.model_files_dir,
self.config.output_dir,
strategy)
return self.extract_predictions(runner.run())
def test_generates_ooutput_file_name(self):
p = PredictionRunner(self.sequence, self.model, self.config,
self.models_dir, self.output_dir)
output_file_name = p.output_file_name
self.assertIn('.bed', output_file_name)
self.assertIn(self.model, output_file_name)
def test_fails_with_missing_config(self):
with self.assertRaises(ValueError):
PredictionRunner(self.sequence, self.model, None, self.models_dir,
self.output_dir)
def test_writes_json_order(self):
p = PredictionRunner(self.sequence, self.model, self.config,
self.models_dir, self.output_dir)
p.write_json_order()