def test_load_CWLKERNEL_BOOT_DIRECTORY(self):
conf = CWLExecuteConfigurator()
self.assertEqual(conf.CWLKERNEL_BOOT_DIRECTORY, '/tmp/CWLKERNEL_DATA')
os.environ['CWLKERNEL_BOOT_DIRECTORY'] = '/tmp/CWLKERNEL_DATA1'
conf = CWLExecuteConfigurator()
os.environ['CWLKERNEL_BOOT_DIRECTORY'] = '/tmp/CWLKERNEL_DATA'
self.assertEqual(conf.CWLKERNEL_BOOT_DIRECTORY, '/tmp/CWLKERNEL_DATA1')
def test_load_CWLKERNEL_MODE(self):
conf = CWLExecuteConfigurator()
self.assertEqual(conf.CWLKERNEL_MODE, 'SIMPLE')
os.environ['CWLKERNEL_MODE'] = 'simple'
conf = CWLExecuteConfigurator()
self.assertEqual(conf.CWLKERNEL_MODE, 'simple')
os.environ['CWLKERNEL_MODE'] = 'something new'
self.assertRaises(RuntimeError, CWLExecuteConfigurator)
def test_file_repository(self):
conf = CWLExecuteConfigurator()
location = os.sep.join(
[conf.CWLKERNEL_BOOT_DIRECTORY,
str(uuid.uuid4()), 'repo'])
repo = WorkflowRepository(Path(location))
head_tool: WorkflowComponent = CWLTool(
'head', {
'class':
'CommandLineTool',
'cwlVersion':
'v1.0',
'id':
'head',
'baseCommand': ['head'],
'inputs': [{
'id': 'number_of_lines',
'type': 'int?',
'inputBinding': {
'position': 0,
'prefix': '-n'
}
}, {
'id': 'headinput',
'type': 'File',
'inputBinding': {
'position': 1
}
}],
'outputs': [{
'id': 'headoutput',
'type': 'stdout'
}],
'label':
'head',
'stdout':
'head.out'
})
repo.register_tool(head_tool)
self.assertEqual(
os.path.realpath(repo.get_tools_path_by_id('head').absolute()),
os.path.realpath(os.path.join(location, 'head.cwl')))
def test_all_properties_have_default_value(self):
conf = CWLExecuteConfigurator()
for property in conf.properties:
self.assertIsNotNone(conf.__getattribute__(property))