def test_categories_and_order(self):
fil = op.join(
op.split(bfile)[0], 'schema/examples/test_pretty_print.json')
prettystring = bosh.prettyprint(fil)
i_tl_descs = prettystring.index("Tool name")
i_con_info = prettystring.index("Container Information")
i_sugg_res = prettystring.index("Suggested Resources")
i_er_codes = prettystring.index("Error Codes")
i_inp_grps = prettystring.index("Input Groups")
i_pos_args = prettystring.index("positional arguments")
i_opt_args = prettystring.index("optional arguments")
i_req_args = prettystring.index("required arguments")
i_conf_fil = prettystring.index("Config Files")
i_out_file = prettystring.index("Output Files")
# Fluff asserts for easy debugging
self.assertTrue(i_tl_descs < i_con_info)
self.assertTrue(i_con_info < i_sugg_res)
self.assertTrue(i_sugg_res < i_er_codes)
self.assertTrue(i_er_codes < i_inp_grps)
self.assertTrue(i_inp_grps < i_pos_args)
self.assertTrue(i_pos_args < i_opt_args)
self.assertTrue(i_opt_args < i_req_args)
self.assertTrue(i_req_args < i_conf_fil)
self.assertTrue(i_conf_fil < i_out_file)
def test_input_optionality_separation(self):
fil = op.join(
op.split(bfile)[0], 'schema/examples/test_pretty_print.json')
prettystring = bosh.prettyprint(fil)
inputs = prettystring.split("=" * 80)[6].split("arguments:")
positional_inputs = inputs[1]
optional_inputs = inputs[2]
required_inputs = inputs[3]
self.assertFalse("Optional: False" in positional_inputs)
self.assertFalse("Optional: False" in optional_inputs)
self.assertFalse("Optional: True" in required_inputs)
def test_output_config_separation(self):
self.maxDiff = None
fil = op.join(
op.split(bfile)[0], 'schema/examples/test_pretty_print.json')
prettystring = bosh.prettyprint(fil)
categories = prettystring.split("=" * 80)
configs = categories[7]
outputs = categories[8]
self.assertTrue("Config Files:" in configs)
self.assertTrue("Template:" in configs)
self.assertTrue("Output Files:" in outputs)
self.assertFalse("Template:" in outputs)
def function(descriptor):
'''
Returns a function to invoke bosh.execute on a descriptor.
args:
descriptor: Zenodo id, file name, or JSON string representing a
descriptor.
name: name of the function to create. Defaults to the tool name in the
descriptor.
'''
validate(descriptor)
descriptor_json = loadJson(descriptor)
def f(*args, **kwargs):
# Set default mode to 'launch'
if len(args) > 0:
mode = args[0]
else:
mode = 'launch'
if mode not in ['launch', 'simulate']:
mode = 'launch'
else:
args = args[1:]
# Call bosh execute
if mode == 'launch':
return execute(mode, descriptor, json.dumps(kwargs), *args)
if len(kwargs) > 0:
return execute(mode, descriptor, '-i', json.dumps(kwargs), *args)
return execute(mode, descriptor, *args)
f.__name__ = str(descriptor_json['name'])
# Documentation
doc = []
doc.append(r'''Runs {0} through its Boutiques interface.
*args:
- mode: 'launch' or 'simulate'. Defaults to 'launch'.
- other arguments: will be passed to bosh execute. Examples: '-s',
'-x'. See help(bosh.execute) for a complete list.
*kwargs:
{1} arguments as defined in the Boutiques descriptor, referenced
from input ids. Example: {2}='some_value'. See complete
list in descriptor help below.
'''.format(f.__name__, f.__name__, descriptor_json['inputs'][0]['id']))
doc.append(prettyprint(descriptor))
f.__doc__ = ''.join(doc)
return f
def test_doesntcrash(self):
fil = op.join(
op.split(bfile)[0], 'schema/examples/test_pretty_print.json')
prettystring = bosh.prettyprint(fil)
self.assertIsInstance(prettystring, string_types)
def test_duplcate_flags(self):
fil = op.join(op.split(bfile)[0], 'schema/examples/good_dupFlags.json')
prettystring = bosh.prettyprint(fil)
self.assertIn("-duplicate", prettystring)
self.assertIn("-duplicate_DUP1", prettystring)
self.assertIn("-duplicate_DUP2", prettystring)