def complete_input_references_in_outputs(cli_outputs, inputs_to_reference):
"""
Takes the cli outputs and inputs to reference and returns the cli outputs, but with resolved input references
:param cli_outputs: The cli outputs to resolve input references for
:param inputs_to_reference: The inputs to reference
"""
resolved_outputs = deepcopy(cli_outputs)
for output_key, output_value in resolved_outputs.items():
if output_value['type'] == 'stdout' or output_value['type'] == 'stderr':
continue
output_binding = output_value['outputBinding']
try:
resolved_glob = resolve_input_references(output_binding['glob'],
inputs_to_reference)
except InvalidInputReference as e:
raise InvalidInputReference(
'Invalid Input Reference for output key "{}":\n{}'.format(
output_key, str(e)))
output_binding['glob'] = resolved_glob
return resolved_outputs
def test_recursive_references():
glob = '$(inputs.$(inputs.a_file.basename).basename'
with pytest.raises(InvalidInputReference):
resolve_input_references(glob, INPUT_TO_REFERENCE)
def test_multiple_references():
glob = '$(inputs.a_file.basename) - $(inputs.a_file.class)'
result = resolve_input_references(glob, INPUT_TO_REFERENCE)
assert result == 'a_file - File'
def test_not_closed_bracket():
glob = '$(inputs["a_file.basename)'
with pytest.raises(InvalidInputReference):
resolve_input_references(glob, INPUT_TO_REFERENCE)
def test_could_not_resolve_attribute():
glob = '$(inputs.a_file.invalid)'
with pytest.raises(InvalidInputReference):
resolve_input_references(glob, INPUT_TO_REFERENCE)
def test_file_list():
glob = 'PRE-$(inputs.a_file[0].basename)-POST'
result = resolve_input_references(glob, INPUT_LIST_TO_REFERENCE)
assert result == 'PRE-a_file-POST'
def test_bracket_dots():
glob = 'PRE-$(inputs.a_file.basename)-POST'
result = resolve_input_references(glob, INPUT_TO_REFERENCE)
assert result == 'PRE-a_file-POST'
def test_bracket_single_quote():
glob = 'PRE-$(inputs[\'a_file\'][\'basename\'])-POST'
result = resolve_input_references(glob, INPUT_TO_REFERENCE)
assert result == 'PRE-a_file-POST'
def test_bracket_double_quote():
glob = 'PRE-$(inputs["a_file"]["basename"])-POST'
result = resolve_input_references(glob, INPUT_TO_REFERENCE)
assert result == 'PRE-a_file-POST'
def test_int_value():
glob = '$(inputs.a_file.size)'
result = resolve_input_references(glob, INPUT_TO_REFERENCE)
assert result == '1000'
def test_wrong_order():
glob = '$(inputs.a_file["basename)"]'
with pytest.raises(InvalidInputReference):
resolve_input_references(glob, INPUT_TO_REFERENCE)
def test_missing_inputs():
glob = '$(invalid.a_file.basename)'
with pytest.raises(InvalidInputReference):
resolve_input_references(glob, INPUT_TO_REFERENCE)
def test_could_not_resolve_identifier():
glob = '$(inputs["invalid"])'
with pytest.raises(InvalidInputReference):
resolve_input_references(glob, INPUT_TO_REFERENCE)
def test_string_index_in_list():
glob = '$(inputs.a_file[invalid].basename)'
with pytest.raises(InvalidInputReference):
resolve_input_references(glob, INPUT_LIST_TO_REFERENCE)
def test_string_index_and_dot():
glob = '$(inputs["a_file"].basename)'
result = resolve_input_references(glob, INPUT_TO_REFERENCE)
assert result == 'a_file'
def test_recursive_attributes():
glob = '$(inputs["inputs["a_file"]"].basename)'
with pytest.raises(InvalidInputReference):
resolve_input_references(glob, INPUT_TO_REFERENCE)
