"""This module contains a linting functions for tool outputs."""
[docs]def lint_output(tool_xml, lint_ctx):
"""Check output elements, ensure there is at least one and check attributes."""
outputs = tool_xml.findall("./outputs")
if len(outputs) == 0:
lint_ctx.warn("Tool contains no outputs section, most tools should produce outputs.")
if len(outputs) > 1:
lint_ctx.warn("Tool contains multiple output sections, behavior undefined.")
num_outputs = 0
if len(outputs) == 0:
lint_ctx.warn("No outputs found")
return
for output in list(outputs[0]):
if output.tag not in ["data", "collection"]:
lint_ctx.warn("Unknown element found in outputs [%s]" % output.tag)
continue
num_outputs += 1
output_attrib = output.attrib
if "name" not in output_attrib:
lint_ctx.warn("Tool output doesn't define a name - this is likely a problem.")
if output.tag == "data":
format_set = False
if "format" in output_attrib:
format_set = True
format = output_attrib["format"]
if format == "input":
lint_ctx.warn("Using format='input' on output data, format_source attribute is less ambiguous and should be used instead.")
elif "format_source" in output_attrib:
format_set = True
if not format_set:
lint_ctx.warn("Tool data output doesn't define an output format.")
elif output.tag == "collection":
if "type" not in output_attrib:
lint_ctx.warn("Collection output with undefined 'type' found.")
lint_ctx.info("%d outputs found.", num_outputs)