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Source code for galaxy.tool_util.linters.outputs

"""This module contains a linting functions for tool outputs."""
from ._util import is_valid_cheetah_placeholder

[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.") else: if not is_valid_cheetah_placeholder(output_attrib["name"]): lint_ctx.warn("Tool output name [%s] is not a valid Cheetah placeholder.", output_attrib["name"]) 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)