This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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)