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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 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"]) format_set = False if output.tag == "data": if __check_format(output, lint_ctx): format_set = True elif "auto_format" in output.attrib and output.attrib["auto_format"]: format_set = True elif output.tag == "collection": if "type" not in output.attrib: lint_ctx.warn("Collection output with undefined 'type' found.") if "structured_like" in output.attrib and "inherit_format" in output.attrib: format_set = True if "format_source" in output.attrib: format_set = True for sub in output: if __check_pattern(sub): format_set = True elif __check_format(sub, lint_ctx): format_set = True if not format_set: lint_ctx.warn("Tool {} output {} doesn't define an output format.".format(output.tag, output.attrib.get("name", "with missing name"))) lint_ctx.info("%d outputs found.", num_outputs)
def __check_format(node, lint_ctx): """ check if format/ext attribute is set in a given node issue a warning if the value is input return true (node defines format/ext) / false (else) """ fmt = node.attrib.get("format", node.attrib.get("ext", None)) if fmt == "input": lint_ctx.warn("Using format='input' on %s, format_source attribute is less ambiguous and should be used instead." % node.tag) return fmt is not None def __check_pattern(node): """ check if pattern attribute is set and defines the extension """ if node.tag != "discover_datasets": return False if "pattern" not in node.attrib: return False if node.attrib["pattern"] == "__default__": return True if "ext" in node.attrib["pattern"] and node.attrib["pattern"].startswith("__") and node.attrib["pattern"].endswith("__"): return True