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Source code for galaxy.tool_util.linters.outputs

"""This module contains a linting functions for tool outputs."""
from galaxy.util import string_as_bool
from ._util import is_valid_cheetah_placeholder
from ..parser.output_collection_def import NAMED_PATTERNS

[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(f"Unknown element found in outputs [{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 __check_format(output, lint_ctx): format_set = True if output.tag == "data": if "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 for sub in output: if __check_pattern(sub): format_set = True elif __check_format(sub, lint_ctx, allow_ext=True): format_set = True if not format_set: lint_ctx.warn(f"Tool {output.tag} output {output.attrib.get('name', 'with missing name')} doesn't define an output format.") lint_ctx.info("%d outputs found.", num_outputs)
def __check_format(node, lint_ctx, allow_ext=False): """ check if format/ext/format_source attribute is set in a given node issue a warning if the value is input return true (node defines format/ext) / false (else) """ if "format_source" in node.attrib and ("ext" in node.attrib or "format" in node.attrib): lint_ctx.warn(f"Tool {node.tag} output {node.attrib.get('name', 'with missing name')} should use either format_source or format/ext") if "format_source" in node.attrib: return True # if allowed (e.g. for discover_datasets), ext takes precedence over format fmt = None if allow_ext: fmt = node.attrib.get("ext") if fmt is None: fmt = node.attrib.get("format") if fmt == "input": lint_ctx.warn(f"Using format='input' on {node.tag}, format_source attribute is less ambiguous and should be used instead.") return fmt is not None def __check_pattern(node): """ check if - pattern attribute is set and defines the extension or - from_tool_provided_metadata is true """ if node.tag != "discover_datasets": return False if "from_tool_provided_metadata" in node.attrib and string_as_bool(node.attrib.get("from_tool_provided_metadata", "false")): return True if "pattern" not in node.attrib: return False pattern = node.attrib["pattern"] regex_pattern = NAMED_PATTERNS.get(pattern, pattern) if "(?P<ext>" in regex_pattern: return True