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Source code for galaxy.tool_util.linters.cwl

"""Linter for CWL tools."""

lint_tool_types = ["cwl"]

from galaxy.tool_util.cwl.schema import schema_loader

[docs]def lint_cwl_validation(tool_source, lint_ctx): """Determine in CWL tool validates against spec.""" raw_reference = schema_loader.raw_process_reference(tool_source._source_path) validation_exception = None try: schema_loader.process_definition(raw_reference) except Exception as e: validation_exception = e if validation_exception: lint_ctx.error(f"Failed to valdiate CWL artifact: {validation_exception}") else: lint_ctx.info("CWL appears to be valid.")
[docs]def lint_new_draft(tool_source, lint_ctx): """Determine in CWL tool is valid, modern draft.""" raw_reference = schema_loader.raw_process_reference(tool_source._source_path) cwl_version = raw_reference.process_object.get("cwlVersion", None) if cwl_version is None: lint_ctx.error("CWL file does not contain a 'cwlVersion'") if cwl_version not in ["v1.0"]: lint_ctx.warn(f"CWL version [{cwl_version}] is unknown, we recommend the v1.0 the stable release.") else: lint_ctx.info(f"Modern CWL version [{cwl_version}].")
[docs]def lint_docker_image(tool_source, lint_ctx): _, containers, *_ = tool_source.parse_requirements_and_containers() if len(containers) == 0: lint_ctx.warn("Tool does not specify a DockerPull source.") else: identifier = containers[0].identifier lint_ctx.info(f"Tool will run in Docker image [{identifier}].")
[docs]def lint_description(tool_source, lint_ctx): help = tool_source.parse_help() if not help: lint_ctx.warn("Description of tool is empty or absent.") elif "TODO" in help: lint_ctx.warn("Help contains TODO text.")