Mercurial > repos > shellac > sam_consensus_v3
view env/lib/python3.9/site-packages/galaxy/tool_util/linters/cwl.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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"""Linter for CWL tools.""" lint_tool_types = ["cwl"] from galaxy.tool_util.cwl.schema import schema_loader 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("Failed to valdiate CWL artifact [%s]", validation_exception) else: lint_ctx.info("CWL appears to be valid.") 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("CWL version [%s] is unknown, we recommend the v1.0 the stable release." % cwl_version) else: lint_ctx.info("Modern CWL version [%s]", cwl_version) 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("Tool will run in Docker image [%s]." % identifier) 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.")