Mercurial > repos > guerler > springsuite
comparison planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/cwl.py @ 1:56ad4e20f292 draft
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
| author | guerler |
|---|---|
| date | Fri, 31 Jul 2020 00:32:28 -0400 |
| parents | |
| children |
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| 0:d30785e31577 | 1:56ad4e20f292 |
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| 1 """Linter for CWL tools.""" | |
| 2 | |
| 3 lint_tool_types = ["cwl"] | |
| 4 | |
| 5 from galaxy.tool_util.cwl.schema import schema_loader | |
| 6 | |
| 7 | |
| 8 def lint_cwl_validation(tool_source, lint_ctx): | |
| 9 """Determine in CWL tool validates against spec.""" | |
| 10 raw_reference = schema_loader.raw_process_reference(tool_source._source_path) | |
| 11 validation_exception = None | |
| 12 try: | |
| 13 schema_loader.process_definition(raw_reference) | |
| 14 except Exception as e: | |
| 15 validation_exception = e | |
| 16 if validation_exception: | |
| 17 lint_ctx.error("Failed to valdiate CWL artifact [%s]", validation_exception) | |
| 18 else: | |
| 19 lint_ctx.info("CWL appears to be valid.") | |
| 20 | |
| 21 | |
| 22 def lint_new_draft(tool_source, lint_ctx): | |
| 23 """Determine in CWL tool is valid, modern draft.""" | |
| 24 raw_reference = schema_loader.raw_process_reference(tool_source._source_path) | |
| 25 cwl_version = raw_reference.process_object.get("cwlVersion", None) | |
| 26 if cwl_version is None: | |
| 27 lint_ctx.error("CWL file does not contain a 'cwlVersion'") | |
| 28 if cwl_version not in ["v1.0"]: | |
| 29 lint_ctx.warn("CWL version [%s] is unknown, we recommend the v1.0 the stable release." % cwl_version) | |
| 30 else: | |
| 31 lint_ctx.info("Modern CWL version [%s]", cwl_version) | |
| 32 | |
| 33 | |
| 34 def lint_docker_image(tool_source, lint_ctx): | |
| 35 _, containers = tool_source.parse_requirements_and_containers() | |
| 36 if len(containers) == 0: | |
| 37 lint_ctx.warn("Tool does not specify a DockerPull source.") | |
| 38 else: | |
| 39 identifier = containers[0].identifier | |
| 40 lint_ctx.info("Tool will run in Docker image [%s]." % identifier) | |
| 41 | |
| 42 | |
| 43 def lint_description(tool_source, lint_ctx): | |
| 44 help = tool_source.parse_help() | |
| 45 if not help: | |
| 46 lint_ctx.warn("Description of tool is empty or absent.") | |
| 47 elif "TODO" in help: | |
| 48 lint_ctx.warn("Help contains TODO text.") |