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annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/cwl.py @ 1:56ad4e20f292 draft

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