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annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/linters/outputs.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 """This module contains a linting functions for tool outputs."""
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2 from ._util import is_valid_cheetah_placeholder
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3
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4
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5 def lint_output(tool_xml, lint_ctx):
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6 """Check output elements, ensure there is at least one and check attributes."""
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7 outputs = tool_xml.findall("./outputs")
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8 if len(outputs) == 0:
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9 lint_ctx.warn("Tool contains no outputs section, most tools should produce outputs.")
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10 if len(outputs) > 1:
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11 lint_ctx.warn("Tool contains multiple output sections, behavior undefined.")
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12
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13 num_outputs = 0
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14 if len(outputs) == 0:
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15 lint_ctx.warn("No outputs found")
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16 return
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17
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18 for output in list(outputs[0]):
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19 if output.tag not in ["data", "collection"]:
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20 lint_ctx.warn("Unknown element found in outputs [%s]" % output.tag)
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21 continue
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22 num_outputs += 1
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23 if "name" not in output.attrib:
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24 lint_ctx.warn("Tool output doesn't define a name - this is likely a problem.")
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25 else:
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26 if not is_valid_cheetah_placeholder(output.attrib["name"]):
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27 lint_ctx.warn("Tool output name [%s] is not a valid Cheetah placeholder.", output.attrib["name"])
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28
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29 format_set = False
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30 if output.tag == "data":
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31 if __check_format(output, lint_ctx):
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32 format_set = True
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33 elif "auto_format" in output.attrib and output.attrib["auto_format"]:
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34 format_set = True
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35
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36 elif output.tag == "collection":
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37 if "type" not in output.attrib:
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38 lint_ctx.warn("Collection output with undefined 'type' found.")
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39 if "structured_like" in output.attrib and "inherit_format" in output.attrib:
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40 format_set = True
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41 if "format_source" in output.attrib:
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42 format_set = True
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43 for sub in output:
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44 if __check_pattern(sub):
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45 format_set = True
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46 elif __check_format(sub, lint_ctx):
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47 format_set = True
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48
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49 if not format_set:
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50 lint_ctx.warn("Tool %s output %s doesn't define an output format." % (output.tag, output.attrib.get("name", "with missing name")))
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51
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52 lint_ctx.info("%d outputs found.", num_outputs)
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53
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54
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55 def __check_format(node, lint_ctx):
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56 """
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57 check if format/ext attribute is set in a given node
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58 issue a warning if the value is input
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59 return true (node defines format/ext) / false (else)
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60 """
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61 fmt = node.attrib.get("format", node.attrib.get("ext", None))
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62 if fmt == "input":
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63 lint_ctx.warn("Using format='input' on %s, format_source attribute is less ambiguous and should be used instead." % node.tag)
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64 return fmt is not None
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65
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66
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67 def __check_pattern(node):
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68 """
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69 check if pattern attribute is set and defines the extension
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70 """
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71 if node.tag != "discover_datasets":
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72 return False
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73 if "pattern" not in node.attrib:
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74 return False
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75 if node.attrib["pattern"] == "__default__":
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76 return True
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77 if "ext" in node.attrib["pattern"] and node.attrib["pattern"].startswith("__") and node.attrib["pattern"].endswith("__"):
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78 return True