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comparison 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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0:d30785e31577 1:56ad4e20f292
1 """This module contains a linting functions for tool outputs."""
2 from ._util import is_valid_cheetah_placeholder
3
4
5 def lint_output(tool_xml, lint_ctx):
6 """Check output elements, ensure there is at least one and check attributes."""
7 outputs = tool_xml.findall("./outputs")
8 if len(outputs) == 0:
9 lint_ctx.warn("Tool contains no outputs section, most tools should produce outputs.")
10 if len(outputs) > 1:
11 lint_ctx.warn("Tool contains multiple output sections, behavior undefined.")
12
13 num_outputs = 0
14 if len(outputs) == 0:
15 lint_ctx.warn("No outputs found")
16 return
17
18 for output in list(outputs[0]):
19 if output.tag not in ["data", "collection"]:
20 lint_ctx.warn("Unknown element found in outputs [%s]" % output.tag)
21 continue
22 num_outputs += 1
23 if "name" not in output.attrib:
24 lint_ctx.warn("Tool output doesn't define a name - this is likely a problem.")
25 else:
26 if not is_valid_cheetah_placeholder(output.attrib["name"]):
27 lint_ctx.warn("Tool output name [%s] is not a valid Cheetah placeholder.", output.attrib["name"])
28
29 format_set = False
30 if output.tag == "data":
31 if __check_format(output, lint_ctx):
32 format_set = True
33 elif "auto_format" in output.attrib and output.attrib["auto_format"]:
34 format_set = True
35
36 elif output.tag == "collection":
37 if "type" not in output.attrib:
38 lint_ctx.warn("Collection output with undefined 'type' found.")
39 if "structured_like" in output.attrib and "inherit_format" in output.attrib:
40 format_set = True
41 if "format_source" in output.attrib:
42 format_set = True
43 for sub in output:
44 if __check_pattern(sub):
45 format_set = True
46 elif __check_format(sub, lint_ctx):
47 format_set = True
48
49 if not format_set:
50 lint_ctx.warn("Tool %s output %s doesn't define an output format." % (output.tag, output.attrib.get("name", "with missing name")))
51
52 lint_ctx.info("%d outputs found.", num_outputs)
53
54
55 def __check_format(node, lint_ctx):
56 """
57 check if format/ext attribute is set in a given node
58 issue a warning if the value is input
59 return true (node defines format/ext) / false (else)
60 """
61 fmt = node.attrib.get("format", node.attrib.get("ext", None))
62 if fmt == "input":
63 lint_ctx.warn("Using format='input' on %s, format_source attribute is less ambiguous and should be used instead." % node.tag)
64 return fmt is not None
65
66
67 def __check_pattern(node):
68 """
69 check if pattern attribute is set and defines the extension
70 """
71 if node.tag != "discover_datasets":
72 return False
73 if "pattern" not in node.attrib:
74 return False
75 if node.attrib["pattern"] == "__default__":
76 return True
77 if "ext" in node.attrib["pattern"] and node.attrib["pattern"].startswith("__") and node.attrib["pattern"].endswith("__"):
78 return True