Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/planemo/tool_lint.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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-1:000000000000 0:26e78fe6e8c4
1 from __future__ import absolute_import
2
3 from os.path import basename
4
5 from galaxy.tool_util.lint import lint_tool_source
6
7 from planemo.exit_codes import (
8 EXIT_CODE_GENERIC_FAILURE,
9 EXIT_CODE_OK,
10 )
11 from planemo.io import (
12 coalesce_return_codes,
13 error,
14 info,
15 )
16 from planemo.tools import (
17 is_tool_load_error,
18 yield_tool_sources_on_paths,
19 )
20
21 LINTING_TOOL_MESSAGE = "Linting tool %s"
22
23
24 def lint_tools_on_path(ctx, paths, lint_args, **kwds):
25 assert_tools = kwds.get("assert_tools", True)
26 recursive = kwds.get("recursive", False)
27 exit_codes = []
28 for (tool_path, tool_xml) in yield_tool_sources_on_paths(ctx, paths, recursive):
29 if handle_tool_load_error(tool_path, tool_xml):
30 exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
31 continue
32 info("Linting tool %s" % tool_path)
33 if not lint_tool_source(tool_xml, name=basename(tool_path), **lint_args):
34 error("Failed linting")
35 exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
36 else:
37 exit_codes.append(EXIT_CODE_OK)
38 return coalesce_return_codes(exit_codes, assert_at_least_one=assert_tools)
39
40
41 def handle_tool_load_error(tool_path, tool_xml):
42 """ Return True if tool_xml is tool load error (invalid XML), and
43 print a helpful error message.
44 """
45 is_error = False
46 if is_tool_load_error(tool_xml):
47 info("Could not lint %s due to malformed xml." % tool_path)
48 is_error = True
49 return is_error