Mercurial > repos > shellac > sam_consensus_v3
comparison env/lib/python3.9/site-packages/planemo/commands/cmd_lint.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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-1:000000000000 | 0:4f3585e2f14b |
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1 """Module describing the planemo ``lint`` command.""" | |
2 import click | |
3 | |
4 from planemo import options | |
5 from planemo.cli import command_function | |
6 from planemo.tool_lint import build_tool_lint_args, lint_tools_on_path | |
7 | |
8 | |
9 @click.command('lint') | |
10 @options.optional_tools_arg(multiple=True, allow_uris=True) | |
11 @options.report_level_option() | |
12 @options.report_xunit() | |
13 @options.fail_level_option() | |
14 @options.skip_option() | |
15 @options.lint_xsd_option() | |
16 @options.recursive_option() | |
17 @click.option( | |
18 "--urls", | |
19 is_flag=True, | |
20 default=False, | |
21 help="Check validity of URLs in XML files", | |
22 ) | |
23 @click.option( | |
24 "--doi", | |
25 is_flag=True, | |
26 default=False, | |
27 help="Check validity of DOIs in XML files", | |
28 ) | |
29 @click.option( | |
30 "--conda_requirements", | |
31 is_flag=True, | |
32 default=False, | |
33 help="Check tool requirements for availability in best practice Conda channels.", | |
34 ) | |
35 @click.option( | |
36 "biocontainer", | |
37 "--biocontainer", | |
38 "--biocontainers", | |
39 is_flag=True, | |
40 default=False, | |
41 help="Check best practice BioContainer namespaces for a container definition applicable for this tool.", | |
42 ) | |
43 # @click.option( | |
44 # "--verify", | |
45 # is_flag=True, | |
46 # help="If an sha256sum is available, download the entire file AND validate it.", | |
47 # default=False, | |
48 # ) | |
49 @command_function | |
50 def cli(ctx, uris, **kwds): | |
51 """Check for common errors and best practices.""" | |
52 lint_args = build_tool_lint_args(ctx, **kwds) | |
53 exit_code = lint_tools_on_path( | |
54 ctx, | |
55 uris, | |
56 lint_args, | |
57 recursive=kwds["recursive"] | |
58 ) | |
59 | |
60 # TODO: rearchitect XUnit. | |
61 # if kwds['urls']: | |
62 # collected_data, url_exit_code = check_urls(ctx, paths, **kwds) | |
63 # if kwds.get('report_xunit', False): | |
64 # with open(kwds['report_xunit'], 'w') as handle: | |
65 # handle.write(build_report.template_data( | |
66 # collected_data, template_name='xunit.tpl')) | |
67 ctx.exit(exit_code) |