Mercurial > repos > shellac > guppy_basecaller
comparison env/lib/python3.7/site-packages/planemo/commands/cmd_lint.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
| author | shellac |
|---|---|
| date | Sat, 02 May 2020 07:14:21 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:26e78fe6e8c4 |
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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.lint import build_lint_args | |
| 7 from planemo.tool_lint import lint_tools_on_path | |
| 8 | |
| 9 | |
| 10 @click.command('lint') | |
| 11 @options.optional_tools_arg(multiple=True, allow_uris=True) | |
| 12 @options.report_level_option() | |
| 13 @options.report_xunit() | |
| 14 @options.fail_level_option() | |
| 15 @options.skip_option() | |
| 16 @options.lint_xsd_option() | |
| 17 @options.recursive_option() | |
| 18 @click.option( | |
| 19 "--urls", | |
| 20 is_flag=True, | |
| 21 default=False, | |
| 22 help="Check validity of URLs in XML files", | |
| 23 ) | |
| 24 @click.option( | |
| 25 "--doi", | |
| 26 is_flag=True, | |
| 27 default=False, | |
| 28 help="Check validity of DOIs in XML files", | |
| 29 ) | |
| 30 @click.option( | |
| 31 "--conda_requirements", | |
| 32 is_flag=True, | |
| 33 default=False, | |
| 34 help="Check tool requirements for availability in best practice Conda channels.", | |
| 35 ) | |
| 36 @click.option( | |
| 37 "biocontainer", | |
| 38 "--biocontainer", | |
| 39 "--biocontainers", | |
| 40 is_flag=True, | |
| 41 default=False, | |
| 42 help="Check best practice BioContainer namespaces for a container definition applicable for this tool.", | |
| 43 ) | |
| 44 # @click.option( | |
| 45 # "--verify", | |
| 46 # is_flag=True, | |
| 47 # help="If an sha256sum is available, download the entire file AND validate it.", | |
| 48 # default=False, | |
| 49 # ) | |
| 50 @command_function | |
| 51 def cli(ctx, uris, **kwds): | |
| 52 """Check for common errors and best practices.""" | |
| 53 lint_args = build_lint_args(ctx, **kwds) | |
| 54 exit_code = lint_tools_on_path( | |
| 55 ctx, | |
| 56 uris, | |
| 57 lint_args, | |
| 58 recursive=kwds["recursive"] | |
| 59 ) | |
| 60 | |
| 61 # TODO: rearchitect XUnit. | |
| 62 # if kwds['urls']: | |
| 63 # collected_data, url_exit_code = check_urls(ctx, paths, **kwds) | |
| 64 # if kwds.get('report_xunit', False): | |
| 65 # with open(kwds['report_xunit'], 'w') as handle: | |
| 66 # handle.write(build_report.template_data( | |
| 67 # collected_data, template_name='xunit.tpl')) | |
| 68 ctx.exit(exit_code) |