Mercurial > repos > shellac > sam_consensus_v3
view 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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"""Module describing the planemo ``lint`` command.""" import click from planemo import options from planemo.cli import command_function from planemo.tool_lint import build_tool_lint_args, lint_tools_on_path @click.command('lint') @options.optional_tools_arg(multiple=True, allow_uris=True) @options.report_level_option() @options.report_xunit() @options.fail_level_option() @options.skip_option() @options.lint_xsd_option() @options.recursive_option() @click.option( "--urls", is_flag=True, default=False, help="Check validity of URLs in XML files", ) @click.option( "--doi", is_flag=True, default=False, help="Check validity of DOIs in XML files", ) @click.option( "--conda_requirements", is_flag=True, default=False, help="Check tool requirements for availability in best practice Conda channels.", ) @click.option( "biocontainer", "--biocontainer", "--biocontainers", is_flag=True, default=False, help="Check best practice BioContainer namespaces for a container definition applicable for this tool.", ) # @click.option( # "--verify", # is_flag=True, # help="If an sha256sum is available, download the entire file AND validate it.", # default=False, # ) @command_function def cli(ctx, uris, **kwds): """Check for common errors and best practices.""" lint_args = build_tool_lint_args(ctx, **kwds) exit_code = lint_tools_on_path( ctx, uris, lint_args, recursive=kwds["recursive"] ) # TODO: rearchitect XUnit. # if kwds['urls']: # collected_data, url_exit_code = check_urls(ctx, paths, **kwds) # if kwds.get('report_xunit', False): # with open(kwds['report_xunit'], 'w') as handle: # handle.write(build_report.template_data( # collected_data, template_name='xunit.tpl')) ctx.exit(exit_code)