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annotate env/lib/python3.7/site-packages/planemo/commands/cmd_lint.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 """Module describing the planemo ``lint`` command."""
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2 import click
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3
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4 from planemo import options
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5 from planemo.cli import command_function
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6 from planemo.lint import build_lint_args
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7 from planemo.tool_lint import lint_tools_on_path
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8
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9
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10 @click.command('lint')
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11 @options.optional_tools_arg(multiple=True, allow_uris=True)
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12 @options.report_level_option()
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13 @options.report_xunit()
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14 @options.fail_level_option()
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15 @options.skip_option()
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16 @options.lint_xsd_option()
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17 @options.recursive_option()
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18 @click.option(
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19 "--urls",
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20 is_flag=True,
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21 default=False,
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22 help="Check validity of URLs in XML files",
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23 )
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24 @click.option(
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25 "--doi",
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26 is_flag=True,
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27 default=False,
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28 help="Check validity of DOIs in XML files",
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29 )
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30 @click.option(
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31 "--conda_requirements",
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32 is_flag=True,
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33 default=False,
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34 help="Check tool requirements for availability in best practice Conda channels.",
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35 )
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36 @click.option(
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37 "biocontainer",
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38 "--biocontainer",
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39 "--biocontainers",
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40 is_flag=True,
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41 default=False,
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42 help="Check best practice BioContainer namespaces for a container definition applicable for this tool.",
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43 )
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44 # @click.option(
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45 # "--verify",
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46 # is_flag=True,
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47 # help="If an sha256sum is available, download the entire file AND validate it.",
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48 # default=False,
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49 # )
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50 @command_function
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51 def cli(ctx, uris, **kwds):
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52 """Check for common errors and best practices."""
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53 lint_args = build_lint_args(ctx, **kwds)
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54 exit_code = lint_tools_on_path(
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55 ctx,
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56 uris,
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57 lint_args,
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58 recursive=kwds["recursive"]
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59 )
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60
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61 # TODO: rearchitect XUnit.
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62 # if kwds['urls']:
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63 # collected_data, url_exit_code = check_urls(ctx, paths, **kwds)
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64 # if kwds.get('report_xunit', False):
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65 # with open(kwds['report_xunit'], 'w') as handle:
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66 # handle.write(build_report.template_data(
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67 # collected_data, template_name='xunit.tpl'))
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68 ctx.exit(exit_code)