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annotate env/lib/python3.7/site-packages/planemo/commands/cmd_serve.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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26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1 """Module describing the planemo ``serve`` 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.galaxy import galaxy_serve
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7 from planemo.runnable import for_paths
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8 from planemo.tools import uris_to_paths
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9
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10
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11 @click.command('serve')
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12 @options.optional_tools_arg(multiple=True, allow_uris=True)
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13 @options.galaxy_serve_options()
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14 @options.enable_cwl_option()
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15 @options.galaxy_cwl_root_option()
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16 @command_function
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17 def cli(ctx, uris, **kwds):
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18 """Launch Galaxy instance with specified tools.
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19
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20 The Galaxy tool panel will include just the referenced tool or tools (by
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21 default all the tools in the current working directory) and the upload
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22 tool.
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23
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24 planemo will search parent directories to see if any is a Galaxy instance
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25 - but one can pick the Galaxy instance to use with the ``--galaxy_root``
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26 option or force planemo to download a disposable instance with the
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27 ``--install_galaxy`` flag.
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28
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29 ``planemo`` will run the Galaxy instance in an existing virtualenv if one
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30 exists in a ``.venv`` directory in the specified ``--galaxy_root``.
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31 Otherwise, the Galaxy instance will run in a clean virtualenv created in
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32 ``/tmp``.
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33
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34 ``planemo`` uses temporarily generated config files and environment
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35 variables to attempt to shield this execution of Galaxy from manually
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36 launched runs against that same Galaxy root - but this may not be bullet
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37 proof yet, so please be careful and do not try this against a production
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38 Galaxy instance.
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39 """
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40 paths = uris_to_paths(ctx, uris)
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41 runnables = for_paths(paths)
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42 kwds['galaxy_skip_client_build'] = False
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43 galaxy_serve(ctx, runnables, **kwds)