Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/commands/cmd_run.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 """Module describing the planemo ``cwl_run`` command."""
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2 from __future__ import print_function
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3
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4 import json
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5
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6 import click
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7 from galaxy.util import unicodify
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8
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9 from planemo import options
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10 from planemo.cli import command_function
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11 from planemo.engine import engine_context
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12 from planemo.io import warn
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13 from planemo.tools import uri_to_path
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14
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15
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16 @click.command('run')
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17 @options.required_tool_arg(allow_uris=True)
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18 @options.required_job_arg()
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19 @options.galaxy_run_options()
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20 @options.galaxy_config_options()
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21 @options.enable_cwl_option()
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22 @options.galaxy_cwl_root_option()
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23 @options.run_output_directory_option()
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24 @options.run_output_json_option()
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25 @options.engine_options()
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26 @command_function
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27 def cli(ctx, uri, job_path, **kwds):
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28 """Planemo command for running tools and jobs.
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29
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30 \b
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31 % planemo run cat1-tool.cwl cat-job.json
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32 """
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33 path = uri_to_path(ctx, uri)
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34 # TODO: convert UI to runnable and do a better test of cwl.
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35 is_cwl = path.endswith(".cwl")
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36 kwds["cwl"] = is_cwl
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37 if kwds.get("engine", None) is None:
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38 kwds["engine"] = "galaxy" if not is_cwl else "cwltool"
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39
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40 with engine_context(ctx, **kwds) as engine:
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41 run_result = engine.run(path, job_path)
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42
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43 if not run_result.was_successful:
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44 warn("Run failed [%s]" % unicodify(run_result))
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45 ctx.exit(1)
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46
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47 outputs_dict = run_result.outputs_dict
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48 print(outputs_dict)
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49 output_json = kwds.get("output_json", None)
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50 if output_json:
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51 with open(output_json, "w") as f:
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52 json.dump(outputs_dict, f)
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53
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54 return 0