Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/commands/cmd_test.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 ``test`` 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.engine import (
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7 engine_context,
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8 )
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9 from planemo.galaxy import galaxy_config
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10 from planemo.galaxy.config import _find_test_data
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11 from planemo.galaxy.test import (
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12 handle_reports_and_summary,
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13 run_in_config,
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14 )
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15 from planemo.io import temp_directory
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16 from planemo.runnable import (
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17 for_paths,
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18 RunnableType,
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19 )
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20
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21
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22 @click.command('test')
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23 @options.optional_tools_arg(multiple=True)
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24 @click.option(
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25 "--failed",
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26 is_flag=True,
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27 help="Re-run only failed tests. This command will read "
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28 "tool_test_output.json to determine which tests failed so this "
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29 "file must have been produced with the same set of tool ids "
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30 "previously.",
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31 default=False,
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32 )
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33 @click.option(
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34 "--polling_backoff",
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35 type=int,
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36 help="Poll resources with an increasing interval between requests. "
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37 "Useful when testing against remote and/or production "
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38 "instances to limit generated traffic.",
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39 default="0",
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40 )
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41 @click.option(
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42 "--history_name",
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43 help="Name for history (if a history is generated as part of testing.)"
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44 )
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45 @options.galaxy_target_options()
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46 @options.galaxy_config_options()
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47 @options.test_options()
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48 @options.engine_options()
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49 @command_function
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50 def cli(ctx, paths, **kwds):
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51 """Run specified tool's tests within Galaxy.
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52
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53 All referenced tools (by default all the tools in the current working
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54 directory) will be tested and the results quickly summarized.
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55
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56 To run these tests planemo needs a Galaxy instance to utilize, planemo
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57 will search parent directories to see if any is a Galaxy instance
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58 - but one can pick the Galaxy instance to use with the --galaxy_root
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59 option or force planemo to download a disposable instance with the
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60 ``--install_galaxy`` flag.
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61
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62 In additon to to quick summary printed to the console - various detailed
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63 output summaries can be configured. ``tool_test_output.html`` (settable
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64 via ``--test_output``) will contain a human consumable HTML report
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65 describing the test run. A JSON file (settable via ``--test_output_json``
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66 and defaulting to ``tool_test_output.json``) will also be created. These
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67 files can can be disabled by passing in empty arguments or globally by
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68 setting the values ``default_test_output`` and/or
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69 ``default_test_output_json`` in ``~/.planemo.yml`` to ``null``. For
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70 continuous integration testing a xUnit-style report can be confiured using
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71 the ``--test_output_xunit``.
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72
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73 planemo uses temporarily generated config files and environment variables
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74 to attempt to shield this execution of Galaxy from manually launched runs
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75 against that same Galaxy root - but this may not be bullet proof yet so
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76 please careful and do not try this against production Galaxy instances.
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77 """
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78 with temp_directory(dir=ctx.planemo_directory) as temp_path:
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79 # Create temp dir(s) outside of temp, docker can't mount $TEMPDIR on OSX
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80 runnables = for_paths(paths, temp_path=temp_path)
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81 is_cwl = all(r.type in {RunnableType.cwl_tool, RunnableType.cwl_workflow} for r in runnables)
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82 if kwds.get("engine") is None:
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83 kwds["engine"] = "galaxy" if not is_cwl else "cwltool"
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84
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85 engine_type = kwds["engine"]
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86 test_engine_testable = {RunnableType.galaxy_tool, RunnableType.galaxy_datamanager, RunnableType.directory}
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87 enable_test_engines = any(r.type not in test_engine_testable for r in runnables)
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88 enable_test_engines = enable_test_engines or engine_type != "galaxy"
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89 if enable_test_engines:
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90 ctx.vlog("Using test engine type %s" % engine_type)
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91 with engine_context(ctx, **kwds) as engine:
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92 test_data = engine.test(runnables)
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93 return_value = handle_reports_and_summary(ctx, test_data.structured_data, kwds=kwds)
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94 else:
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95 ctx.vlog("Running traditional Galaxy tool tests using run_tests.sh in Galaxy root %s" % engine_type)
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96 kwds["for_tests"] = True
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97 if kwds.get('update_test_data'):
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98 non_copied_runnables = for_paths(paths)
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99 kwds['test_data_target_dir'] = _find_test_data(non_copied_runnables, **kwds)
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100 with galaxy_config(ctx, runnables, **kwds) as config:
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101 return_value = run_in_config(ctx, config, **kwds)
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102
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103 ctx.exit(return_value)