Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/engine/galaxy.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 contianing the :class:`GalaxyEngine` implementation of :class:`Engine`."""
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2 from __future__ import absolute_import
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3
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4 import abc
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5 import contextlib
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6
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7 from galaxy.tool_util.verify import interactor
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8
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9 from planemo.galaxy.activity import execute
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10 from planemo.galaxy.config import external_galaxy_config
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11 from planemo.galaxy.serve import serve_daemon
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12 from planemo.runnable import RunnableType
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13 from .interface import BaseEngine
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14
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15
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16 class GalaxyEngine(BaseEngine):
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17 """An :class:`Engine` implementation backed by a managed Galaxy.
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18
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19 More information on Galaxy can be found at http://galaxyproject.org/.
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20 """
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21
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22 __metaclass__ = abc.ABCMeta
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23
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24 handled_runnable_types = [
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25 RunnableType.cwl_tool,
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26 RunnableType.cwl_workflow,
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27 RunnableType.galaxy_workflow,
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28 RunnableType.galaxy_tool,
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29 RunnableType.galaxy_datamanager,
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30 ]
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31
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32 def _run(self, runnable, job_path):
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33 """Run CWL job in Galaxy."""
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34 self._ctx.vlog("Serving artifact [%s] with Galaxy." % (runnable,))
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35 with self.ensure_runnables_served([runnable]) as config:
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36 self._ctx.vlog("Running job path [%s]" % job_path)
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37 run_response = execute(self._ctx, config, runnable, job_path, **self._kwds)
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38
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39 return run_response
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40
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41 @abc.abstractmethod
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42 def ensure_runnables_served(self, runnables):
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43 """Use a context manager and describe Galaxy instance with runnables being served."""
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44
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45 def _run_test_case(self, test_case):
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46 if hasattr(test_case, "job_path"):
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47 # Simple file-based job path.
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48 return super(GalaxyEngine, self)._run_test_case(test_case)
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49 else:
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50 with self.ensure_runnables_served([test_case.runnable]) as config:
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51 galaxy_interactor_kwds = {
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52 "galaxy_url": config.galaxy_url,
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53 "master_api_key": config.master_api_key,
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54 "api_key": config.user_api_key,
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55 "keep_outputs_dir": "", # TODO: this...
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56 }
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57 tool_id = test_case.tool_id
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58 test_index = test_case.test_index
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59 tool_version = test_case.tool_version
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60 galaxy_interactor = interactor.GalaxyInteractorApi(**galaxy_interactor_kwds)
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61
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62 test_results = []
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63
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64 def _register_job_data(job_data):
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65 test_results.append({
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66 'id': tool_id + "-" + str(test_index),
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67 'has_data': True,
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68 'data': job_data,
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69 })
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70
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71 verbose = self._ctx.verbose
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72 try:
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73 if verbose:
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74 # TODO: this is pretty hacky, it'd be better to send a stream
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75 # and capture the output information somehow.
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76 interactor.VERBOSE_GALAXY_ERRORS = True
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77
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78 interactor.verify_tool(
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79 tool_id,
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80 galaxy_interactor,
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81 test_index=test_index,
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82 tool_version=tool_version,
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83 register_job_data=_register_job_data,
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84 quiet=not verbose,
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85 )
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86 except Exception:
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87 pass
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88
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89 return test_results[0]
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90
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91
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92 class LocalManagedGalaxyEngine(GalaxyEngine):
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93 """An :class:`Engine` implementation backed by a managed Galaxy.
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94
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95 More information on Galaxy can be found at http://galaxyproject.org/.
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96 """
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97
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98 @contextlib.contextmanager
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99 def ensure_runnables_served(self, runnables):
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100 # TODO: define an interface for this - not everything in config would make sense for a
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101 # pre-existing Galaxy interface.
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102 with serve_daemon(self._ctx, runnables, **self._serve_kwds()) as config:
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103 yield config
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104
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105 def _serve_kwds(self):
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106 return self._kwds.copy()
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107
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108
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109 class DockerizedManagedGalaxyEngine(LocalManagedGalaxyEngine):
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110 """An :class:`Engine` implementation backed by Galaxy running in Docker.
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111
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112 More information on Galaxy can be found at http://galaxyproject.org/.
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113 """
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114
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115 def _serve_kwds(self):
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116 serve_kwds = self._kwds.copy()
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117 serve_kwds["dockerize"] = True
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118 return serve_kwds
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119
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120
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121 class ExternalGalaxyEngine(GalaxyEngine):
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122 """An :class:`Engine` implementation backed by an external Galaxy instance.
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123 """
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124
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125 @contextlib.contextmanager
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126 def ensure_runnables_served(self, runnables):
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127 # TODO: ensure tools are available
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128 with external_galaxy_config(self._ctx, runnables, **self._kwds) as config:
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129 config.install_workflows()
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130 yield config
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131
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132
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133 __all__ = (
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134 "DockerizedManagedGalaxyEngine",
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135 "ExternalGalaxyEngine",
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136 "LocalManagedGalaxyEngine",
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137 )