annotate env/lib/python3.9/site-packages/planemo/engine/galaxy.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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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 from six import add_metaclass
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9
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10 from planemo.galaxy.activity import execute
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11 from planemo.galaxy.config import external_galaxy_config
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12 from planemo.galaxy.serve import serve_daemon
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13 from planemo.runnable import RunnableType
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14 from .interface import BaseEngine
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15
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16
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17 @add_metaclass(abc.ABCMeta)
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18 class GalaxyEngine(BaseEngine):
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19 """An :class:`Engine` implementation backed by a managed Galaxy.
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20
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21 More information on Galaxy can be found at http://galaxyproject.org/.
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22 """
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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 if self._ctx.verbose:
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38 self._ctx.log("Running Galaxy with API configuration [%s]" % config.user_api_config)
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39 run_response = execute(self._ctx, config, runnable, job_path, **self._kwds)
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40
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41 return run_response
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42
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43 @abc.abstractmethod
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44 def ensure_runnables_served(self, runnables):
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45 """Use a context manager and describe Galaxy instance with runnables being served."""
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46
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47 def _run_test_case(self, test_case):
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48 if hasattr(test_case, "job_path"):
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49 # Simple file-based job path.
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50 return super(GalaxyEngine, self)._run_test_case(test_case)
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51 else:
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52 with self.ensure_runnables_served([test_case.runnable]) as config:
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53 galaxy_interactor_kwds = {
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54 "galaxy_url": config.galaxy_url,
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55 "master_api_key": config.master_api_key,
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56 "api_key": config.user_api_key,
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57 "keep_outputs_dir": "", # TODO: this...
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58 }
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59 tool_id = test_case.tool_id
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60 test_index = test_case.test_index
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61 tool_version = test_case.tool_version
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62 galaxy_interactor = interactor.GalaxyInteractorApi(**galaxy_interactor_kwds)
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63
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64 test_results = []
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65
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66 def _register_job_data(job_data):
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67 test_results.append({
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68 'id': tool_id + "-" + str(test_index),
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69 'has_data': True,
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70 'data': job_data,
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71 })
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72
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73 verbose = self._ctx.verbose
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74 try:
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75 if verbose:
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76 # TODO: this is pretty hacky, it'd be better to send a stream
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77 # and capture the output information somehow.
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78 interactor.VERBOSE_GALAXY_ERRORS = True
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79
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80 interactor.verify_tool(
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81 tool_id,
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82 galaxy_interactor,
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83 test_index=test_index,
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84 tool_version=tool_version,
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85 register_job_data=_register_job_data,
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86 quiet=not verbose,
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87 )
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88 except Exception:
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89 pass
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90
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91 return test_results[0]
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92
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93
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94 class LocalManagedGalaxyEngine(GalaxyEngine):
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95 """An :class:`Engine` implementation backed by a managed Galaxy.
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96
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97 More information on Galaxy can be found at http://galaxyproject.org/.
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98 """
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99
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100 @contextlib.contextmanager
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101 def ensure_runnables_served(self, runnables):
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102 # TODO: define an interface for this - not everything in config would make sense for a
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103 # pre-existing Galaxy interface.
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104 with serve_daemon(self._ctx, runnables, **self._serve_kwds()) as config:
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105 yield config
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106
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107 def _serve_kwds(self):
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108 return self._kwds.copy()
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109
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110
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111 class DockerizedManagedGalaxyEngine(LocalManagedGalaxyEngine):
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112 """An :class:`Engine` implementation backed by Galaxy running in Docker.
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113
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114 More information on Galaxy can be found at http://galaxyproject.org/.
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115 """
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116
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117 def _serve_kwds(self):
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118 serve_kwds = self._kwds.copy()
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119 serve_kwds["dockerize"] = True
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120 return serve_kwds
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121
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122
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123 class ExternalGalaxyEngine(GalaxyEngine):
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124 """An :class:`Engine` implementation backed by an external Galaxy instance.
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125 """
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126
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127 @contextlib.contextmanager
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128 def ensure_runnables_served(self, runnables):
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129 # TODO: ensure tools are available
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130 with external_galaxy_config(self._ctx, runnables, **self._kwds) as config:
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131 config.install_workflows()
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132 yield config
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133
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134
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135 __all__ = (
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136 "DockerizedManagedGalaxyEngine",
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137 "ExternalGalaxyEngine",
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138 "LocalManagedGalaxyEngine",
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139 )