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

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 """Module contianing the :class:`Engine` abstraction."""
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2
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3 import abc
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4 import json
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5 import os
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6 import tempfile
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7 from typing import List
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8
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9 from six import add_metaclass
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10
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11 from planemo.exit_codes import EXIT_CODE_UNSUPPORTED_FILE_TYPE
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12 from planemo.io import error
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13 from planemo.runnable import (
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14 cases,
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15 RunnableType,
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16 )
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17 from planemo.test.results import StructuredData
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18
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19
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20 @add_metaclass(abc.ABCMeta)
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21 class Engine(object):
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22 """Abstract description of an external process for running tools or workflows.
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23 """
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24
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25 @abc.abstractmethod
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26 def run(self, path, job_path):
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27 """Run a job using a compatible artifact (workflow or tool)."""
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28
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29 @abc.abstractmethod
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30 def cleanup(self):
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31 """Release any resources used to run/test with this engine."""
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32
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33 @abc.abstractmethod
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34 def test(self, runnables):
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35 """Test runnable artifacts (workflow or tool)."""
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36
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37
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38 class BaseEngine(Engine):
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39 """Base class providing context and keywords for Engine implementations."""
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40
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41 handled_runnable_types = [] # type: List[RunnableType]
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42
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43 def __init__(self, ctx, **kwds):
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44 """Store context and kwds."""
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45 self._ctx = ctx
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46 self._kwds = kwds
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47
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48 def can_run(self, runnable):
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49 """Use subclass's ``handled_runnable_types`` variable to infer ``can_run``."""
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50 return runnable.type in self.handled_runnable_types
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51
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52 def cleanup(self):
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53 """Default no-op cleanup method."""
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54
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55 def run(self, runnable, job_path):
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56 """Run a job using a compatible artifact (workflow or tool)."""
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57 self._check_can_run(runnable)
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58 run_response = self._run(runnable, job_path)
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59 return run_response
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60
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61 @abc.abstractmethod
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62 def _run(self, runnable, job_path):
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63 """Run a job using a compatible artifact (workflow or tool) wrapped as a runnable."""
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64
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65 def _check_can_run(self, runnable):
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66 if not self.can_run(runnable):
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67 template = "Engine type [%s] cannot execute [%s]s"
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68 message = template % (self.__class__, runnable.type)
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69 error(message)
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70 self._ctx.exit(EXIT_CODE_UNSUPPORTED_FILE_TYPE)
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71
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72 def _check_can_run_all(self, runnables):
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73 for runnable in runnables:
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74 self._check_can_run(runnable)
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75
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76 def test(self, runnables):
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77 """Test runnable artifacts (workflow or tool)."""
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78 self._check_can_run_all(runnables)
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79 test_cases = [t for tl in map(cases, runnables) for t in tl]
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80 test_results = self._collect_test_results(test_cases)
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81 tests = []
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82 for (test_case, run_response) in test_results:
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83 test_case_data = test_case.structured_test_data(run_response)
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84 tests.append(test_case_data)
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85 test_data = {
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86 'version': '0.1',
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87 'tests': tests,
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88 }
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89 structured_results = StructuredData(data=test_data)
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90 structured_results.calculate_summary_data()
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91 return structured_results
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92
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93 def _collect_test_results(self, test_cases):
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94 test_results = []
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95 for test_case in test_cases:
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96 self._ctx.vlog(
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97 "Running tests %s" % test_case
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98 )
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99 run_response = self._run_test_case(test_case)
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100 self._ctx.vlog(
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101 "Test case [%s] resulted in run response [%s]",
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102 test_case,
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103 run_response,
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104 )
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105 test_results.append((test_case, run_response))
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106 return test_results
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107
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108 def _run_test_case(self, test_case):
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109 runnable = test_case.runnable
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110 job_path = test_case.job_path
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111 tmp_path = None
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112 if job_path is None:
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113 job = test_case.job
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114 f = tempfile.NamedTemporaryFile(
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115 dir=test_case.tests_directory,
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116 suffix=".json",
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117 prefix="plnmotmptestjob",
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118 delete=False,
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119 mode="w+",
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120 )
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121 tmp_path = f.name
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122 job_path = tmp_path
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123 json.dump(job, f)
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124 f.close()
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125 try:
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126 run_response = self._run(runnable, job_path)
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127 finally:
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128 if tmp_path:
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129 os.remove(tmp_path)
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130 return run_response
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131
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132
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133 __all__ = (
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134 "Engine",
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135 "BaseEngine",
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136 )