Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/engine/interface.py @ 4:79f47841a781 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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:`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
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8 from planemo.exit_codes import EXIT_CODE_UNSUPPORTED_FILE_TYPE
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9 from planemo.io import error
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10 from planemo.runnable import (
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11 cases,
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12 for_path,
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13 )
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14 from planemo.test.results import StructuredData
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15
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16
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17 class Engine(object):
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18 """Abstract description of an external process for running tools or workflows.
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19 """
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20
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21 __metaclass__ = abc.ABCMeta
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22
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23 @abc.abstractmethod
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24 def run(self, path, job_path):
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25 """Run a job using a compatible artifact (workflow or tool)."""
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26
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27 @abc.abstractmethod
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28 def cleanup(self):
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29 """Release any resources used to run/test with this engine."""
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30
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31 @abc.abstractmethod
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32 def test(self, runnables):
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33 """Test runnable artifacts (workflow or tool)."""
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34
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35
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36 class BaseEngine(Engine):
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37 """Base class providing context and keywords for Engine implementations."""
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38
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39 handled_runnable_types = []
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40
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41 def __init__(self, ctx, **kwds):
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42 """Store context and kwds."""
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43 self._ctx = ctx
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44 self._kwds = kwds
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45
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46 def can_run(self, runnable):
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47 """Use subclass's ``handled_runnable_types`` variable to infer ``can_run``."""
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48 return runnable.type in self.handled_runnable_types
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49
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50 def cleanup(self):
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51 """Default no-op cleanup method."""
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52
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53 def run(self, path, job_path):
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54 """Run a job using a compatible artifact (workflow or tool)."""
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55 runnable = for_path(path)
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56 self._check_can_run(runnable)
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57 run_response = self._run(runnable, job_path)
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58 return run_response
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59
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60 @abc.abstractmethod
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61 def _run(self, runnable, job_path):
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62 """Run a job using a compatible artifact (workflow or tool) wrapped as a runnable."""
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63
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64 def _check_can_run(self, runnable):
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65 if not self.can_run(runnable):
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66 template = "Engine type [%s] cannot execute [%s]s"
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67 message = template % (self.__class__, runnable.type)
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68 error(message)
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69 self._ctx.exit(EXIT_CODE_UNSUPPORTED_FILE_TYPE)
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70
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71 def _check_can_run_all(self, runnables):
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72 for runnable in runnables:
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73 self._check_can_run(runnable)
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74
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75 def test(self, runnables):
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76 """Test runnable artifacts (workflow or tool)."""
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77 self._check_can_run_all(runnables)
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78 test_cases = [t for tl in map(cases, runnables) for t in tl]
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79 test_results = self._collect_test_results(test_cases)
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80 tests = []
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81 for (test_case, run_response) in test_results:
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82 test_case_data = test_case.structured_test_data(run_response)
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83 tests.append(test_case_data)
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84 test_data = {
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85 'version': '0.1',
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86 'tests': tests,
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87 }
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88 structured_results = StructuredData(data=test_data)
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89 structured_results.calculate_summary_data()
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90 return structured_results
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91
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92 def _collect_test_results(self, test_cases):
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93 test_results = []
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94 for test_case in test_cases:
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95 self._ctx.vlog(
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96 "Running tests %s" % test_case
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97 )
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98 run_response = self._run_test_case(test_case)
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99 self._ctx.vlog(
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100 "Test case [%s] resulted in run response [%s]",
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101 test_case,
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102 run_response,
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103 )
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104 test_results.append((test_case, run_response))
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105 return test_results
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106
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107 def _run_test_case(self, test_case):
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108 runnable = test_case.runnable
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109 job_path = test_case.job_path
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110 tmp_path = None
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111 if job_path is None:
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112 job = test_case.job
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113 f = tempfile.NamedTemporaryFile(
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114 dir=test_case.tests_directory,
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115 suffix=".json",
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116 prefix="plnmotmptestjob",
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117 delete=False,
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118 mode="w+",
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119 )
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120 tmp_path = f.name
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121 job_path = tmp_path
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122 json.dump(job, f)
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123 f.close()
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124 try:
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125 run_response = self._run(runnable, job_path)
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126 finally:
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127 if tmp_path:
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128 os.remove(tmp_path)
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129 return run_response
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130
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131 def _process_test_results(self, test_results):
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132 for (test_case, run_response) in test_results:
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133 pass
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134
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135
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136 __all__ = (
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137 "Engine",
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138 "BaseEngine",
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139 )