annotate toolfactory/galaxy-tool-test @ 121:2050b2475ae5 draft

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author fubar
date Thu, 07 Jan 2021 09:24:17 +0000
parents d4d88d393285
children
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99
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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import datetime as dt
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5 import json
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6 import logging
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7 import os
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8 import sys
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9 import tempfile
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10 from collections import namedtuple
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11 from concurrent.futures import thread, ThreadPoolExecutor
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12
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13 import yaml
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14
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15 from galaxy.tool_util.verify.interactor import (
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16 DictClientTestConfig,
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17 GalaxyInteractorApi,
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18 verify_tool,
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19 )
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20
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21 DESCRIPTION = """Script to quickly run a tool test against a running Galaxy instance."""
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22 DEFAULT_SUITE_NAME = "Galaxy Tool Tests"
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23 ALL_TESTS = -1
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24 ALL_TOOLS = "*"
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25 ALL_VERSION = "*"
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26 LATEST_VERSION = None
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27
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28
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29 TestReference = namedtuple("TestReference", ["tool_id", "tool_version", "test_index"])
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30 TestException = namedtuple("TestException", ["tool_id", "exception", "was_recorded"])
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31
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32
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33 class Results:
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34
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35 def __init__(self, default_suitename, test_json, append=False):
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36 self.test_json = test_json or "-"
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37 test_results = []
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38 test_exceptions = []
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39 suitename = default_suitename
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40 if append:
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41 assert test_json != "-"
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42 with open(test_json) as f:
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43 previous_results = json.load(f)
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44 test_results = previous_results["tests"]
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45 if "suitename" in previous_results:
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46 suitename = previous_results["suitename"]
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47 self.test_results = test_results
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48 self.test_exceptions = test_exceptions
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49 self.suitename = suitename
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50
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51 def register_result(self, result):
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52 self.test_results.append(result)
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53
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54 def register_exception(self, test_exception):
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55 self.test_exceptions.append(test_exception)
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56
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57 def already_successful(self, test_reference):
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58 test_id = _test_id_for_reference(test_reference)
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59 for test_result in self.test_results:
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60 if test_result.get('id') != test_id:
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61 continue
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62
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63 has_data = test_result.get('has_data', False)
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64 if has_data:
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65 test_data = test_result.get("data", {})
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66 if 'status' in test_data and test_data['status'] == 'success':
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67 return True
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68
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69 return False
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70
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71 def write(self):
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72 tests = sorted(self.test_results, key=lambda el: el['id'])
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73 n_passed, n_failures, n_skips = 0, 0, 0
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74 n_errors = len([e for e in self.test_exceptions if not e.was_recorded])
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75 for test in tests:
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76 has_data = test.get('has_data', False)
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77 if has_data:
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78 test_data = test.get("data", {})
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79 if 'status' not in test_data:
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80 raise Exception(f"Test result data {test_data} doesn't contain a status key.")
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81 status = test_data['status']
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82 if status == "success":
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83 n_passed += 1
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84 elif status == "error":
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85 n_errors += 1
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86 elif status == "skip":
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87 n_skips += 1
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88 elif status == "failure":
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89 n_failures += 1
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90 report_obj = {
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91 'version': '0.1',
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92 'suitename': self.suitename,
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93 'results': {
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94 'total': n_passed + n_failures + n_skips + n_errors,
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95 'errors': n_errors,
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96 'failures': n_failures,
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97 'skips': n_skips,
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98 },
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99 'tests': tests,
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100 }
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101 if self.test_json == "-":
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102 print(json.dumps(report_obj))
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103 else:
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104 with open(self.test_json, "w") as f:
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105 json.dump(report_obj, f)
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106
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107 def info_message(self):
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108 messages = []
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109 passed_tests = self._tests_with_status('success')
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110 messages.append("Passed tool tests ({}): {}".format(
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111 len(passed_tests),
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112 [t["id"] for t in passed_tests]
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113 ))
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114 failed_tests = self._tests_with_status('failure')
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115 messages.append("Failed tool tests ({}): {}".format(
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116 len(failed_tests),
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117 [t["id"] for t in failed_tests]
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118 ))
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119 skiped_tests = self._tests_with_status('skip')
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120 messages.append("Skipped tool tests ({}): {}".format(
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121 len(skiped_tests),
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122 [t["id"] for t in skiped_tests]
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123 ))
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124 errored_tests = self._tests_with_status('error')
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125 messages.append("Errored tool tests ({}): {}".format(
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126 len(errored_tests),
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127 [t["id"] for t in errored_tests]
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128 ))
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129 return "\n".join(messages)
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130
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131 @property
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132 def success_count(self):
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133 self._tests_with_status('success')
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134
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135 @property
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136 def skip_count(self):
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137 self._tests_with_status('skip')
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138
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139 @property
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140 def error_count(self):
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141 return self._tests_with_status('error') + len(self.test_exceptions)
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142
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143 @property
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144 def failure_count(self):
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145 return self._tests_with_status('failure')
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146
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147 def _tests_with_status(self, status):
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148 return [t for t in self.test_results if t.get("data", {}).get("status") == status]
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149
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150
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151 def test_tools(
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152 galaxy_interactor,
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153 test_references,
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154 results,
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155 log=None,
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156 parallel_tests=1,
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157 history_per_test_case=False,
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158 no_history_cleanup=False,
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159 retries=0,
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160 verify_kwds=None,
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161 ):
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162 """Run through tool tests and write report.
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163
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164 Refactor this into Galaxy in 21.01.
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165 """
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166 verify_kwds = (verify_kwds or {}).copy()
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167 tool_test_start = dt.datetime.now()
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168 history_created = False
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169 if history_per_test_case:
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170 test_history = None
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171 else:
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172 history_created = True
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173 test_history = galaxy_interactor.new_history(history_name=f"History for {results.suitename}")
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174 verify_kwds.update({
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175 "no_history_cleanup": no_history_cleanup,
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176 "test_history": test_history,
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177 })
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178 with ThreadPoolExecutor(max_workers=parallel_tests) as executor:
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179 try:
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180 for test_reference in test_references:
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181 _test_tool(
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182 executor=executor,
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183 test_reference=test_reference,
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184 results=results,
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185 galaxy_interactor=galaxy_interactor,
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186 log=log,
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187 retries=retries,
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188 verify_kwds=verify_kwds,
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189 )
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190 finally:
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191 # Always write report, even if test was cancelled.
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192 try:
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193 executor.shutdown(wait=True)
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194 except KeyboardInterrupt:
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195 executor._threads.clear()
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196 thread._threads_queues.clear()
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197 results.write()
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198 if log:
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199 log.info("Report written to '%s'", os.path.abspath(results.test_json))
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200 log.info(results.info_message())
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201 log.info("Total tool test time: {}".format(dt.datetime.now() - tool_test_start))
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202 if history_created and not no_history_cleanup:
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203 galaxy_interactor.delete_history(test_history)
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204
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205
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206 def _test_id_for_reference(test_reference):
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207 tool_id = test_reference.tool_id
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208 tool_version = test_reference.tool_version
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209 test_index = test_reference.test_index
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210
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211 if tool_version and tool_id.endswith("/" + tool_version):
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212 tool_id = tool_id[:-len("/" + tool_version)]
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213
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214 label_base = tool_id
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215 if tool_version:
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216 label_base += "/" + str(tool_version)
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217
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218 test_id = label_base + "-" + str(test_index)
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219 return test_id
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diff changeset
220
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221
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diff changeset
222 def _test_tool(
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223 executor,
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diff changeset
224 test_reference,
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diff changeset
225 results,
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parents:
diff changeset
226 galaxy_interactor,
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parents:
diff changeset
227 log,
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parents:
diff changeset
228 retries,
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parents:
diff changeset
229 verify_kwds,
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parents:
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230 ):
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parents:
diff changeset
231 tool_id = test_reference.tool_id
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232 tool_version = test_reference.tool_version
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233 test_index = test_reference.test_index
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234 # If given a tool_id with a version suffix, strip it off so we can treat tool_version
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235 # correctly at least in client_test_config.
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236 if tool_version and tool_id.endswith("/" + tool_version):
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237 tool_id = tool_id[:-len("/" + tool_version)]
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238
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239 test_id = _test_id_for_reference(test_reference)
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240
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241 def run_test():
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242 run_retries = retries
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243 job_data = None
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244 job_exception = None
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245
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246 def register(job_data_):
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247 nonlocal job_data
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248 job_data = job_data_
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249
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250 try:
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251 while run_retries >= 0:
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252 job_exception = None
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253 try:
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254 if log:
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255 log.info("Executing test '%s'", test_id)
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256 verify_tool(
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257 tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version,
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258 register_job_data=register, **verify_kwds
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259 )
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260 if log:
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261 log.info("Test '%s' passed", test_id)
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262 break
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263 except Exception as e:
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264 if log:
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265 log.warning("Test '%s' failed", test_id, exc_info=True)
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266
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267 job_exception = e
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268 run_retries -= 1
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269 finally:
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270 if job_data is not None:
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271 results.register_result({
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272 "id": test_id,
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273 "has_data": True,
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274 "data": job_data,
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275 })
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276 if job_exception is not None:
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277 was_recorded = job_data is not None
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278 test_exception = TestException(tool_id, job_exception, was_recorded)
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279 results.register_exception(test_exception)
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280
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281 executor.submit(run_test)
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282
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283
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diff changeset
284 def build_case_references(
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285 galaxy_interactor,
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diff changeset
286 tool_id=ALL_TOOLS,
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diff changeset
287 tool_version=LATEST_VERSION,
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diff changeset
288 test_index=ALL_TESTS,
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289 page_size=0,
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parents:
diff changeset
290 page_number=0,
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parents:
diff changeset
291 check_against=None,
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parents:
diff changeset
292 log=None,
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293 ):
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diff changeset
294 test_references = []
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parents:
diff changeset
295 if tool_id == ALL_TOOLS:
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parents:
diff changeset
296 tests_summary = galaxy_interactor.get_tests_summary()
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parents:
diff changeset
297 for tool_id, tool_versions_dict in tests_summary.items():
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parents:
diff changeset
298 for tool_version, summary in tool_versions_dict.items():
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parents:
diff changeset
299 for test_index in range(summary["count"]):
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diff changeset
300 test_reference = TestReference(tool_id, tool_version, test_index)
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diff changeset
301 test_references.append(test_reference)
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parents:
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302 else:
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303 assert tool_id
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parents:
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304 tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version) or {}
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parents:
diff changeset
305 for i, tool_test_dict in enumerate(tool_test_dicts):
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diff changeset
306 this_tool_version = tool_test_dict.get("tool_version", tool_version)
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307 this_test_index = i
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parents:
diff changeset
308 if test_index == ALL_TESTS or i == test_index:
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diff changeset
309 test_reference = TestReference(tool_id, this_tool_version, this_test_index)
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diff changeset
310 test_references.append(test_reference)
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311
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312 if check_against:
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diff changeset
313 filtered_test_references = []
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parents:
diff changeset
314 for test_reference in test_references:
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parents:
diff changeset
315 if check_against.already_successful(test_reference):
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parents:
diff changeset
316 if log is not None:
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parents:
diff changeset
317 log.debug(f"Found successful test for {test_reference}, skipping")
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parents:
diff changeset
318 continue
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diff changeset
319 filtered_test_references.append(test_reference)
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320 log.info(f"Skipping {len(test_references)-len(filtered_test_references)} out of {len(test_references)} tests.")
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diff changeset
321 test_references = filtered_test_references
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diff changeset
322
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parents:
diff changeset
323 if page_size > 0:
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parents:
diff changeset
324 slice_start = page_size * page_number
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parents:
diff changeset
325 slice_end = page_size * (page_number + 1)
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parents:
diff changeset
326 test_references = test_references[slice_start:slice_end]
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diff changeset
327
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diff changeset
328 return test_references
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diff changeset
329
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diff changeset
330
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parents:
diff changeset
331 def main(argv=None):
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parents:
diff changeset
332 if argv is None:
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parents:
diff changeset
333 argv = sys.argv[1:]
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334
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parents:
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335 args = _arg_parser().parse_args(argv)
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parents:
diff changeset
336 log = setup_global_logger(__name__, verbose=args.verbose)
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parents:
diff changeset
337 client_test_config_path = args.client_test_config
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parents:
diff changeset
338 if client_test_config_path is not None:
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parents:
diff changeset
339 log.debug(f"Reading client config path {client_test_config_path}")
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parents:
diff changeset
340 with open(client_test_config_path) as f:
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parents:
diff changeset
341 client_test_config = yaml.full_load(f)
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parents:
diff changeset
342 else:
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diff changeset
343 client_test_config = {}
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diff changeset
344
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parents:
diff changeset
345 def get_option(key):
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diff changeset
346 arg_val = getattr(args, key, None)
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parents:
diff changeset
347 if arg_val is None and key in client_test_config:
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diff changeset
348 val = client_test_config.get(key)
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parents:
diff changeset
349 else:
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diff changeset
350 val = arg_val
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parents:
diff changeset
351 return val
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diff changeset
352
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parents:
diff changeset
353 output_json_path = get_option("output_json")
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parents:
diff changeset
354 galaxy_interactor_kwds = {
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parents:
diff changeset
355 "galaxy_url": get_option("galaxy_url"),
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parents:
diff changeset
356 "master_api_key": get_option("admin_key"),
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parents:
diff changeset
357 "api_key": get_option("key"),
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parents:
diff changeset
358 "keep_outputs_dir": args.output,
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parents:
diff changeset
359 "download_attempts": get_option("download_attempts"),
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parents:
diff changeset
360 "download_sleep": get_option("download_sleep"),
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parents:
diff changeset
361 }
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parents:
diff changeset
362 tool_id = args.tool_id
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parents:
diff changeset
363 tool_version = args.tool_version
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parents:
diff changeset
364 tools_client_test_config = DictClientTestConfig(client_test_config.get("tools"))
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parents:
diff changeset
365 verbose = args.verbose
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parents:
diff changeset
366
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parents:
diff changeset
367 galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
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parents:
diff changeset
368 results = Results(args.suite_name, output_json_path, append=args.append)
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parents:
diff changeset
369 check_against = None if not args.skip_successful else results
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parents:
diff changeset
370 test_references = build_case_references(
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parents:
diff changeset
371 galaxy_interactor,
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parents:
diff changeset
372 tool_id=tool_id,
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parents:
diff changeset
373 tool_version=tool_version,
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parents:
diff changeset
374 test_index=args.test_index,
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parents:
diff changeset
375 page_size=args.page_size,
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parents:
diff changeset
376 page_number=args.page_number,
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parents:
diff changeset
377 check_against=check_against,
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parents:
diff changeset
378 log=log,
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parents:
diff changeset
379 )
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parents:
diff changeset
380 log.debug(f"Built {len(test_references)} test references to executed.")
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parents:
diff changeset
381 verify_kwds = dict(
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parents:
diff changeset
382 client_test_config=tools_client_test_config,
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parents:
diff changeset
383 force_path_paste=args.force_path_paste,
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parents:
diff changeset
384 skip_with_reference_data=not args.with_reference_data,
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parents:
diff changeset
385 quiet=not verbose,
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parents:
diff changeset
386 )
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parents:
diff changeset
387 test_tools(
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parents:
diff changeset
388 galaxy_interactor,
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parents:
diff changeset
389 test_references,
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parents:
diff changeset
390 results,
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parents:
diff changeset
391 log=log,
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parents:
diff changeset
392 parallel_tests=args.parallel_tests,
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parents:
diff changeset
393 history_per_test_case=args.history_per_test_case,
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parents:
diff changeset
394 no_history_cleanup=args.no_history_cleanup,
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parents:
diff changeset
395 verify_kwds=verify_kwds,
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parents:
diff changeset
396 )
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parents:
diff changeset
397 exceptions = results.test_exceptions
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parents:
diff changeset
398 if exceptions:
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parents:
diff changeset
399 exception = exceptions[0]
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parents:
diff changeset
400 if hasattr(exception, "exception"):
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parents:
diff changeset
401 exception = exception.exception
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parents:
diff changeset
402 raise exception
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parents:
diff changeset
403
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parents:
diff changeset
404
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parents:
diff changeset
405 def setup_global_logger(name, log_file=None, verbose=False):
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parents:
diff changeset
406 formatter = logging.Formatter('%(asctime)s %(levelname)-5s - %(message)s')
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parents:
diff changeset
407 console = logging.StreamHandler()
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parents:
diff changeset
408 console.setFormatter(formatter)
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parents:
diff changeset
409
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parents:
diff changeset
410 logger = logging.getLogger(name)
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parents:
diff changeset
411 logger.setLevel(logging.DEBUG if verbose else logging.INFO)
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parents:
diff changeset
412 logger.addHandler(console)
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parents:
diff changeset
413
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parents:
diff changeset
414 if not log_file:
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parents:
diff changeset
415 # delete = false is chosen here because it is always nice to have a log file
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parents:
diff changeset
416 # ready if you need to debug. Not having the "if only I had set a log file"
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parents:
diff changeset
417 # moment after the fact.
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parents:
diff changeset
418 temp = tempfile.NamedTemporaryFile(prefix="ephemeris_", delete=False)
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parents:
diff changeset
419 log_file = temp.name
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parents:
diff changeset
420 file_handler = logging.FileHandler(log_file)
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parents:
diff changeset
421 logger.addHandler(file_handler)
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parents:
diff changeset
422 logger.info(f"Storing log file in: {log_file}")
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parents:
diff changeset
423 return logger
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parents:
diff changeset
424
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parents:
diff changeset
425
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parents:
diff changeset
426 def _arg_parser():
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427 parser = argparse.ArgumentParser(description=DESCRIPTION)
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428 parser.add_argument('-u', '--galaxy-url', default="http://localhost:8080", help='Galaxy URL')
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429 parser.add_argument('-k', '--key', default=None, help='Galaxy User API Key')
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430 parser.add_argument('-a', '--admin-key', default=None, help='Galaxy Admin API Key')
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431 parser.add_argument('--force_path_paste', default=False, action="store_true", help='This requires Galaxy-side config option "allow_path_paste" enabled. Allows for fetching test data locally. Only for admins.')
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432 parser.add_argument('-t', '--tool-id', default=ALL_TOOLS, help='Tool ID')
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433 parser.add_argument('--tool-version', default=None, help='Tool Version (if tool id supplied). Defaults to just latest version, use * to test all versions')
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434 parser.add_argument('-i', '--test-index', default=ALL_TESTS, type=int, help='Tool Test Index (starting at 0) - by default all tests will run.')
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435 parser.add_argument('-o', '--output', default=None, help='directory to dump outputs to')
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436 parser.add_argument('--append', default=False, action="store_true", help="Extend a test record json (created with --output-json) with additional tests.")
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437 parser.add_argument('--skip-successful', default=False, action="store_true", help="When used with --append, skip previously run successful tests.")
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438 parser.add_argument('-j', '--output-json', default=None, help='output metadata json')
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439 parser.add_argument('--verbose', default=False, action="store_true", help="Verbose logging.")
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440 parser.add_argument('-c', '--client-test-config', default=None, help="Test config YAML to help with client testing")
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441 parser.add_argument('--suite-name', default=DEFAULT_SUITE_NAME, help="Suite name for tool test output")
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442 parser.add_argument('--with-reference-data', dest="with_reference_data", default=False, action="store_true")
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443 parser.add_argument('--skip-with-reference-data', dest="with_reference_data", action="store_false", help="Skip tests the Galaxy server believes use data tables or loc files.")
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444 parser.add_argument('--history-per-suite', dest="history_per_test_case", default=False, action="store_false", help="Create new history per test suite (all tests in same history).")
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445 parser.add_argument('--history-per-test-case', dest="history_per_test_case", action="store_true", help="Create new history per test case.")
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446 parser.add_argument('--no-history-cleanup', default=False, action="store_true", help="Perserve histories created for testing.")
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447 parser.add_argument('--parallel-tests', default=1, type=int, help="Parallel tests.")
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448 parser.add_argument('--retries', default=0, type=int, help="Retry failed tests.")
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449 parser.add_argument('--page-size', default=0, type=int, help="If positive, use pagination and just run one 'page' to tool tests.")
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450 parser.add_argument('--page-number', default=0, type=int, help="If page size is used, run this 'page' of tests - starts with 0.")
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451 parser.add_argument('--download-attempts', default=1, type=int, help="Galaxy may return a transient 500 status code for download if test results are written but not yet accessible.")
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452 parser.add_argument('--download-sleep', default=1, type=int, help="If download attempts is greater than 1, the amount to sleep between download attempts.")
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453 return parser
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454
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455
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456 if __name__ == "__main__":
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457 main()