Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/planemo/galaxy/test/actions.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """Actions related to running and reporting on Galaxy-specific testing.""" |
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2 |
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3 import io |
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4 import json |
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5 import os |
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6 from distutils.dir_util import copy_tree |
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7 |
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8 import click |
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9 from galaxy.util import unicodify |
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10 |
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11 from planemo.exit_codes import ( |
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12 EXIT_CODE_GENERIC_FAILURE, |
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13 EXIT_CODE_NO_SUCH_TARGET, |
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14 EXIT_CODE_OK, |
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15 ) |
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16 from planemo.galaxy.run import ( |
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17 run_galaxy_command, |
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18 setup_venv, |
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19 ) |
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20 from planemo.io import error, info, shell_join, warn |
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21 from planemo.reports import ( |
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22 allure, |
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23 build_report, |
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24 ) |
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25 from planemo.test.results import get_dict_value |
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26 from . import structures as test_structures |
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27 |
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28 |
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29 NO_XUNIT_REPORT_MESSAGE = ("Cannot locate xUnit report [%s] for tests - " |
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30 "required to build planemo report and summarize " |
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31 "tests.") |
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32 NO_JSON_REPORT_MESSAGE = ("Cannot locate JSON report [%s] for tests - " |
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33 "required to build planemo report and summarize " |
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34 "tests.") |
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35 REPORT_NOT_CHANGED = ("Galaxy failed to update test report [%s] for tests - " |
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36 "required to build planemo report and summarize " |
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37 "tests.") |
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38 NO_TESTS_MESSAGE = "No tests were executed - see Galaxy output for details." |
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39 ALL_TESTS_PASSED_MESSAGE = "All %d test(s) executed passed." |
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40 PROBLEM_COUNT_MESSAGE = ("There were problems with %d test(s) - out of %d " |
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41 "test(s) executed. See %s for detailed breakdown.") |
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42 GENERIC_PROBLEMS_MESSAGE = ("One or more tests failed. See %s for detailed " |
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43 "breakdown.") |
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44 GENERIC_TESTS_PASSED_MESSAGE = "No failing tests encountered." |
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45 TEST_DATA_UPDATED_MESSAGE = "Test data were updated and tests were rerun." |
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46 TEST_DATA_NOT_UPDATED_MESSAGE = "%s Therefore, no test data were updated." % ALL_TESTS_PASSED_MESSAGE |
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47 |
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48 |
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49 def run_in_config(ctx, config, run=run_galaxy_command, test_data_target_dir=None, **kwds): |
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50 """Run Galaxy tests with the run_tests.sh command. |
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51 |
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52 The specified `config` object describes the context for tool |
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53 execution. |
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54 """ |
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55 config_directory = config.config_directory |
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56 html_report_file = kwds["test_output"] |
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57 |
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58 job_output_files = kwds.get("job_output_files", None) |
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59 if job_output_files is None: |
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60 job_output_files = os.path.join(config_directory, "jobfiles") |
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61 |
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62 xunit_report_file = _xunit_state(kwds, config) |
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63 xunit_report_file_tracker = _FileChangeTracker(xunit_report_file) |
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64 structured_report_file = _structured_report_file(kwds, config) |
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65 structured_report_file_tracker = _FileChangeTracker(structured_report_file) |
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66 |
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67 info("Testing using galaxy_root %s", config.galaxy_root) |
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68 # TODO: Allow running dockerized Galaxy here instead. |
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69 server_ini = os.path.join(config_directory, "galaxy.ini") |
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70 config.env["GALAXY_CONFIG_FILE"] = server_ini |
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71 config.env["GALAXY_TEST_VERBOSE_ERRORS"] = "true" |
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72 config.env["GALAXY_TEST_SAVE"] = job_output_files |
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73 |
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74 cd_to_galaxy_command = ['cd', config.galaxy_root] |
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75 test_cmd = test_structures.GalaxyTestCommand( |
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76 html_report_file, |
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77 xunit_report_file, |
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78 structured_report_file, |
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79 failed=kwds.get("failed", False), |
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80 installed=kwds.get("installed", False), |
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81 ).build() |
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82 setup_common_startup_args = "" |
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83 if kwds.get("skip_venv", False): |
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84 setup_common_startup_args = shell_join( |
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85 'COMMON_STARTUP_ARGS=--skip-venv', |
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86 'export COMMON_STARTUP_ARGS', |
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87 'echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"', |
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88 ) |
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89 setup_venv_command = setup_venv(ctx, kwds) |
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90 cmd = shell_join( |
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91 cd_to_galaxy_command, |
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92 setup_common_startup_args, |
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93 setup_venv_command, |
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94 test_cmd, |
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95 ) |
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96 action = "Testing tools" |
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97 return_code = run( |
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98 ctx, |
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99 cmd, |
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100 config.env, |
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101 action |
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102 ) |
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103 if return_code != 0 and kwds.get('update_test_data', False): |
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104 for test_data_dir in [config.test_data_dir, test_data_target_dir]: |
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105 if test_data_dir: |
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106 copy_tree(job_output_files, test_data_dir) |
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107 kwds['test_data_updated'] = True |
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108 info('Test data updated. Rerunning...') |
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109 return_code = run( |
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110 ctx, |
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111 cmd, |
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112 config.env, |
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113 action |
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114 ) |
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115 |
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116 _check_test_outputs(xunit_report_file_tracker, structured_report_file_tracker) |
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117 test_results = test_structures.GalaxyTestResults( |
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118 structured_report_file, |
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119 xunit_report_file, |
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120 html_report_file, |
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121 return_code, |
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122 ) |
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123 |
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124 structured_data = test_results.structured_data |
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125 return handle_reports_and_summary( |
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126 ctx, |
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127 structured_data, |
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128 exit_code=test_results.exit_code, |
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129 kwds=kwds |
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130 ) |
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131 |
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132 |
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133 def handle_reports_and_summary(ctx, structured_data, exit_code=None, kwds=None): |
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134 """Produce reports and print summary, return 0 if tests passed. |
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135 |
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136 If ``exit_code`` is set - use underlying test source for return |
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137 code and test success determination, otherwise infer from supplied |
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138 test data. |
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139 """ |
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140 if kwds is None: |
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141 kwds = {} |
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142 handle_reports(ctx, structured_data, kwds) |
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143 summary_exit_code = _handle_summary( |
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144 structured_data, |
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145 **kwds |
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146 ) |
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147 return exit_code if exit_code is not None else summary_exit_code |
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148 |
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149 |
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150 def merge_reports(input_paths, output_path): |
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151 reports = [] |
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152 for path in input_paths: |
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153 with io.open(path, encoding='utf-8') as f: |
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154 reports.append(json.load(f)) |
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155 tests = [] |
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156 for report in reports: |
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157 tests.extend(report["tests"]) |
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158 tests = sorted(tests, key=lambda k: k['id']) |
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159 merged_report = {"tests": tests} |
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160 with io.open(output_path, mode="w", encoding='utf-8') as out: |
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161 out.write(unicodify(json.dumps(merged_report))) |
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162 |
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163 |
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164 def handle_reports(ctx, structured_data, kwds): |
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165 """Write reports based on user specified kwds.""" |
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166 exceptions = [] |
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167 structured_report_file = kwds.get("test_output_json", None) |
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168 if structured_report_file and not os.path.exists(structured_report_file): |
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169 try: |
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170 with io.open(structured_report_file, mode="w", encoding='utf-8') as f: |
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171 f.write(unicodify(json.dumps(structured_data))) |
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172 except Exception as e: |
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173 exceptions.append(e) |
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174 |
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175 for report_type in ["html", "markdown", "text", "xunit", "junit", "allure"]: |
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176 try: |
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177 _handle_test_output_file( |
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178 ctx, report_type, structured_data, kwds |
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179 ) |
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180 except Exception as e: |
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181 exceptions.append(e) |
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182 |
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183 if len(exceptions) > 0: |
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184 raise exceptions[0] |
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185 |
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186 |
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187 def _handle_test_output_file(ctx, report_type, test_data, kwds): |
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188 kwd_name = "test_output" |
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189 if report_type != "html": |
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190 kwd_name = "test_output_%s" % report_type |
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191 |
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192 path = kwds.get(kwd_name, None) |
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193 if path is None: |
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194 message = "No file specified for %s, skipping test output." % kwd_name |
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195 ctx.vlog(message) |
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196 return |
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197 |
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198 if report_type == "allure": |
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199 file_modication_datatime = kwds.get("file_modication_datatime") |
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200 allure.write_results(path, test_data, file_modication_datatime=file_modication_datatime) |
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201 return |
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202 |
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203 try: |
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204 contents = build_report.build_report( |
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205 test_data, report_type=report_type |
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206 ) |
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207 except Exception: |
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208 message = "Problem producing report file %s for %s" % ( |
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209 path, kwd_name |
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210 ) |
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211 ctx.vlog(message, exception=True) |
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212 raise |
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213 |
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214 try: |
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215 with io.open(path, mode='w', encoding='utf-8') as handle: |
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216 handle.write(unicodify(contents)) |
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217 except Exception: |
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218 message = "Problem writing output file %s for %s" % ( |
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219 kwd_name, path |
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220 ) |
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221 ctx.vlog(message, exception=True) |
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222 raise |
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223 |
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224 |
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225 def _handle_summary( |
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226 structured_data, |
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227 **kwds |
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228 ): |
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229 summary_dict = get_dict_value("summary", structured_data) |
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230 num_tests = get_dict_value("num_tests", summary_dict) |
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231 num_failures = get_dict_value("num_failures", summary_dict) |
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232 num_errors = get_dict_value("num_errors", summary_dict) |
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233 num_problems = num_failures + num_errors |
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234 |
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235 summary_exit_code = EXIT_CODE_OK |
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236 if num_problems > 0: |
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237 summary_exit_code = EXIT_CODE_GENERIC_FAILURE |
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238 elif num_tests == 0: |
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239 summary_exit_code = EXIT_CODE_NO_SUCH_TARGET |
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240 |
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241 summary_style = kwds.get("summary") |
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242 if kwds.get('test_data_updated'): |
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243 info(TEST_DATA_UPDATED_MESSAGE) |
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244 if summary_style != "none": |
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245 if num_tests == 0: |
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246 warn(NO_TESTS_MESSAGE) |
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247 elif num_problems == 0: |
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248 if kwds.get('update_test_data') and not kwds.get('test_data_updated'): |
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249 info(TEST_DATA_NOT_UPDATED_MESSAGE % num_tests) |
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250 else: |
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251 info(ALL_TESTS_PASSED_MESSAGE % num_tests) |
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252 elif num_problems: |
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253 html_report_file = kwds.get("test_output") |
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254 message_args = (num_problems, num_tests, html_report_file) |
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255 message = PROBLEM_COUNT_MESSAGE % message_args |
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256 warn(message) |
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257 |
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258 _summarize_tests_full( |
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259 structured_data, |
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260 **kwds |
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261 ) |
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262 |
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263 return summary_exit_code |
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264 |
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265 |
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266 def _summarize_tests_full( |
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267 structured_data, |
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268 **kwds |
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269 ): |
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270 tests = get_dict_value("tests", structured_data) |
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271 for test_case_data in tests: |
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272 _summarize_test_case(test_case_data, **kwds) |
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273 |
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274 |
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275 def passed(xunit_testcase_el): |
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276 did_pass = True |
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277 for child_el in list(xunit_testcase_el): |
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278 if child_el.tag in ["failure", "error"]: |
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279 did_pass = False |
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280 return did_pass |
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281 |
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282 |
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283 def _summarize_test_case(structured_data, **kwds): |
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284 summary_style = kwds.get("summary") |
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285 test_id = test_structures.case_id( |
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286 raw_id=get_dict_value("id", structured_data) |
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287 ) |
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288 status = get_dict_value( |
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289 "status", |
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290 get_dict_value("data", structured_data) |
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291 ) |
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292 if status != "success": |
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293 state = click.style("failed", bold=True, fg='red') |
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294 else: |
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295 state = click.style("passed", bold=True, fg='green') |
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296 click.echo(test_id.label + ": " + state) |
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297 if summary_style != "minimal": |
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298 _print_command_line(structured_data, test_id) |
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299 |
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300 |
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301 def _print_command_line(test, test_id): |
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302 execution_problem = test.get("execution_problem", None) |
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303 if execution_problem: |
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304 click.echo("| command: *could not execute job, no command generated* ") |
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305 return |
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306 |
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307 job = None |
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308 try: |
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309 job = test["job"] |
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310 except (KeyError, IndexError): |
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311 click.echo("| command: *failed to find job for test object [%s]" % test) |
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312 return |
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313 try: |
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314 command = job["command_line"] |
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315 except (KeyError, IndexError): |
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316 click.echo("| command: *failed to find command_line for job object [%s]" % job) |
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317 return |
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318 |
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319 click.echo("| command: %s" % command) |
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320 |
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321 |
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322 def _check_test_outputs( |
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323 xunit_report_file_tracker, |
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324 structured_report_file_tracker |
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325 ): |
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326 if not os.path.exists(xunit_report_file_tracker.path): |
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327 message = NO_XUNIT_REPORT_MESSAGE % xunit_report_file_tracker.path |
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328 error(message) |
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329 raise Exception(message) |
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330 |
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331 if not os.path.exists(structured_report_file_tracker.path): |
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332 message = NO_JSON_REPORT_MESSAGE % structured_report_file_tracker.path |
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333 error(message) |
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334 raise Exception(message) |
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335 |
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336 if not xunit_report_file_tracker.changed(): |
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337 message = REPORT_NOT_CHANGED % xunit_report_file_tracker.path |
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338 error(message) |
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339 raise Exception(message) |
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340 |
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341 if not structured_report_file_tracker.changed(): |
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342 message = REPORT_NOT_CHANGED % structured_report_file_tracker.path |
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343 error(message) |
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344 raise Exception(message) |
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345 |
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346 |
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347 def _xunit_state(kwds, config): |
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348 # This has been supported in Galaxy for well over a year, just going to assume |
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349 # it from here on out. |
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350 # xunit_supported = True |
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351 # if shell("grep -q xunit '%s'/run_tests.sh" % config.galaxy_root): |
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352 # xunit_supported = False |
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353 |
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354 xunit_report_file = kwds.get("test_output_xunit", None) |
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355 if xunit_report_file is None: |
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356 xunit_report_file = os.path.join(config.config_directory, "xunit.xml") |
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357 |
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358 return xunit_report_file |
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359 |
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360 |
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361 def _structured_report_file(kwds, config): |
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362 # This has been supported in Galaxy for well over a year, just going to assume |
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363 # it from here on out. |
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364 # structured_data_supported = True |
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365 # if shell("grep -q structured_data '%s'/run_tests.sh" % config.galaxy_root): |
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366 # structured_data_supported = False |
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367 |
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368 structured_report_file = None |
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369 structured_report_file = kwds.get("test_output_json", None) |
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370 if structured_report_file is None: |
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371 conf_dir = config.config_directory |
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372 structured_report_file = os.path.join(conf_dir, "structured_data.json") |
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373 |
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374 return structured_report_file |
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375 |
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376 |
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377 class _FileChangeTracker(object): |
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378 |
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379 def __init__(self, path): |
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380 modification_time = None |
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381 if os.path.exists(path): |
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382 modification_time = os.path.getmtime(path) |
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383 |
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384 self.path = path |
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385 self.modification_time = modification_time |
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386 |
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387 def changed(self): |
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388 if self.modification_time: |
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389 new_modification_time = os.path.getmtime(self.path) |
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390 return self.modification_time != new_modification_time |
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391 else: |
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392 return os.path.exists(self.path) |
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393 |
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394 |
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395 __all__ = ( |
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396 "run_in_config", |
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397 "handle_reports", |
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398 "handle_reports_and_summary", |
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399 ) |