Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/galaxy/test/actions.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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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 build_report
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22 from planemo.test.results import get_dict_value
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23 from . import structures as test_structures
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24
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25
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26 NO_XUNIT_REPORT_MESSAGE = ("Cannot locate xUnit report [%s] for tests - "
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27 "required to build planemo report and summarize "
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28 "tests.")
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29 NO_JSON_REPORT_MESSAGE = ("Cannot locate JSON 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 REPORT_NOT_CHANGED = ("Galaxy failed to update test 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 NO_TESTS_MESSAGE = "No tests were executed - see Galaxy output for details."
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36 ALL_TESTS_PASSED_MESSAGE = "All %d test(s) executed passed."
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37 PROBLEM_COUNT_MESSAGE = ("There were problems with %d test(s) - out of %d "
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38 "test(s) executed. See %s for detailed breakdown.")
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39 GENERIC_PROBLEMS_MESSAGE = ("One or more tests failed. See %s for detailed "
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40 "breakdown.")
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41 GENERIC_TESTS_PASSED_MESSAGE = "No failing tests encountered."
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42
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43
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44 def run_in_config(ctx, config, run=run_galaxy_command, test_data_target_dir=None, **kwds):
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45 """Run Galaxy tests with the run_tests.sh command.
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46
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47 The specified `config` object describes the context for tool
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48 execution.
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49 """
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50 config_directory = config.config_directory
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51 html_report_file = kwds["test_output"]
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52
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53 job_output_files = kwds.get("job_output_files", None)
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54 if job_output_files is None:
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55 job_output_files = os.path.join(config_directory, "jobfiles")
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56
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57 xunit_report_file = _xunit_state(kwds, config)
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58 xunit_report_file_tracker = _FileChangeTracker(xunit_report_file)
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59 structured_report_file = _structured_report_file(kwds, config)
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60 structured_report_file_tracker = _FileChangeTracker(structured_report_file)
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61
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62 info("Testing using galaxy_root %s", config.galaxy_root)
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63 # TODO: Allow running dockerized Galaxy here instead.
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64 server_ini = os.path.join(config_directory, "galaxy.ini")
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65 config.env["GALAXY_CONFIG_FILE"] = server_ini
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66 config.env["GALAXY_TEST_VERBOSE_ERRORS"] = "true"
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67 config.env["GALAXY_TEST_SAVE"] = job_output_files
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68
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69 cd_to_galaxy_command = ['cd', config.galaxy_root]
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70 test_cmd = test_structures.GalaxyTestCommand(
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71 html_report_file,
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72 xunit_report_file,
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73 structured_report_file,
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74 failed=kwds.get("failed", False),
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75 installed=kwds.get("installed", False),
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76 ).build()
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77 setup_common_startup_args = ""
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78 if kwds.get("skip_venv", False):
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79 setup_common_startup_args = shell_join(
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80 'COMMON_STARTUP_ARGS=--skip-venv',
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81 'export COMMON_STARTUP_ARGS',
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82 'echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"',
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83 )
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84 setup_venv_command = setup_venv(ctx, kwds)
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85 cmd = shell_join(
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86 cd_to_galaxy_command,
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87 setup_common_startup_args,
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88 setup_venv_command,
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89 test_cmd,
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90 )
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91 action = "Testing tools"
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92 return_code = run(
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93 ctx,
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94 cmd,
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95 config.env,
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96 action
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97 )
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98 if kwds.get('update_test_data', False):
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99 copy_tree(job_output_files, test_data_target_dir or config.test_data_dir)
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100
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101 _check_test_outputs(xunit_report_file_tracker, structured_report_file_tracker)
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102 test_results = test_structures.GalaxyTestResults(
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103 structured_report_file,
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104 xunit_report_file,
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105 html_report_file,
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106 return_code,
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107 )
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108
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109 structured_data = test_results.structured_data
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110 return handle_reports_and_summary(
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111 ctx,
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112 structured_data,
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113 exit_code=test_results.exit_code,
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114 kwds=kwds
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115 )
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116
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117
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118 def handle_reports_and_summary(ctx, structured_data, exit_code=None, kwds={}):
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119 """Produce reports and print summary, return 0 if tests passed.
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120
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121 If ``exit_code`` is set - use underlying test source for return
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122 code and test success determination, otherwise infer from supplied
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123 test data.
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124 """
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diff changeset
125 handle_reports(ctx, structured_data, kwds)
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126 summary_exit_code = _handle_summary(
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diff changeset
127 structured_data,
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diff changeset
128 **kwds
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129 )
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130 return exit_code if exit_code is not None else summary_exit_code
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131
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132
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133 def merge_reports(input_paths, output_path):
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diff changeset
134 reports = []
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parents:
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135 for path in input_paths:
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diff changeset
136 with io.open(path, encoding='utf-8') as f:
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137 reports.append(json.load(f))
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diff changeset
138 tests = []
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139 for report in reports:
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140 tests.extend(report["tests"])
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141 merged_report = {"tests": tests}
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diff changeset
142 with io.open(output_path, mode="w", encoding='utf-8') as out:
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143 out.write(unicodify(json.dumps(merged_report)))
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144
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145
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146 def handle_reports(ctx, structured_data, kwds):
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147 """Write reports based on user specified kwds."""
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148 exceptions = []
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149 structured_report_file = kwds.get("test_output_json", None)
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150 if structured_report_file and not os.path.exists(structured_report_file):
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diff changeset
151 try:
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152 with io.open(structured_report_file, mode="w", encoding='utf-8') as f:
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153 f.write(unicodify(json.dumps(structured_data)))
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154 except Exception as e:
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155 exceptions.append(e)
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156
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157 for report_type in ["html", "markdown", "text", "xunit", "junit"]:
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158 try:
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159 _handle_test_output_file(
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160 ctx, report_type, structured_data, kwds
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161 )
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162 except Exception as e:
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163 exceptions.append(e)
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164
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165 if len(exceptions) > 0:
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166 raise exceptions[0]
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167
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168
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169 def _handle_test_output_file(ctx, report_type, test_data, kwds):
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170 kwd_name = "test_output"
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171 if report_type != "html":
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172 kwd_name = "test_output_%s" % report_type
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173
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174 path = kwds.get(kwd_name, None)
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parents:
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175 if path is None:
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176 message = "No file specified for %s, skipping test output." % kwd_name
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177 ctx.vlog(message)
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178 return
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179
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180 try:
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181 contents = build_report.build_report(
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parents:
diff changeset
182 test_data, report_type=report_type
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diff changeset
183 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
184 except Exception:
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shellac
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diff changeset
185 message = "Problem producing report file %s for %s" % (
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186 path, kwd_name
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187 )
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188 ctx.vlog(message, exception=True)
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189 raise
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190
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shellac
parents:
diff changeset
191 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
192 with io.open(path, mode='w', encoding='utf-8') as handle:
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shellac
parents:
diff changeset
193 handle.write(unicodify(contents))
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shellac
parents:
diff changeset
194 except Exception:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
195 message = "Problem writing output file %s for %s" % (
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parents:
diff changeset
196 kwd_name, path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
197 )
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parents:
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198 ctx.vlog(message, exception=True)
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shellac
parents:
diff changeset
199 raise
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
200
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
201
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shellac
parents:
diff changeset
202 def _handle_summary(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
203 structured_data,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
204 **kwds
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
205 ):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
206 summary_dict = get_dict_value("summary", structured_data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
207 num_tests = get_dict_value("num_tests", summary_dict)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
208 num_failures = get_dict_value("num_failures", summary_dict)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
209 num_errors = get_dict_value("num_errors", summary_dict)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
210 num_problems = num_failures + num_errors
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shellac
parents:
diff changeset
211
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
212 summary_exit_code = EXIT_CODE_OK
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
213 if num_problems > 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
214 summary_exit_code = EXIT_CODE_GENERIC_FAILURE
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
215 elif num_tests == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
216 summary_exit_code = EXIT_CODE_NO_SUCH_TARGET
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shellac
parents:
diff changeset
217
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
218 summary_style = kwds.get("summary")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
219 if summary_style != "none":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
220 if num_tests == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
221 warn(NO_TESTS_MESSAGE)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
222 elif num_problems == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
223 info(ALL_TESTS_PASSED_MESSAGE % num_tests)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
224 elif num_problems:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
225 html_report_file = kwds.get("test_output")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
226 message_args = (num_problems, num_tests, html_report_file)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
227 message = PROBLEM_COUNT_MESSAGE % message_args
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
228 warn(message)
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shellac
parents:
diff changeset
229
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
230 _summarize_tests_full(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
231 structured_data,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
232 **kwds
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
233 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
234
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
235 return summary_exit_code
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
236
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
237
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
238 def _summarize_tests_full(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
239 structured_data,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
240 **kwds
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
241 ):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
242 tests = get_dict_value("tests", structured_data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
243 for test_case_data in tests:
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shellac
parents:
diff changeset
244 _summarize_test_case(test_case_data, **kwds)
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shellac
parents:
diff changeset
245
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shellac
parents:
diff changeset
246
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
247 def passed(xunit_testcase_el):
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shellac
parents:
diff changeset
248 did_pass = True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
249 for child_el in list(xunit_testcase_el):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
250 if child_el.tag in ["failure", "error"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
251 did_pass = False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
252 return did_pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
253
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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254
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255 def _summarize_test_case(structured_data, **kwds):
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256 summary_style = kwds.get("summary")
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257 test_id = test_structures.case_id(
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258 raw_id=get_dict_value("id", structured_data)
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259 )
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260 status = get_dict_value(
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261 "status",
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262 get_dict_value("data", structured_data)
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263 )
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264 if status != "success":
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265 state = click.style("failed", bold=True, fg='red')
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266 else:
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267 state = click.style("passed", bold=True, fg='green')
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268 click.echo(test_id.label + ": " + state)
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269 if summary_style != "minimal":
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270 _print_command_line(structured_data, test_id)
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271
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272
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273 def _print_command_line(test, test_id):
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274 execution_problem = test.get("execution_problem", None)
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275 if execution_problem:
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276 click.echo("| command: *could not execute job, no command generated* ")
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277 return
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278
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279 try:
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280 command = test["job"]["command_line"]
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281 except (KeyError, IndexError):
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282 click.echo("| command: *failed to determine command for job* ")
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283 return
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284
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285 click.echo("| command: %s" % command)
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286
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287
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288 def _check_test_outputs(
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289 xunit_report_file_tracker,
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290 structured_report_file_tracker
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291 ):
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292 if not os.path.exists(xunit_report_file_tracker.path):
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293 message = NO_XUNIT_REPORT_MESSAGE % xunit_report_file_tracker.path
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294 error(message)
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295 raise Exception(message)
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296
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297 if not os.path.exists(structured_report_file_tracker.path):
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298 message = NO_JSON_REPORT_MESSAGE % structured_report_file_tracker.path
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299 error(message)
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300 raise Exception(message)
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301
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302 if not xunit_report_file_tracker.changed():
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303 message = REPORT_NOT_CHANGED % xunit_report_file_tracker.path
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304 error(message)
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305 raise Exception(message)
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306
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307 if not structured_report_file_tracker.changed():
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308 message = REPORT_NOT_CHANGED % structured_report_file_tracker.path
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309 error(message)
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310 raise Exception(message)
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311
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312
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313 def _xunit_state(kwds, config):
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314 # This has been supported in Galaxy for well over a year, just going to assume
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315 # it from here on out.
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316 # xunit_supported = True
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317 # if shell("grep -q xunit '%s'/run_tests.sh" % config.galaxy_root):
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318 # xunit_supported = False
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319
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320 xunit_report_file = kwds.get("test_output_xunit", None)
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321 if xunit_report_file is None:
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322 xunit_report_file = os.path.join(config.config_directory, "xunit.xml")
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323
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324 return xunit_report_file
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325
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326
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327 def _structured_report_file(kwds, config):
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328 # This has been supported in Galaxy for well over a year, just going to assume
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329 # it from here on out.
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330 # structured_data_supported = True
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331 # if shell("grep -q structured_data '%s'/run_tests.sh" % config.galaxy_root):
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332 # structured_data_supported = False
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333
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334 structured_report_file = None
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335 structured_report_file = kwds.get("test_output_json", None)
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336 if structured_report_file is None:
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337 conf_dir = config.config_directory
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338 structured_report_file = os.path.join(conf_dir, "structured_data.json")
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339
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340 return structured_report_file
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341
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342
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343 class _FileChangeTracker(object):
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344
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345 def __init__(self, path):
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346 modification_time = None
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347 if os.path.exists(path):
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348 modification_time = os.path.getmtime(path)
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349
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350 self.path = path
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351 self.modification_time = modification_time
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352
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353 def changed(self):
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354 if self.modification_time:
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355 new_modification_time = os.path.getmtime(self.path)
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356 return self.modification_time != new_modification_time
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357 else:
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358 return os.path.exists(self.path)
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359
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360
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361 __all__ = (
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362 "run_in_config",
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363 "handle_reports",
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364 "handle_reports_and_summary",
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365 )