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annotate venv/lib/python2.7/site-packages/planemo/galaxy_test/structures.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 """ Utilities for reasoning about Galaxy test results.
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2 """
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3 from __future__ import print_function
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4 from __future__ import absolute_import
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5
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6 from collections import namedtuple
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7 import json
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8 import xml.etree.ElementTree as ET
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9
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10 RUN_TESTS_CMD = (
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11 "sh run_tests.sh --report_file %s %s %s %s"
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12 )
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13
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14
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15 class GalaxyTestCommand(object):
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16
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17 def __init__(
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18 self,
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19 html_report_file,
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20 xunit_report_file,
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21 structured_report_file,
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22 failed=False,
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23 installed=False,
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24 ):
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25 self.html_report_file = html_report_file
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26 self.xunit_report_file = xunit_report_file
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27 self.structured_report_file = structured_report_file
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28 self.failed = failed
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29 self.installed = installed
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30
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31 def build(self):
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32 xunit_report_file = self.xunit_report_file
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33 sd_report_file = self.structured_report_file
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34 html_report_file = self.html_report_file
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35 if xunit_report_file:
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36 xunit_arg = "--xunit_report_file %s" % xunit_report_file
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37 else:
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38 xunit_arg = ""
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39 if sd_report_file:
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40 sd_arg = "--structured_data_report_file %s" % sd_report_file
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41 else:
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42 sd_arg = ""
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43 if self.installed:
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44 tests = "-installed"
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45 else:
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46 tests = "functional.test_toolbox"
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47 if self.failed:
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48 sd = StructuredData(self.structured_report_file)
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49 failed_ids = sd.failed_ids
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50 tests = " ".join(failed_ids)
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51 return RUN_TESTS_CMD % (html_report_file, xunit_arg, sd_arg, tests)
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52
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53
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54 class StructuredData(object):
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55 """ Abstraction around Galaxy's structured test data output.
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56 """
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57
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58 def __init__(self, json_path):
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59 self.json_path = json_path
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60 try:
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61 with open(json_path, "r") as output_json_f:
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62 structured_data = json.load(output_json_f)
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63 structured_data_tests = structured_data["tests"]
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64 except Exception:
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65 print("Warning: Targetting older Galaxy which did not "
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66 "produce a structured test results files.")
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67 structured_data = {}
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68 structured_data_tests = {}
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69 self.structured_data = structured_data
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70 self.structured_data_tests = structured_data_tests
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71 structured_data_by_id = {}
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72 for test in self.structured_data_tests:
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73 structured_data_by_id[test["id"]] = test["data"]
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74 self.structured_data_by_id = structured_data_by_id
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75 self.has_details = "summary" in structured_data
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76 if self.has_details:
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77 self._read_summary()
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78
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79 def update(self):
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80 with open(self.json_path, "w") as out_f:
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81 json.dump(self.structured_data, out_f)
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82
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83 def merge_xunit(self, xunit_root):
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84 self.has_details = True
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85 xunit_attrib = xunit_root.attrib
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86 num_tests = int(xunit_attrib.get("tests", 0))
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87 num_failures = int(xunit_attrib.get("failures", 0))
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88 num_errors = int(xunit_attrib.get("errors", 0))
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89 num_skips = int(xunit_attrib.get("skips", 0))
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90 summary = dict(
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91 num_tests=num_tests,
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92 num_failures=num_failures,
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93 num_errors=num_errors,
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94 num_skips=num_skips,
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95 )
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96
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97 self.structured_data["summary"] = summary
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98 self.num_tests = num_tests
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99 self.num_problems = num_skips + num_errors + num_failures
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100
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101 for testcase_el in xunit_t_elements_from_root(xunit_root):
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102 test = case_id(testcase_el)
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103 test_data = self.structured_data_by_id.get(test.id)
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104 if not test_data:
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105 continue
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106 problem_el = None
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107 for problem_type in ["skip", "failure", "error"]:
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108 problem_el = testcase_el.find(problem_type)
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109 if problem_el is not None:
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110 break
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111 if problem_el is not None:
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112 status = problem_el.tag
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113 test_data["problem_type"] = problem_el.attrib["type"]
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114 test_data["problem_log"] = problem_el.text
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115 else:
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116 status = "success"
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117 test_data["status"] = status
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118
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119 def _read_summary(self):
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120 # TODO: read relevant data out of summary object.
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121 pass
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122
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123 @property
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124 def failed_ids(self):
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125 ids = set([])
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126 for test_data in self.structured_data_tests:
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127 if test_data["data"]["status"] == "success":
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128 continue
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129 test_case = test_data["id"].replace(".test_toolbox.", ".test_toolbox:")
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130 ids.add(test_case)
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131 return ids
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132
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133
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134 class GalaxyTestResults(object):
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135 """ Class that combine the test-centric xunit output
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136 with the Galaxy centric structured data output - and
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137 abstracts away the difference (someday).
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138 """
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139
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140 def __init__(
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141 self,
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142 output_json_path,
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143 output_xml_path,
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144 output_html_path,
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145 exit_code,
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146 ):
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147 self.output_html_path = output_html_path
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148 self.exit_code = exit_code
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149 sd = StructuredData(output_json_path)
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150 self.sd = sd
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151 self.structured_data = sd.structured_data
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152 self.structured_data_tests = sd.structured_data_tests
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153 self.structured_data_by_id = sd.structured_data_by_id
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154
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155 if output_xml_path:
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156 self.xunit_tree = parse_xunit_report(output_xml_path)
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157 sd.merge_xunit(self._xunit_root)
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158 else:
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159 self.xunit_tree = ET.fromstring("<testsuite />")
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160 self.sd.update()
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161
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162 @property
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163 def has_details(self):
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164 return self.sd.has_details
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165
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166 @property
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167 def num_tests(self):
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168 return self.sd.num_tests
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169
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170 @property
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171 def num_problems(self):
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172 return self.sd.num_problems
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173
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174 @property
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175 def _xunit_root(self):
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176 return self.xunit_tree.getroot()
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177
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178 @property
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179 def all_tests_passed(self):
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180 return self.sd.num_problems == 0
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181
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182 @property
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183 def xunit_testcase_elements(self):
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184 return xunit_t_elements_from_root(self._xunit_root)
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185
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186
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187 def xunit_t_elements_from_root(xunit_root):
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188 for testcase_el in find_cases(xunit_root):
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189 yield testcase_el
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190
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191
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192 def parse_xunit_report(xunit_report_path):
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193 return ET.parse(xunit_report_path)
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194
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195
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196 def find_cases(xunit_root):
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197 return xunit_root.findall("testcase")
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198
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199
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200 def case_id(testcase_el):
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201 name_raw = testcase_el.attrib["name"]
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202 if "TestForTool_" in name_raw:
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203 raw_id = name_raw
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204 else:
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205 class_name = testcase_el.attrib["classname"]
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206 raw_id = "{0}.{1}".format(class_name, name_raw)
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207
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208 name = None
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209 num = None
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210 if "TestForTool_" in raw_id:
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211 tool_and_num = raw_id.split("TestForTool_")[-1]
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212 if ".test_tool_" in tool_and_num:
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213 name, num_str = tool_and_num.split(".test_tool_", 1)
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214 num = _parse_num(num_str)
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215 # Tempted to but something human friendly in here like
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216 # num + 1 - but then it doesn't match HTML report.
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217 else:
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218 name = tool_and_num
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219 else:
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220 name = raw_id
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221
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222 return TestId(name, num, raw_id)
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223
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224
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225 def _parse_num(num_str):
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226 try:
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227 num = int(num_str)
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228 except ValueError:
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229 num = None
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230 return num
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231
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232
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233 TestId = namedtuple("TestId", ["name", "num", "id"])
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234
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235
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236 @property
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237 def _label(self):
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238 if self.num is not None:
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239 return "{0}[{1}]".format(self.name, self.num)
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240 else:
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241 return self.id
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242
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243
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244 TestId.label = _label