Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/galaxy/test/structures.py @ 2:6af9afd405e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 """Utilities for reasoning about Galaxy test results."""
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2 from __future__ import absolute_import
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3 from __future__ import print_function
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4
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5 import os
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6 from collections import namedtuple
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7 from xml.etree import ElementTree as ET
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8
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9 from six.moves import shlex_quote
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10
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11 from planemo.io import error
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12 from planemo.test.results import StructuredData as BaseStructuredData
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13
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14
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15 NO_STRUCTURED_FILE = (
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16 "Warning: Problem with target Galaxy, it did not "
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17 "produce a structured test results file [%s] - summary "
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18 "information and planemo reports will be incorrect."
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19 )
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20
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21
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22 class GalaxyTestCommand(object):
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23 """Abstraction around building a ``run_tests.sh`` command for Galaxy tests."""
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24
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25 def __init__(
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26 self,
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27 html_report_file,
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28 xunit_report_file,
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29 structured_report_file,
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30 failed=False,
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31 installed=False,
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32 ):
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33 self.html_report_file = html_report_file
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34 self.xunit_report_file = xunit_report_file
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35 self.structured_report_file = structured_report_file
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36 self.failed = failed
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37 self.installed = installed
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38
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39 def build(self):
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40 xunit_report_file = self.xunit_report_file
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41 sd_report_file = self.structured_report_file
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42 cmd = "sh run_tests.sh $COMMON_STARTUP_ARGS --report_file %s" % shlex_quote(self.html_report_file)
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43 if xunit_report_file:
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44 cmd += " --xunit_report_file %s" % shlex_quote(xunit_report_file)
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45 if sd_report_file:
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46 cmd += " --structured_data_report_file %s" % shlex_quote(sd_report_file)
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47 if self.installed:
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48 cmd += ' -installed'
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49 elif self.failed:
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50 sd = StructuredData(sd_report_file)
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51 tests = " ".join(sd.failed_ids)
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52 cmd += " %s" % tests
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53 else:
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54 cmd += ' functional.test_toolbox'
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55 return cmd
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56
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57
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58 class StructuredData(BaseStructuredData):
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59 """Abstraction around Galaxy's structured test data output."""
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60
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61 def __init__(self, json_path):
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62 if not json_path or not os.path.exists(json_path):
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63 error(NO_STRUCTURED_FILE % json_path)
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64 super(StructuredData, self).__init__(json_path)
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65
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66 def merge_xunit(self, xunit_root):
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67 self.has_details = True
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68 xunit_attrib = xunit_root.attrib
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69 num_tests = int(xunit_attrib.get("tests", 0))
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70 num_failures = int(xunit_attrib.get("failures", 0))
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71 num_errors = int(xunit_attrib.get("errors", 0))
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72 num_skips = int(xunit_attrib.get("skips", 0))
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73 summary = dict(
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74 num_tests=num_tests,
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75 num_failures=num_failures,
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76 num_errors=num_errors,
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77 num_skips=num_skips,
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78 )
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79
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80 self.structured_data["summary"] = summary
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81
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82 for testcase_el in xunit_t_elements_from_root(xunit_root):
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83 test = case_id(testcase_el)
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84 test_data = self.structured_data_by_id.get(test.id)
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85 if not test_data:
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86 continue
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87 problem_el = None
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88 for problem_type in ["skip", "failure", "error"]:
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89 problem_el = testcase_el.find(problem_type)
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90 if problem_el is not None:
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91 break
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92 if problem_el is not None:
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93 status = problem_el.tag
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94 test_data["problem_type"] = problem_el.attrib["type"]
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95 test_data["problem_log"] = problem_el.text
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96 else:
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97 status = "success"
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98 test_data["status"] = status
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99
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100
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101 class GalaxyTestResults(object):
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102 """ Class that combine the test-centric xunit output
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103 with the Galaxy centric structured data output - and
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104 abstracts away the difference (someday).
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105 """
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106
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107 def __init__(
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108 self,
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109 output_json_path,
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110 output_xml_path,
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111 output_html_path,
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112 exit_code,
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113 ):
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114 self.output_html_path = output_html_path
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115 sd = StructuredData(output_json_path)
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116 self.sd = sd
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117 self.structured_data = sd.structured_data
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118 self.structured_data_tests = sd.structured_data_tests
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119 self.structured_data_by_id = sd.structured_data_by_id
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120
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121 self.xunit_tree = parse_xunit_report(output_xml_path)
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122 sd.merge_xunit(self._xunit_root)
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123
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124 self.sd.set_exit_code(exit_code)
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125 self.sd.read_summary()
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126 self.sd.update()
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127
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128 @property
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129 def exit_code(self):
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130 return self.sd.exit_code
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131
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132 @property
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133 def has_details(self):
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134 return self.sd.has_details
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135
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136 @property
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137 def num_tests(self):
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138 return self.sd.num_tests
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139
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140 @property
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141 def num_problems(self):
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142 return self.sd.num_problems
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143
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144 @property
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145 def _xunit_root(self):
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146 return self.xunit_tree.getroot()
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147
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148 @property
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149 def all_tests_passed(self):
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150 return self.sd.num_problems == 0
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151
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152 @property
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153 def xunit_testcase_elements(self):
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154 return xunit_t_elements_from_root(self._xunit_root)
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155
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156
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157 def xunit_t_elements_from_root(xunit_root):
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158 for testcase_el in find_cases(xunit_root):
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159 yield testcase_el
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160
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161
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162 def parse_xunit_report(xunit_report_path):
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163 return ET.parse(xunit_report_path)
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164
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165
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166 def find_cases(xunit_root):
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167 return xunit_root.findall("testcase")
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168
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169
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170 def case_id(testcase_el=None, raw_id=None):
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171 if raw_id is None:
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172 assert testcase_el is not None
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173 name_raw = testcase_el.attrib["name"]
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174 if "TestForTool_" in name_raw:
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175 raw_id = name_raw
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176 else:
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177 class_name = testcase_el.attrib["classname"]
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178 raw_id = "{0}.{1}".format(class_name, name_raw)
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179
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180 name = None
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181 num = None
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182 if "TestForTool_" in raw_id:
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183 tool_and_num = raw_id.split("TestForTool_")[-1]
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184 if ".test_tool_" in tool_and_num:
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185 name, num_str = tool_and_num.split(".test_tool_", 1)
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186 num = _parse_num(num_str)
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187 # Tempted to but something human friendly in here like
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188 # num + 1 - but then it doesn't match HTML report.
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189 else:
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190 name = tool_and_num
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191 else:
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192 name = raw_id
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193
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194 return TestId(name, num, raw_id)
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195
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196
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197 def _parse_num(num_str):
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198 try:
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199 num = int(num_str)
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200 except ValueError:
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201 num = None
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202 return num
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203
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204
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205 TestId = namedtuple("TestId", ["name", "num", "id"])
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206
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207
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208 @property
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209 def _label(self):
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210 if self.num is not None:
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211 return "{0}[{1}]".format(self.name, self.num)
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212 else:
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213 return self.id
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214
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215
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216 TestId.label = _label