Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/prov/tests/test_xml.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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0
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1 from __future__ import (absolute_import, division, print_function,
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2 unicode_literals)
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3
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4 import difflib
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5 import glob
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6 import inspect
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7 import io
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8 from lxml import etree
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9 import os
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10 import unittest
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11 import warnings
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12
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13 from prov.identifier import Namespace, QualifiedName
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14 from prov.constants import PROV
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15 import prov.model as prov
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16 from prov.tests.test_model import AllTestsBase
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17 from prov.tests.utility import RoundTripTestCase
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18
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19
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20 EX_NS = ('ex', 'http://example.com/ns/ex#')
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21 EX_TR = ('tr', 'http://example.com/ns/tr#')
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22
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23 # Most general way to get the path.
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24 DATA_PATH = os.path.join(os.path.dirname(os.path.abspath(inspect.getfile(
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25 inspect.currentframe()))), "xml")
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26
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27
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28 def remove_empty_tags(tree):
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29 if tree.text is not None and tree.text.strip() == "":
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30 tree.text = None
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31 for elem in tree:
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32 if etree.iselement(elem):
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33 remove_empty_tags(elem)
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34
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35
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36 def compare_xml(doc1, doc2):
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37 """
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38 Helper function to compare two XML files. It will parse both once again
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39 and write them in a canonical fashion.
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40 """
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41 try:
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42 doc1.seek(0, 0)
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43 except AttributeError:
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44 pass
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45 try:
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46 doc2.seek(0, 0)
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47 except AttributeError:
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48 pass
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49
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50 obj1 = etree.parse(doc1)
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51 obj2 = etree.parse(doc2)
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52
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53 # Remove comments from both.
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54 for c in obj1.getroot().xpath("//comment()"):
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55 p = c.getparent()
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56 p.remove(c)
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57 for c in obj2.getroot().xpath("//comment()"):
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58 p = c.getparent()
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59 p.remove(c)
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60
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61 remove_empty_tags(obj1.getroot())
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62 remove_empty_tags(obj2.getroot())
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63
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64 buf = io.BytesIO()
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65 obj1.write_c14n(buf)
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66 buf.seek(0, 0)
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67 str1 = buf.read().decode()
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68 str1 = [_i.strip() for _i in str1.splitlines() if _i.strip()]
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69
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70 buf = io.BytesIO()
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71 obj2.write_c14n(buf)
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72 buf.seek(0, 0)
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73 str2 = buf.read().decode()
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74 str2 = [_i.strip() for _i in str2.splitlines() if _i.strip()]
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75
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76 unified_diff = difflib.unified_diff(str1, str2)
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77
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78 err_msg = "\n".join(unified_diff)
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79 if err_msg:
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80 msg = "Strings are not equal.\n"
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81 raise AssertionError(msg + err_msg)
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82
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83
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84 class ProvXMLTestCase(unittest.TestCase):
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85 def test_serialization_example_6(self):
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86 """
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87 Test the serialization of example 6 which is a simple entity
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88 description.
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89 """
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90 document = prov.ProvDocument()
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91 ex_ns = document.add_namespace(*EX_NS)
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92 document.add_namespace(*EX_TR)
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93
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94 document.entity("tr:WD-prov-dm-20111215", (
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95 (prov.PROV_TYPE, ex_ns["Document"]),
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96 ("ex:version", "2")
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97 ))
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98
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99 with io.BytesIO() as actual:
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100 document.serialize(format='xml', destination=actual)
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101 compare_xml(os.path.join(DATA_PATH, "example_06.xml"), actual)
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102
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103 def test_serialization_example_7(self):
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104 """
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105 Test the serialization of example 7 which is a basic activity.
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106 """
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107 document = prov.ProvDocument()
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108 document.add_namespace(*EX_NS)
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109
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110 document.activity(
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111 "ex:a1",
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112 "2011-11-16T16:05:00",
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113 "2011-11-16T16:06:00", [
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114 (prov.PROV_TYPE, prov.Literal("ex:edit", prov.XSD_QNAME)),
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115 ("ex:host", "server.example.org")])
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116
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117 with io.BytesIO() as actual:
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118 document.serialize(format='xml', destination=actual)
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119 compare_xml(os.path.join(DATA_PATH, "example_07.xml"), actual)
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120
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121 def test_serialization_example_8(self):
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122 """
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123 Test the serialization of example 8 which deals with generation.
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124 """
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125 document = prov.ProvDocument()
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126 document.add_namespace(*EX_NS)
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127
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128 e1 = document.entity("ex:e1")
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129 a1 = document.activity("ex:a1")
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130
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131 document.wasGeneratedBy(entity=e1, activity=a1,
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132 time="2001-10-26T21:32:52",
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133 other_attributes={"ex:port": "p1"})
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134
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135 e2 = document.entity("ex:e2")
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136
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137 document.wasGeneratedBy(entity=e2, activity=a1,
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138 time="2001-10-26T10:00:00",
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139 other_attributes={"ex:port": "p2"})
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140
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141 with io.BytesIO() as actual:
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142 document.serialize(format='xml', destination=actual)
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143 compare_xml(os.path.join(DATA_PATH, "example_08.xml"), actual)
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144
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145 def test_deserialization_example_6(self):
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146 """
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147 Test the deserialization of example 6 which is a simple entity
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148 description.
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149 """
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150 actual_doc = prov.ProvDocument.deserialize(
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151 source=os.path.join(DATA_PATH, "example_06.xml"),
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152 format="xml")
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153
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154 expected_document = prov.ProvDocument()
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155 ex_ns = expected_document.add_namespace(*EX_NS)
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156 expected_document.add_namespace(*EX_TR)
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157
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158 expected_document.entity("tr:WD-prov-dm-20111215", (
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159 (prov.PROV_TYPE, ex_ns["Document"]),
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160 ("ex:version", "2")
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161 ))
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162
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163 self.assertEqual(actual_doc, expected_document)
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164
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165 def test_deserialization_example_7(self):
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166 """
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167 Test the deserialization of example 7 which is a simple activity
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168 description.
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169 """
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170 actual_doc = prov.ProvDocument.deserialize(
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171 source=os.path.join(DATA_PATH, "example_07.xml"),
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172 format="xml")
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173
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174 expected_document = prov.ProvDocument()
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175 ex_ns = Namespace(*EX_NS)
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176 expected_document.add_namespace(ex_ns)
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177
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178 expected_document.activity(
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179 "ex:a1",
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180 "2011-11-16T16:05:00",
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181 "2011-11-16T16:06:00", [
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182 (prov.PROV_TYPE, QualifiedName(ex_ns, "edit")),
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183 ("ex:host", "server.example.org")])
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184
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185 self.assertEqual(actual_doc, expected_document)
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186
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187 def test_deserialization_example_04_and_05(self):
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188 """
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189 Example 4 and 5 have a different type specification. They use an
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190 xsi:type as an attribute on an entity. This can be read but if
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191 written again it will become an XML child element. This is
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192 semantically identical but cannot be tested with a round trip.
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193 """
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194 # Example 4.
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195 xml_string = """
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196 <prov:document
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197 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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198 xmlns:xsd="http://www.w3.org/2001/XMLSchema"
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199 xmlns:prov="http://www.w3.org/ns/prov#"
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200 xmlns:ex="http://example.com/ns/ex#"
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201 xmlns:tr="http://example.com/ns/tr#">
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202
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203 <prov:entity prov:id="tr:WD-prov-dm-20111215" xsi:type="prov:Plan">
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204 <prov:type xsi:type="xsd:QName">ex:Workflow</prov:type>
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205 </prov:entity>
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206
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207 </prov:document>
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208 """
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209 with io.StringIO() as xml:
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210 xml.write(xml_string)
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211 xml.seek(0, 0)
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212 actual_document = prov.ProvDocument.deserialize(source=xml,
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213 format="xml")
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214
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215 expected_document = prov.ProvDocument()
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216 ex_ns = Namespace(*EX_NS)
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217 expected_document.add_namespace(ex_ns)
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218 expected_document.add_namespace(*EX_TR)
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219
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220 # The xsi:type attribute is mapped to a proper PROV attribute.
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221 expected_document.entity("tr:WD-prov-dm-20111215", (
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222 (prov.PROV_TYPE, QualifiedName(ex_ns, "Workflow")),
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223 (prov.PROV_TYPE, PROV["Plan"])))
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224
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225 self.assertEqual(actual_document, expected_document, "example_04")
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226
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227 # Example 5.
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228 xml_string = """
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229 <prov:document
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230 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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231 xmlns:xsd="http://www.w3.org/2001/XMLSchema"
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232 xmlns:prov="http://www.w3.org/ns/prov#"
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233 xmlns:ex="http://example.com/ns/ex#"
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234 xmlns:tr="http://example.com/ns/tr#">
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235
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236 <prov:entity prov:id="tr:WD-prov-dm-20111215" xsi:type="prov:Plan">
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237 <prov:type xsi:type="xsd:QName">ex:Workflow</prov:type>
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238 <prov:type xsi:type="xsd:QName">prov:Plan</prov:type> <!-- inferred -->
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239 <prov:type xsi:type="xsd:QName">prov:Entity</prov:type> <!-- inferred -->
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240 </prov:entity>
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241
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242 </prov:document>
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243 """
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244 with io.StringIO() as xml:
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245 xml.write(xml_string)
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246 xml.seek(0, 0)
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247 actual_document = prov.ProvDocument.deserialize(source=xml,
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248 format="xml")
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249
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250 expected_document = prov.ProvDocument()
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251 expected_document.add_namespace(*EX_NS)
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252 expected_document.add_namespace(*EX_TR)
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253
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254 # The xsi:type attribute is mapped to a proper PROV attribute.
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255 expected_document.entity("tr:WD-prov-dm-20111215", (
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256 (prov.PROV_TYPE, QualifiedName(ex_ns, "Workflow")),
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257 (prov.PROV_TYPE, PROV["Entity"]),
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258 (prov.PROV_TYPE, PROV["Plan"])
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259 ))
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260
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261 self.assertEqual(actual_document, expected_document, "example_05")
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262
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263 def test_other_elements(self):
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264 """
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265 PROV XML uses the <prov:other> element to enable the storage of non
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266 PROV information in a PROV XML document. It will be ignored by this
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267 library a warning will be raised informing the user.
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268 """
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269 # This is example 42 from the PROV XML documentation.
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270 xml_string = """
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271 <prov:document
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272 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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273 xmlns:xsd="http://www.w3.org/2001/XMLSchema"
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274 xmlns:prov="http://www.w3.org/ns/prov#"
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275 xmlns:ex="http://example.com/ns/ex#">
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276
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277 <!-- prov statements go here -->
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278
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279 <prov:other>
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280 <ex:foo>
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281 <ex:content>bar</ex:content>
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282 </ex:foo>
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283 </prov:other>
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284
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285 <!-- more prov statements can go here -->
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286
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287 </prov:document>
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288 """
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289 with warnings.catch_warnings(record=True) as w:
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290 warnings.simplefilter("always")
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291
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292 with io.StringIO() as xml:
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293 xml.write(xml_string)
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294 xml.seek(0, 0)
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295 doc = prov.ProvDocument.deserialize(source=xml, format="xml")
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296
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297 self.assertEqual(len(w), 1)
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298 self.assertTrue(
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299 "Document contains non-PROV information in <prov:other>. It will "
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300 "be ignored in this package." in str(w[0].message))
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301
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302 # This document contains nothing else.
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303 self.assertEqual(len(doc._records), 0)
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304
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305 def test_nested_default_namespace(self):
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306 """
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307 Tests that a default namespace that is defined in a lower level tag is
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308 written to a bundle.
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309 """
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310 filename = os.path.join(DATA_PATH, "nested_default_namespace.xml")
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311 doc = prov.ProvDocument.deserialize(source=filename, format="xml")
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312
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313 ns = Namespace("", "http://example.org/0/")
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314
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315 self.assertEqual(len(doc._records), 1)
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316 self.assertEqual(doc.get_default_namespace(), ns)
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317 self.assertEqual(doc._records[0].identifier.namespace, ns)
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318 self.assertEqual(doc._records[0].identifier.localpart, "e001")
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319
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320 def test_redefining_namespaces(self):
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321 """
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322 Test the behaviour when namespaces are redefined at the element level.
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323 """
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324 filename = os.path.join(DATA_PATH,
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325 "namespace_redefined_but_does_not_change.xml")
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326 doc = prov.ProvDocument.deserialize(source=filename, format="xml")
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327 # This has one record part of the original namespace.
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328 self.assertEqual(len(doc._records), 1)
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329 ns = Namespace("ex", "http://example.com/ns/ex#")
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330 self.assertEqual(doc._records[0].attributes[0][1].namespace, ns)
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331
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332 # This also has one record but now in a different namespace.
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333 filename = os.path.join(DATA_PATH, "namespace_redefined.xml")
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334 doc = prov.ProvDocument.deserialize(source=filename, format="xml")
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335 new_ns = doc._records[0].attributes[0][1].namespace
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336 self.assertNotEqual(new_ns, ns)
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337 self.assertEqual(new_ns.uri, "http://example.com/ns/new_ex#")
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338
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339
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340 class ProvXMLRoundTripFromFileTestCase(unittest.TestCase):
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341 def _perform_round_trip(self, filename, force_types=False):
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342 document = prov.ProvDocument.deserialize(
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343 source=filename, format="xml")
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344
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345 with io.BytesIO() as new_xml:
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346 document.serialize(format='xml', destination=new_xml,
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347 force_types=force_types)
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348 compare_xml(filename, new_xml)
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349
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350
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351 # Add one test for each found file. Lazy way to do metaprogramming...
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352 # I think parametrized tests are justified in this case as the test
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353 # function names make it clear what is going on.
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354 for filename in glob.iglob(os.path.join(
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355 DATA_PATH, "*" + os.path.extsep + "xml")):
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356 name = os.path.splitext(os.path.basename(filename))[0]
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357 test_name = "test_roundtrip_from_xml_%s" % name
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358
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359 # Cannot round trip this one as the namespace in the PROV data model are
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360 # always defined per bundle and not per element.
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361 if name in ("nested_default_namespace",
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362 "nested_changing_default_namespace",
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363 "namespace_redefined_but_does_not_change",
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364 "namespace_redefined"):
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365 continue
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366
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367 # Python creates closures on function calls...
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368 def get_fct(f):
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369 # Some test files have a lot of type declarations...
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370 if name in ["pc1"]:
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371 force_types = True
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372 else:
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373 force_types = False
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374
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375 def fct(self):
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376 self._perform_round_trip(f, force_types=force_types)
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377 return fct
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378
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379 fct = get_fct(filename)
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380 fct.__name__ = str(test_name)
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381
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382 # Disabled round-trip XML comparisons since deserializing then serializing
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383 # PROV-XML does not maintain XML equivalence. (For example, prov:entity
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384 # elements with type prov:Plan become prov:plan elements)
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385 # TODO: Revisit these tests
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386
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387 # setattr(ProvXMLRoundTripFromFileTestCase, test_name, fct)
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388
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389
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390 class RoundTripXMLTests(RoundTripTestCase, AllTestsBase):
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391 FORMAT = 'xml'
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392
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393
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394 if __name__ == '__main__':
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395 unittest.main()