Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/schema_salad/tests/test_examples.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 from __future__ import absolute_import, print_function
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2
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3 import os
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4
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5 import six
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6
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7 import ruamel.yaml
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8 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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9 import schema_salad.main
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10 import schema_salad.ref_resolver
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11 import schema_salad.schema
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12 from schema_salad.jsonld_context import makerdf
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13 from schema_salad.sourceline import SourceLine, cmap
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14
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15 from .util import get_data
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16
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17
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18 def test_schemas():
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19 loader = schema_salad.ref_resolver.Loader({})
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20
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21 ra, _ = loader.resolve_all(
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22 cmap(
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23 {
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24 u"$schemas": [
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25 schema_salad.ref_resolver.file_uri(get_data("tests/EDAM.owl"))
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26 ],
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27 u"$namespaces": {u"edam": u"http://edamontology.org/"},
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28 u"edam:has_format": u"edam:format_1915",
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29 }
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30 ),
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31 "",
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32 )
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33
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34 assert {
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35 u"$schemas": [schema_salad.ref_resolver.file_uri(get_data("tests/EDAM.owl"))],
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36 u"$namespaces": {u"edam": u"http://edamontology.org/"},
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37 u"http://edamontology.org/has_format": u"http://edamontology.org/format_1915",
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38 } == ra
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39
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40
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41 def test_self_validate():
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42 assert 0 == schema_salad.main.main(argsl=[get_data("metaschema/metaschema.yml")])
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43 assert 0 == schema_salad.main.main(
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44 argsl=[
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45 get_data("metaschema/metaschema.yml"),
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46 get_data("metaschema/metaschema.yml"),
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47 ]
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48 )
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49
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50
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51 def test_avro_regression():
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52 assert 0 == schema_salad.main.main(argsl=[get_data("tests/Process.yml")])
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53
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54
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55 def test_jsonld_ctx():
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56 ldr, _, _, _ = schema_salad.schema.load_schema(
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57 cmap(
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58 {
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59 "$base": "Y",
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60 "name": "X",
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61 "$namespaces": {"foo": "http://example.com/foo#"},
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62 "$graph": [
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63 {"name": "ExampleType", "type": "enum", "symbols": ["asym", "bsym"]}
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64 ],
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65 }
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66 )
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67 )
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68
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69 ra, _ = ldr.resolve_all(cmap({"foo:bar": "asym"}), "X")
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70
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71 assert ra == {"http://example.com/foo#bar": "asym"}
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72
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73
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74 def test_idmap():
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75 ldr = schema_salad.ref_resolver.Loader({})
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76 ldr.add_context(
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77 {
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78 "inputs": {
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79 "@id": "http://example.com/inputs",
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80 "mapSubject": "id",
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81 "mapPredicate": "a",
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82 },
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83 "outputs": {"@type": "@id", "identity": True},
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84 "id": "@id",
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85 }
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86 )
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87
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88 ra, _ = ldr.resolve_all(
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89 cmap(
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90 {
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91 "id": "stuff",
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92 "inputs": {"zip": 1, "zing": 2},
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93 "outputs": ["out"],
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94 "other": {"n": 9},
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95 }
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96 ),
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97 "http://example2.com/",
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98 )
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99
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100 assert "http://example2.com/#stuff" == ra["id"]
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101 for item in ra["inputs"]:
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102 if item["a"] == 2:
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103 assert "http://example2.com/#stuff/zing" == item["id"]
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104 else:
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105 assert "http://example2.com/#stuff/zip" == item["id"]
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106 assert ["http://example2.com/#stuff/out"] == ra["outputs"]
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107 assert {"n": 9} == ra["other"]
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108
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109
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110 def test_scoped_ref():
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111 ldr = schema_salad.ref_resolver.Loader({})
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112 ldr.add_context(
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113 {
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114 "scatter": {"@type": "@id", "refScope": 0},
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115 "source": {"@type": "@id", "refScope": 2},
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116 "in": {"mapSubject": "id", "mapPredicate": "source"},
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117 "out": {"@type": "@id", "identity": True},
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118 "inputs": {"mapSubject": "id", "mapPredicate": "type"},
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119 "outputs": {"mapSubject": "id"},
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120 "steps": {"mapSubject": "id"},
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121 "id": "@id",
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122 }
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123 )
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124
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125 ra, _ = ldr.resolve_all(
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126 cmap(
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127 {
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128 "inputs": {"inp": "string", "inp2": "string"},
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129 "outputs": {"out": {"type": "string", "source": "step2/out"}},
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130 "steps": {
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131 "step1": {
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132 "in": {"inp": "inp", "inp2": "#inp2", "inp3": ["inp", "inp2"]},
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133 "out": ["out"],
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134 "scatter": "inp",
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135 },
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136 "step2": {
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137 "in": {"inp": "step1/out"},
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138 "scatter": "inp",
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139 "out": ["out"],
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140 },
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141 },
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142 }
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143 ),
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144 "http://example2.com/",
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145 )
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146
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147 assert {
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148 "inputs": [
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149 {"id": "http://example2.com/#inp", "type": "string"},
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150 {"id": "http://example2.com/#inp2", "type": "string"},
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151 ],
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152 "outputs": [
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153 {
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154 "id": "http://example2.com/#out",
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155 "type": "string",
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156 "source": "http://example2.com/#step2/out",
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157 }
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158 ],
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159 "steps": [
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160 {
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161 "id": "http://example2.com/#step1",
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162 "scatter": "http://example2.com/#step1/inp",
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163 "in": [
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164 {
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165 "id": "http://example2.com/#step1/inp",
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166 "source": "http://example2.com/#inp",
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167 },
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168 {
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169 "id": "http://example2.com/#step1/inp2",
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170 "source": "http://example2.com/#inp2",
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171 },
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172 {
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173 "id": "http://example2.com/#step1/inp3",
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174 "source": [
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175 "http://example2.com/#inp",
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176 "http://example2.com/#inp2",
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177 ],
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178 },
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179 ],
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180 "out": ["http://example2.com/#step1/out"],
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181 },
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182 {
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183 "id": "http://example2.com/#step2",
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184 "scatter": "http://example2.com/#step2/inp",
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185 "in": [
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186 {
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187 "id": "http://example2.com/#step2/inp",
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188 "source": "http://example2.com/#step1/out",
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189 }
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190 ],
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191 "out": ["http://example2.com/#step2/out"],
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192 },
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193 ],
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194 } == ra
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195
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196
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197 def test_examples():
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198 for a in ["field_name", "ident_res", "link_res", "vocab_res"]:
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199 ldr, _, _, _ = schema_salad.schema.load_schema(
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200 get_data("metaschema/%s_schema.yml" % a)
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201 )
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202 with open(get_data("metaschema/%s_src.yml" % a)) as src_fp:
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203 src = ldr.resolve_all(
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204 ruamel.yaml.round_trip_load(src_fp), "", checklinks=False
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205 )[0]
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206 with open(get_data("metaschema/%s_proc.yml" % a)) as src_proc:
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207 proc = ruamel.yaml.safe_load(src_proc)
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208 assert proc == src
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209
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210
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211 def test_yaml_float_test():
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212 assert ruamel.yaml.safe_load("float-test: 2e-10")["float-test"] == 2e-10
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213
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214
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215 def test_typedsl_ref():
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216 ldr = schema_salad.ref_resolver.Loader({})
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217 ldr.add_context(
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218 {
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219 "File": "http://example.com/File",
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220 "null": "http://example.com/null",
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221 "array": "http://example.com/array",
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222 "type": {"@type": "@vocab", "typeDSL": True},
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223 }
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224 )
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225
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226 ra, _ = ldr.resolve_all(cmap({"type": "File"}), "")
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227 assert {"type": "File"} == ra
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228
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229 ra, _ = ldr.resolve_all(cmap({"type": "File?"}), "")
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230 assert {"type": ["null", "File"]} == ra
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231
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232 ra, _ = ldr.resolve_all(cmap({"type": "File[]"}), "")
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233 assert {"type": {"items": "File", "type": "array"}} == ra
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234
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235 ra, _ = ldr.resolve_all(cmap({"type": "File[]?"}), "")
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236 assert {"type": ["null", {"items": "File", "type": "array"}]} == ra
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237
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238
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239 def test_secondaryFile_dsl_ref():
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240 ldr = schema_salad.ref_resolver.Loader({})
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241 ldr.add_context({"secondaryFiles": {"secondaryFilesDSL": True}})
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242
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243 ra, _ = ldr.resolve_all(cmap({"secondaryFiles": ".foo"}), "")
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244 assert {"secondaryFiles": {"pattern": ".foo", "required": None}} == ra
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245
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246 ra, _ = ldr.resolve_all(cmap({"secondaryFiles": ".foo?"}), "")
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247 assert {"secondaryFiles": {"pattern": ".foo", "required": False}} == ra
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248
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249 ra, _ = ldr.resolve_all(cmap({"secondaryFiles": [".foo"]}), "")
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250 assert {"secondaryFiles": [{"pattern": ".foo", "required": None}]} == ra
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251
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252 ra, _ = ldr.resolve_all(cmap({"secondaryFiles": [".foo?"]}), "")
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253 assert {"secondaryFiles": [{"pattern": ".foo", "required": False}]} == ra
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254
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255
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256 def test_scoped_id():
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257 ldr = schema_salad.ref_resolver.Loader({})
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258 ctx = {
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259 "id": "@id",
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260 "location": {"@id": "@id", "@type": "@id"},
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261 "bar": "http://example.com/bar",
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262 "ex": "http://example.com/",
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parents:
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263 }
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parents:
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264 ldr.add_context(ctx)
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265
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266 ra, _ = ldr.resolve_all(
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parents:
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267 cmap({"id": "foo", "bar": {"id": "baz"}}), "http://example.com"
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parents:
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268 )
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269 assert {
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270 "id": "http://example.com/#foo",
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parents:
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271 "bar": {"id": "http://example.com/#foo/baz"},
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parents:
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272 } == ra
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273
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274 g = makerdf(None, ra, ctx)
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parents:
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275 print(g.serialize(format="n3"))
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parents:
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276
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277 ra, _ = ldr.resolve_all(
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278 cmap({"location": "foo", "bar": {"location": "baz"}}),
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279 "http://example.com",
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280 checklinks=False,
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281 )
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282 assert {
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283 "location": "http://example.com/foo",
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284 "bar": {"location": "http://example.com/baz"},
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parents:
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285 } == ra
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286
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287 g = makerdf(None, ra, ctx)
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288 print(g.serialize(format="n3"))
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289
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290 ra, _ = ldr.resolve_all(
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parents:
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291 cmap({"id": "foo", "bar": {"location": "baz"}}),
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parents:
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292 "http://example.com",
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293 checklinks=False,
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parents:
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294 )
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295 assert {
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296 "id": "http://example.com/#foo",
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297 "bar": {"location": "http://example.com/baz"},
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parents:
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298 } == ra
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299
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300 g = makerdf(None, ra, ctx)
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301 print(g.serialize(format="n3"))
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parents:
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302
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303 ra, _ = ldr.resolve_all(
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parents:
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304 cmap({"location": "foo", "bar": {"id": "baz"}}),
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parents:
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305 "http://example.com",
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306 checklinks=False,
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parents:
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307 )
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308 assert {
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309 "location": "http://example.com/foo",
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310 "bar": {"id": "http://example.com/#baz"},
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parents:
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311 } == ra
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312
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313 g = makerdf(None, ra, ctx)
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314 print(g.serialize(format="n3"))
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parents:
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315
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316
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317 def test_subscoped_id():
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318 ldr = schema_salad.ref_resolver.Loader({})
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319 ctx = {"id": "@id", "bar": {"subscope": "bar"}}
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320 ldr.add_context(ctx)
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321
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322 ra, _ = ldr.resolve_all(
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323 cmap({"id": "foo", "bar": {"id": "baz"}}), "http://example.com"
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parents:
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324 )
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325 assert {
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326 "id": "http://example.com/#foo",
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parents:
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327 "bar": {"id": "http://example.com/#foo/bar/baz"},
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guerler
parents:
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328 } == ra
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parents:
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329
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330
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331 def test_mixin():
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332 base_url = schema_salad.ref_resolver.file_uri(os.path.join(os.getcwd(), "tests"))
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parents:
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333 ldr = schema_salad.ref_resolver.Loader({})
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parents:
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334 ra = ldr.resolve_ref(
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parents:
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335 cmap({"$mixin": get_data("tests/mixin.yml"), "one": "five"}), base_url=base_url
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guerler
parents:
diff changeset
336 )
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parents:
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337 assert {"id": "four", "one": "five"} == ra[0]
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guerler
parents:
diff changeset
338 ldr = schema_salad.ref_resolver.Loader({"id": "@id"})
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guerler
parents:
diff changeset
339
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340 ra = ldr.resolve_all(
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parents:
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341 cmap(
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parents:
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342 [
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parents:
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343 {"id": "a", "m": {"$mixin": get_data("tests/mixin.yml")}},
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parents:
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344 {"id": "b", "m": {"$mixin": get_data("tests/mixin.yml")}},
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parents:
diff changeset
345 ]
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guerler
parents:
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346 ),
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347 base_url=base_url,
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guerler
parents:
diff changeset
348 )
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parents:
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349 assert [
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parents:
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350 {"id": base_url + "#a", "m": {"id": base_url + u"#a/four", "one": "two"}},
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guerler
parents:
diff changeset
351 {"id": base_url + "#b", "m": {"id": base_url + u"#b/four", "one": "two"}},
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guerler
parents:
diff changeset
352 ] == ra[0]
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guerler
parents:
diff changeset
353
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guerler
parents:
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354
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parents:
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355 def test_fragment():
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guerler
parents:
diff changeset
356 ldr = schema_salad.ref_resolver.Loader({"id": "@id"})
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guerler
parents:
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357 b, _ = ldr.resolve_ref(get_data("tests/frag.yml#foo2"))
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guerler
parents:
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358 assert {"id": b["id"], "bar": "b2"} == b
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guerler
parents:
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359
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guerler
parents:
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360
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guerler
parents:
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361 def test_file_uri():
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guerler
parents:
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362 # Note: this test probably won't pass on Windows. Someone with a
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guerler
parents:
diff changeset
363 # windows box should add an alternate test.
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guerler
parents:
diff changeset
364 assert "file:///foo/bar%20baz/quux" == schema_salad.ref_resolver.file_uri(
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guerler
parents:
diff changeset
365 "/foo/bar baz/quux"
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guerler
parents:
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366 )
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guerler
parents:
diff changeset
367 assert os.path.normpath(
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guerler
parents:
diff changeset
368 "/foo/bar baz/quux"
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guerler
parents:
diff changeset
369 ) == schema_salad.ref_resolver.uri_file_path("file:///foo/bar%20baz/quux")
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guerler
parents:
diff changeset
370 assert (
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guerler
parents:
diff changeset
371 "file:///foo/bar%20baz/quux%23zing%20zong"
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guerler
parents:
diff changeset
372 == schema_salad.ref_resolver.file_uri("/foo/bar baz/quux#zing zong")
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guerler
parents:
diff changeset
373 )
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guerler
parents:
diff changeset
374 assert (
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guerler
parents:
diff changeset
375 "file:///foo/bar%20baz/quux#zing%20zong"
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guerler
parents:
diff changeset
376 == schema_salad.ref_resolver.file_uri(
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guerler
parents:
diff changeset
377 "/foo/bar baz/quux#zing zong", split_frag=True
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guerler
parents:
diff changeset
378 )
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guerler
parents:
diff changeset
379 )
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guerler
parents:
diff changeset
380 assert os.path.normpath(
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guerler
parents:
diff changeset
381 "/foo/bar baz/quux#zing zong"
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382 ) == schema_salad.ref_resolver.uri_file_path(
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383 "file:///foo/bar%20baz/quux#zing%20zong"
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384 )
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385
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386
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387 def test_sourceline():
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388 ldr = schema_salad.ref_resolver.Loader({"id": "@id"})
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389 b, _ = ldr.resolve_ref(get_data("tests/frag.yml"))
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390
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391 class TestExp(Exception):
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392 pass
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393
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394 try:
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395 with SourceLine(b, 1, TestExp, False):
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396 raise Exception("Whoops")
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397 except TestExp as e:
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398 assert str(e).endswith("frag.yml:3:3: Whoops"), e
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399 except Exception as exc:
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400 assert False, exc
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401
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402 if six.PY2:
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403 try:
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404 with SourceLine(b, 1, TestExp, True):
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405 raise Exception("Whoops")
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406 except TestExp as e:
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407 assert (
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408 str(e)
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409 .splitlines()[0]
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410 .endswith("frag.yml:3:3: Traceback (most recent call last):")
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411 ), str(e)
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412 except Exception as exc:
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413 assert False, exc
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414
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415
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416 def test_cmap():
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417 # Test bugfix that cmap won't fail when given a CommentedMap with no lc.data
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418 cmap(CommentedMap((("foo", "bar"), ("baz", ["quux"]))))
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419 cmap(CommentedSeq(("foo", [], "bar")))
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420
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421
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422 def test_blank_node_id():
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423 # Test that blank nodes are passed through and not considered
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424 # relative paths. Blank nodes (also called anonymous ids) are
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425 # URIs starting with "_:". They are randomly generated
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426 # placeholders mainly used internally where an id is needed but
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427 # was not given.
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428
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429 ldr = schema_salad.ref_resolver.Loader({})
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430 ctx = {"id": "@id"}
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431 ldr.add_context(ctx)
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432
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433 ra, _ = ldr.resolve_all(cmap({"id": "_:foo"}), "http://example.com")
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434 assert {"id": "_:foo"} == ra