Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/schema_salad/avro/schema.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 # Licensed to the Apache Software Foundation (ASF) under one
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2 # or more contributor license agreements. See the NOTICE file
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3 # distributed with this work for additional information
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4 # regarding copyright ownership. The ASF licenses this file
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5 # to you under the Apache License, Version 2.0 (the
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6 # "License"); you may not use this file except in compliance
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7 # with the License. You may obtain a copy of the License at
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8 #
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9 # http://www.apache.org/licenses/LICENSE-2.0
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10 #
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11 # Unless required by applicable law or agreed to in writing, software
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12 # distributed under the License is distributed on an "AS IS" BASIS,
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13 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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14 # See the License for the specific language governing permissions and
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15 # limitations under the License.
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16 # Modifications copyright (C) 2017-2018 Common Workflow Language.
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17 """
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18 Contains the Schema classes.
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19
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20 A schema may be one of:
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21 A record, mapping field names to field value data;
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22 An enum, containing one of a small set of symbols;
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23 An array of values, all of the same schema;
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24 A union of other schemas;
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25 A unicode string;
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26 A 32-bit signed int;
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27 A 64-bit signed long;
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28 A 32-bit floating-point float;
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29 A 64-bit floating-point double;
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30 A boolean; or
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31 Null.
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32 """
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33 from typing import Any, Dict, List, Optional, Text, Tuple, Union, cast
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34
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35 from schema_salad.exceptions import SchemaException
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36
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37 import six
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38
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39 #
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40 # Constants
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41 #
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42
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43 PRIMITIVE_TYPES = ("null", "boolean", "string", "int", "long", "float", "double")
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44
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45 NAMED_TYPES = ("enum", "record")
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46
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47 VALID_TYPES = PRIMITIVE_TYPES + NAMED_TYPES + ("array", "union")
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48
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49 SCHEMA_RESERVED_PROPS = (
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50 "type",
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51 "name",
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52 "namespace",
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53 "fields", # Record
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54 "items", # Array
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55 "symbols", # Enum
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56 "doc",
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57 )
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58
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59 FIELD_RESERVED_PROPS = ("default", "name", "doc", "order", "type")
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60
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61 VALID_FIELD_SORT_ORDERS = ("ascending", "descending", "ignore")
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62
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63 #
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64 # Exceptions
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65 #
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66
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67
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68 class AvroException(SchemaException):
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69 pass
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70
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71
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72 class SchemaParseException(AvroException):
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73 pass
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74
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75
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76 #
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77 # Base Classes
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78 #
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79
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80
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81 class Schema(object):
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82 """Base class for all Schema classes."""
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83
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84 def __init__(self, atype, other_props=None):
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85 # type: (Text, Optional[Dict[Text, Any]]) -> None
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86 # Ensure valid ctor args
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87 if not isinstance(atype, six.string_types):
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88 raise SchemaParseException(
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89 "Schema type '{}' must be a string, was '{}.".format(atype, type(atype))
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90 )
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91 elif atype not in VALID_TYPES:
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92 fail_msg = "%s is not a valid type." % atype
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93 raise SchemaParseException(fail_msg)
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94
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95 # add members
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96 if not hasattr(self, "_props"):
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97 self._props = {} # type: Dict[Text, Any]
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98 self.set_prop("type", atype)
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99 self.type = atype
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100 self._props.update(other_props or {})
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101
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102 # Read-only properties dict. Printing schemas
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103 # creates JSON properties directly from this dict.
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104 props = property(lambda self: self._props)
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105
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106 # utility functions to manipulate properties dict
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107 def get_prop(self, key): # type: (Text) -> Any
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108 return self._props.get(key)
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109
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110 def set_prop(self, key, value): # type: (Text, Any) -> None
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111 self._props[key] = value
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112
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113
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114 class Name(object):
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115 """Class to describe Avro name."""
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116
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117 def __init__(self, name_attr, space_attr, default_space):
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118 # type: (Text, Optional[Text], Optional[Text]) -> None
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119 """
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120 Formulate full name according to the specification.
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121
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122 @arg name_attr: name value read in schema or None.
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123 @arg space_attr: namespace value read in schema or None.
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124 @ard default_space: the current default space or None.
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125 """
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126 # Ensure valid ctor args
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127 if not (isinstance(name_attr, six.string_types) or (name_attr is None)):
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128 fail_msg = "Name must be non-empty string or None."
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129 raise SchemaParseException(fail_msg)
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130 elif name_attr == "":
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131 fail_msg = "Name must be non-empty string or None."
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132 raise SchemaParseException(fail_msg)
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133
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134 if not (isinstance(space_attr, six.string_types) or (space_attr is None)):
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135 fail_msg = "Space must be non-empty string or None."
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136 raise SchemaParseException(fail_msg)
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137 elif name_attr == "":
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138 fail_msg = "Space must be non-empty string or None."
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139 raise SchemaParseException(fail_msg)
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140
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141 if not (isinstance(default_space, six.string_types) or (default_space is None)):
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142 fail_msg = "Default space must be non-empty string or None."
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143 raise SchemaParseException(fail_msg)
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144 elif name_attr == "":
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145 fail_msg = "Default must be non-empty string or None."
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146 raise SchemaParseException(fail_msg)
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147
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148 self._full = None # type: Optional[Text]
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149
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150 if name_attr is None or name_attr == "":
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151 return
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152
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153 if name_attr.find(".") < 0:
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154 if (space_attr is not None) and (space_attr != ""):
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155 self._full = "%s.%s" % (space_attr, name_attr)
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156 else:
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157 if (default_space is not None) and (default_space != ""):
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158 self._full = "%s.%s" % (default_space, name_attr)
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159 else:
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160 self._full = name_attr
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161 else:
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162 self._full = name_attr
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163
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164 fullname = property(lambda self: self._full)
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165
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166 def get_space(self):
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167 # type: () -> Optional[Text]
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168 """Back out a namespace from full name."""
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169 if self._full is None:
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170 return None
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171
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172 if self._full.find(".") > 0:
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173 return self._full.rsplit(".", 1)[0]
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174 else:
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175 return ""
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176
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177
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178 class Names(object):
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179 """Track name set and default namespace during parsing."""
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180
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181 def __init__(self, default_namespace=None):
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182 # type: (Optional[Text]) -> None
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183 self.names = {} # type: Dict[Text, NamedSchema]
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184 self.default_namespace = default_namespace
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185
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186 def has_name(self, name_attr, space_attr):
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187 # type: (Text, Optional[Text]) -> bool
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188 test = Name(name_attr, space_attr, self.default_namespace).fullname
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189 return test in self.names
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190
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191 def get_name(self, name_attr, space_attr):
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192 # type: (Text, Optional[Text]) -> Optional[NamedSchema]
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193 test = Name(name_attr, space_attr, self.default_namespace).fullname
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194 if test not in self.names:
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195 return None
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196 return self.names[test]
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197
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198 def add_name(self, name_attr, space_attr, new_schema):
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199 # type: (Text, Optional[Text], NamedSchema) -> Name
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200 """
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201 Add a new schema object to the name set.
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202
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203 @arg name_attr: name value read in schema
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204 @arg space_attr: namespace value read in schema.
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205
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206 @return: the Name that was just added.
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207 """
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208 to_add = Name(name_attr, space_attr, self.default_namespace)
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209
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210 if to_add.fullname in VALID_TYPES:
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211 fail_msg = "%s is a reserved type name." % to_add.fullname
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212 raise SchemaParseException(fail_msg)
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213 elif to_add.fullname in self.names:
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214 fail_msg = 'The name "%s" is already in use.' % to_add.fullname
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215 raise SchemaParseException(fail_msg)
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216
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217 self.names[to_add.fullname] = new_schema
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218 return to_add
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219
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220
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221 class NamedSchema(Schema):
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222 """Named Schemas specified in NAMED_TYPES."""
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223
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224 def __init__(
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225 self,
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226 atype, # type: Text
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227 name, # type: Text
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228 namespace=None, # type: Optional[Text]
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229 names=None, # type: Optional[Names]
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230 other_props=None, # type: Optional[Dict[Text, Text]]
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231 ): # type: (...) -> None
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232 # Ensure valid ctor args
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233 if not name:
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234 fail_msg = "Named Schemas must have a non-empty name."
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235 raise SchemaParseException(fail_msg)
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236 elif not isinstance(name, six.string_types):
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237 fail_msg = "The name property must be a string."
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238 raise SchemaParseException(fail_msg)
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239 elif namespace is not None and not isinstance(namespace, six.string_types):
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240 fail_msg = "The namespace property must be a string."
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241 raise SchemaParseException(fail_msg)
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242 if names is None:
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243 raise SchemaParseException("Must provide Names.")
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244
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245 # Call parent ctor
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246 Schema.__init__(self, atype, other_props)
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247
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248 # Add class members
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249 new_name = names.add_name(name, namespace, self)
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250
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251 # Store name and namespace as they were read in origin schema
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252 self.set_prop("name", name)
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253 if namespace is not None:
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254 self.set_prop("namespace", new_name.get_space())
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255
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256 # Store full name as calculated from name, namespace
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257 self._fullname = new_name.fullname
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258
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259 # read-only properties
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260 name = property(lambda self: self.get_prop("name"))
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261
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262
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263 class Field(object):
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264 def __init__(
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265 self,
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266 atype, # type: Union[Text, Dict[Text, Text]]
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267 name, # type: Text
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268 has_default, # type: bool
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269 default=None, # type: Optional[Text]
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270 order=None, # type: Optional[Text]
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271 names=None, # type: Optional[Names]
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272 doc=None, # type: Optional[Text]
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273 other_props=None, # type: Optional[Dict[Text, Text]]
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274 ): # type: (...) -> None
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275 # Ensure valid ctor args
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276 if not name:
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277 fail_msg = "Fields must have a non-empty name."
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278 raise SchemaParseException(fail_msg)
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279 elif not isinstance(name, six.string_types):
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280 fail_msg = "The name property must be a string."
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281 raise SchemaParseException(fail_msg)
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282 elif order is not None and order not in VALID_FIELD_SORT_ORDERS:
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283 fail_msg = "The order property %s is not valid." % order
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284 raise SchemaParseException(fail_msg)
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285
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286 # add members
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287 self._props = {} # type: Dict[Text, Union[Schema, Text, None]]
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288 self._has_default = has_default
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289 self._props.update(other_props or {})
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290
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291 if (
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292 isinstance(atype, six.string_types)
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293 and names is not None
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294 and names.has_name(atype, None)
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295 ):
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296 type_schema = cast(NamedSchema, names.get_name(atype, None)) # type: Schema
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297 else:
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298 try:
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299 type_schema = make_avsc_object(cast(Dict[Text, Text], atype), names)
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300 except Exception as e:
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301 raise SchemaParseException(
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302 'Type property "%s" not a valid Avro schema: %s' % (atype, e)
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303 )
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304 self.set_prop("type", type_schema)
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305 self.set_prop("name", name)
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306 self.type = type_schema
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307 self.name = name
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308 # TODO(hammer): check to ensure default is valid
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309 if has_default:
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310 self.set_prop("default", default)
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311 if order is not None:
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312 self.set_prop("order", order)
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313 if doc is not None:
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314 self.set_prop("doc", doc)
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315
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316 # read-only properties
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317 default = property(lambda self: self.get_prop("default"))
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318
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319 # utility functions to manipulate properties dict
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320 def get_prop(self, key): # type: (Text) -> Union[Schema, Text, None]
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321 return self._props.get(key)
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322
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323 def set_prop(self, key, value):
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324 # type: (Text, Union[Schema, Text, None]) -> None
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325 self._props[key] = value
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326
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327
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328 #
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329 # Primitive Types
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330 #
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331 class PrimitiveSchema(Schema):
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332 """Valid primitive types are in PRIMITIVE_TYPES."""
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333
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334 def __init__(self, atype, other_props=None):
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335 # type: (Text, Optional[Dict[Text, Text]]) -> None
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336 # Ensure valid ctor args
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337 if atype not in PRIMITIVE_TYPES:
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338 raise AvroException("%s is not a valid primitive type." % atype)
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339
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340 # Call parent ctor
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341 Schema.__init__(self, atype, other_props=other_props)
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342
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343 self.fullname = atype
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344
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345
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346 #
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347 # Complex Types (non-recursive)
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348 #
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349
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350
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351 class EnumSchema(NamedSchema):
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352 def __init__(
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353 self,
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354 name, # type: Text
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355 namespace, # type: Text
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356 symbols, # type: List[Text]
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357 names=None, # type: Optional[Names]
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358 doc=None, # type: Optional[Text]
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359 other_props=None, # type: Optional[Dict[Text, Text]]
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360 ): # type: (...) -> None
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361 # Ensure valid ctor args
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362 if not isinstance(symbols, list):
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363 fail_msg = "Enum Schema requires a JSON array for the symbols property."
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364 raise AvroException(fail_msg)
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365 elif False in [isinstance(s, six.string_types) for s in symbols]:
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366 fail_msg = "Enum Schema requires all symbols to be JSON strings."
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367 raise AvroException(fail_msg)
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368 elif len(set(symbols)) < len(symbols):
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369 fail_msg = "Duplicate symbol: %s" % symbols
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370 raise AvroException(fail_msg)
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371
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372 # Call parent ctor
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373 NamedSchema.__init__(self, "enum", name, namespace, names, other_props)
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374
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375 # Add class members
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376 self.set_prop("symbols", symbols)
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377 if doc is not None:
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378 self.set_prop("doc", doc)
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379
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380 # read-only properties
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381 symbols = property(lambda self: self.get_prop("symbols"))
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382
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383
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384 #
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385 # Complex Types (recursive)
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386 #
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387
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388
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389 class ArraySchema(Schema):
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390 def __init__(self, items, names=None, other_props=None):
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391 # type: (List[Any], Optional[Names], Optional[Dict[Text, Text]]) -> None
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392 # Call parent ctor
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393 Schema.__init__(self, "array", other_props)
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394 # Add class members
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395
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396 if names is None:
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397 raise SchemaParseException("Must provide Names.")
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398 if isinstance(items, six.string_types) and names.has_name(items, None):
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399 items_schema = cast(Schema, names.get_name(items, None))
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400 else:
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401 try:
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402 items_schema = make_avsc_object(items, names)
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403 except Exception as err:
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404 raise SchemaParseException(
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405 "Items schema (%s) not a valid Avro schema: %s (known "
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406 "names: %s)" % (items, err, list(names.names.keys()))
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407 )
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408
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409 self.set_prop("items", items_schema)
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410
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411 # read-only properties
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412 items = property(lambda self: self.get_prop("items"))
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413
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414
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415 class UnionSchema(Schema):
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416 """
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417 names is a dictionary of schema objects
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418 """
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419
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420 def __init__(self, schemas, names=None):
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421 # type: (List[Schema], Optional[Names]) -> None
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422 # Ensure valid ctor args
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423 if names is None:
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424 raise SchemaParseException("Must provide Names.")
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425 if not isinstance(schemas, list):
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426 fail_msg = "Union schema requires a list of schemas."
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427 raise SchemaParseException(fail_msg)
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428
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429 # Call parent ctor
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430 Schema.__init__(self, "union")
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431
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432 # Add class members
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433 schema_objects = [] # type: List[Schema]
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434 for schema in schemas:
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435 if isinstance(schema, six.string_types) and names.has_name(schema, None):
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436 new_schema = cast(Schema, names.get_name(schema, None))
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437 else:
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438 try:
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439 new_schema = make_avsc_object(schema, names) # type: ignore
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440 except Exception as err:
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441 raise SchemaParseException(
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442 "Union item must be a valid Avro schema: %s" % Text(err)
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443 )
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444 # check the new schema
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445 if (
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446 new_schema.type in VALID_TYPES
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447 and new_schema.type not in NAMED_TYPES
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448 and new_schema.type in [schema.type for schema in schema_objects]
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449 ):
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450 raise SchemaParseException("%s type already in Union" % new_schema.type)
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451 elif new_schema.type == "union":
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452 raise SchemaParseException("Unions cannot contain other unions.")
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453 else:
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454 schema_objects.append(new_schema)
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455 self._schemas = schema_objects
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456
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457 # read-only properties
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458 schemas = property(lambda self: self._schemas)
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459
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460
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461 class RecordSchema(NamedSchema):
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462 @staticmethod
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463 def make_field_objects(field_data, names):
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464 # type: (List[Dict[Text, Text]], Names) -> List[Field]
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465 """We're going to need to make message parameters too."""
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466 field_objects = []
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467 field_names = [] # type: List[Text]
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468 for field in field_data:
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469 if hasattr(field, "get") and callable(field.get):
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470 atype = cast(Text, field.get("type"))
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471 name = cast(Text, field.get("name"))
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472
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473 # null values can have a default value of None
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474 has_default = False
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475 default = None
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476 if "default" in field:
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477 has_default = True
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478 default = field.get("default")
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479
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480 order = field.get("order")
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481 doc = field.get("doc")
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482 other_props = get_other_props(field, FIELD_RESERVED_PROPS)
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483 new_field = Field(
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484 atype, name, has_default, default, order, names, doc, other_props
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485 )
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486 # make sure field name has not been used yet
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487 if new_field.name in field_names:
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488 fail_msg = "Field name %s already in use." % new_field.name
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489 raise SchemaParseException(fail_msg)
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490 field_names.append(new_field.name)
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491 else:
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492 raise SchemaParseException("Not a valid field: %s" % field)
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493 field_objects.append(new_field)
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494 return field_objects
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495
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496 def __init__(
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497 self,
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498 name, # type: Text
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499 namespace, # type: Text
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500 fields, # type: List[Dict[Text, Text]]
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501 names=None, # type: Optional[Names]
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502 schema_type="record", # type: Text
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503 doc=None, # type: Optional[Text]
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504 other_props=None, # type: Optional[Dict[Text, Text]]
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505 ): # type: (...) -> None
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506 # Ensure valid ctor args
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507 if fields is None:
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508 fail_msg = "Record schema requires a non-empty fields property."
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509 raise SchemaParseException(fail_msg)
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510 elif not isinstance(fields, list):
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511 fail_msg = "Fields property must be a list of Avro schemas."
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512 raise SchemaParseException(fail_msg)
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513 if names is None:
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514 raise SchemaParseException("Must provide Names.")
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515
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516 # Call parent ctor (adds own name to namespace, too)
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517 NamedSchema.__init__(self, schema_type, name, namespace, names, other_props)
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518
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519 if schema_type == "record":
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520 old_default = names.default_namespace
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521 names.default_namespace = Name(
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522 name, namespace, names.default_namespace
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523 ).get_space()
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524
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525 # Add class members
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526 field_objects = RecordSchema.make_field_objects(fields, names)
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527 self.set_prop("fields", field_objects)
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528 if doc is not None:
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529 self.set_prop("doc", doc)
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530
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531 if schema_type == "record":
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532 names.default_namespace = old_default
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533
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534 # read-only properties
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535 fields = property(lambda self: self.get_prop("fields"))
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536
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537
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538 #
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539 # Module Methods
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540 #
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541 def get_other_props(all_props, reserved_props):
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542 # type: (Dict[Text, Text], Tuple[Text, ...]) -> Optional[Dict[Text, Text]]
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543 """
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544 Retrieve the non-reserved properties from a dictionary of properties
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545 @args reserved_props: The set of reserved properties to exclude
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546 """
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547 if hasattr(all_props, "items") and callable(all_props.items):
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548 return dict(
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549 [(k, v) for (k, v) in list(all_props.items()) if k not in reserved_props]
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550 )
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551 return None
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552
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553
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554 def make_avsc_object(json_data, names=None):
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555 # type: (Union[Dict[Text, Text], List[Any], Text], Optional[Names]) -> Schema
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556 """
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557 Build Avro Schema from data parsed out of JSON string.
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558
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559 @arg names: A Name object (tracks seen names and default space)
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560 """
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561 if names is None:
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562 names = Names()
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563 assert isinstance(names, Names)
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564
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565 # JSON object (non-union)
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566 if hasattr(json_data, "get") and callable(json_data.get): # type: ignore
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567 assert isinstance(json_data, Dict)
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568 atype = cast(Text, json_data.get("type"))
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569 other_props = get_other_props(json_data, SCHEMA_RESERVED_PROPS)
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570 if atype in PRIMITIVE_TYPES:
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571 return PrimitiveSchema(atype, other_props)
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572 if atype in NAMED_TYPES:
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573 name = cast(Text, json_data.get("name"))
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574 namespace = cast(Text, json_data.get("namespace", names.default_namespace))
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575 if atype == "enum":
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576 symbols = cast(List[Text], json_data.get("symbols"))
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577 doc = json_data.get("doc")
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578 return EnumSchema(name, namespace, symbols, names, doc, other_props)
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579 if atype in ["record", "error"]:
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580 fields = cast(List[Dict[Text, Text]], json_data.get("fields"))
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581 doc = json_data.get("doc")
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582 return RecordSchema(
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583 name, namespace, fields, names, atype, doc, other_props
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584 )
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585 raise SchemaParseException("Unknown Named Type: %s" % atype)
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586 if atype in VALID_TYPES:
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587 if atype == "array":
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588 items = cast(List[Text], json_data.get("items"))
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589 return ArraySchema(items, names, other_props)
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590 if atype is None:
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591 raise SchemaParseException('No "type" property: %s' % json_data)
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592 raise SchemaParseException("Undefined type: %s" % atype)
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593 # JSON array (union)
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594 if isinstance(json_data, list):
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595 return UnionSchema(json_data, names)
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596 # JSON string (primitive)
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597 if json_data in PRIMITIVE_TYPES:
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598 return PrimitiveSchema(cast(Text, json_data))
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599 # not for us!
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600 fail_msg = "Could not make an Avro Schema object from %s." % json_data
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601 raise SchemaParseException(fail_msg)