Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/plugins/sparql/aggregates.py @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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1 from rdflib import Literal, XSD
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2
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3 from rdflib.plugins.sparql.evalutils import _eval, NotBoundError, _val
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4 from rdflib.plugins.sparql.operators import numeric
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5 from rdflib.plugins.sparql.datatypes import type_promotion
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6
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7 from rdflib.plugins.sparql.sparql import SPARQLTypeError
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8
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9 from decimal import Decimal
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10
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11 """
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12 Aggregation functions
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13 """
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14
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15 class Accumulator(object):
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16 """abstract base class for different aggregation functions """
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17
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18 def __init__(self, aggregation):
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19 self.var = aggregation.res
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20 self.expr = aggregation.vars
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21 if not aggregation.distinct:
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22 self.use_row = self.dont_care
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23 self.distinct = False
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24 else:
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25 self.distinct = aggregation.distinct
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26 self.seen = set()
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27
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28 def dont_care(self, row):
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29 """skips distinct test """
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30 return True
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31
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32 def use_row(self, row):
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33 """tests distinct with set """
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34 return _eval(self.expr, row) not in self.seen
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35
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36 def set_value(self, bindings):
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37 """sets final value in bindings"""
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38 bindings[self.var] = self.get_value()
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39
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40
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41 class Counter(Accumulator):
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42
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43 def __init__(self, aggregation):
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44 super(Counter, self).__init__(aggregation)
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45 self.value = 0
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46 if self.expr == "*":
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47 # cannot eval "*" => always use the full row
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48 self.eval_row = self.eval_full_row
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49
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50 def update(self, row, aggregator):
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51 try:
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52 val = self.eval_row(row)
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53 except NotBoundError:
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54 # skip UNDEF
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55 return
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56 self.value += 1
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57 if self.distinct:
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58 self.seen.add(val)
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59
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60 def get_value(self):
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61 return Literal(self.value)
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62
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63 def eval_row(self, row):
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64 return _eval(self.expr, row)
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65
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66 def eval_full_row(self, row):
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67 return row
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68
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69 def use_row(self, row):
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70 return self.eval_row(row) not in self.seen
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71
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72
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73 def type_safe_numbers(*args):
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74 types = list(map(type, args))
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75 if float in types and Decimal in types:
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76 return list(map(float, args))
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77 return args
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78
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79
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80 class Sum(Accumulator):
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81
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82 def __init__(self, aggregation):
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83 super(Sum, self).__init__(aggregation)
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84 self.value = 0
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85 self.datatype = None
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86
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87 def update(self, row, aggregator):
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88 try:
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89 value = _eval(self.expr, row)
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90 dt = self.datatype
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91 if dt is None:
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92 dt = value.datatype
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93 else:
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94 dt = type_promotion(dt, value.datatype)
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95 self.datatype = dt
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96 self.value = sum(type_safe_numbers(self.value, numeric(value)))
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97 if self.distinct:
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98 self.seen.add(value)
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99 except NotBoundError:
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100 # skip UNDEF
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101 pass
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102
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103 def get_value(self):
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104 return Literal(self.value, datatype=self.datatype)
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105
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106 class Average(Accumulator):
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107
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108 def __init__(self, aggregation):
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109 super(Average, self).__init__(aggregation)
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110 self.counter = 0
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111 self.sum = 0
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112 self.datatype = None
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113
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114 def update(self, row, aggregator):
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115 try:
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116 value = _eval(self.expr, row)
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117 dt = self.datatype
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118 self.sum = sum(type_safe_numbers(self.sum, numeric(value)))
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119 if dt is None:
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120 dt = value.datatype
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121 else:
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122 dt = type_promotion(dt, value.datatype)
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123 self.datatype = dt
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124 if self.distinct:
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125 self.seen.add(value)
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126 self.counter += 1
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127 # skip UNDEF or BNode => SPARQLTypeError
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128 except NotBoundError:
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129 pass
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130 except SPARQLTypeError:
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131 pass
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132
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133 def get_value(self):
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134 if self.counter == 0:
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135 return Literal(0)
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136 if self.datatype in (XSD.float, XSD.double):
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137 return Literal(self.sum / self.counter)
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138 else:
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139 return Literal(Decimal(self.sum) / Decimal(self.counter))
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140
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141
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142 class Extremum(Accumulator):
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143 """abstract base class for Minimum and Maximum"""
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144
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145 def __init__(self, aggregation):
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146 super(Extremum, self).__init__(aggregation)
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147 self.value = None
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148 # DISTINCT would not change the value for MIN or MAX
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149 self.use_row = self.dont_care
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150
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151 def set_value(self, bindings):
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152 if self.value is not None:
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153 # simply do not set if self.value is still None
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154 bindings[self.var] = Literal(self.value)
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155
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156 def update(self, row, aggregator):
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157 try:
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158 if self.value is None:
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159 self.value = _eval(self.expr, row)
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160 else:
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161 # self.compare is implemented by Minimum/Maximum
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162 self.value = self.compare(self.value, _eval(self.expr, row))
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163 # skip UNDEF or BNode => SPARQLTypeError
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164 except NotBoundError:
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165 pass
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166 except SPARQLTypeError:
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167 pass
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168
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169
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170 class Minimum(Extremum):
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171
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172 def compare(self, val1, val2):
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173 return min(val1, val2, key=_val)
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174
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175
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176 class Maximum(Extremum):
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177
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178 def compare(self, val1, val2):
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179 return max(val1, val2, key=_val)
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180
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181
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182 class Sample(Accumulator):
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183 """takes the first eligable value"""
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184
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185 def __init__(self, aggregation):
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186 super(Sample, self).__init__(aggregation)
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187 # DISTINCT would not change the value
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188 self.use_row = self.dont_care
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189
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190 def update(self, row, aggregator):
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191 try:
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192 # set the value now
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193 aggregator.bindings[self.var] = _eval(self.expr, row)
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194 # and skip this accumulator for future rows
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195 del aggregator.accumulators[self.var]
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196 except NotBoundError:
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197 pass
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198
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199 def get_value(self):
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200 # set None if no value was set
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201 return None
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202
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203 class GroupConcat(Accumulator):
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204
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205 def __init__(self, aggregation):
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206 super(GroupConcat, self).__init__(aggregation)
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207 # only GROUPCONCAT needs to have a list as accumlator
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208 self.value = []
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209 self.separator = aggregation.separator or " "
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210
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211 def update(self, row, aggregator):
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212 try:
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213 value = _eval(self.expr, row)
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214 self.value.append(value)
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215 if self.distinct:
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216 self.seen.add(value)
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217 # skip UNDEF
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218 except NotBoundError:
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219 pass
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220
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221 def get_value(self):
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222 return Literal(self.separator.join(str(v) for v in self.value))
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223
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224
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225 class Aggregator(object):
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226 """combines different Accumulator objects"""
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227
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228 accumulator_classes = {
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229 "Aggregate_Count": Counter,
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230 "Aggregate_Sample": Sample,
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231 "Aggregate_Sum": Sum,
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232 "Aggregate_Avg": Average,
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233 "Aggregate_Min": Minimum,
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234 "Aggregate_Max": Maximum,
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235 "Aggregate_GroupConcat": GroupConcat,
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236 }
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237
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238 def __init__(self, aggregations):
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239 self.bindings = {}
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240 self.accumulators = {}
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241 for a in aggregations:
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242 accumulator_class = self.accumulator_classes.get(a.name)
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243 if accumulator_class is None:
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244 raise Exception("Unknown aggregate function " + a.name)
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245 self.accumulators[a.res] = accumulator_class(a)
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246
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247 def update(self, row):
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248 """update all own accumulators"""
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249 # SAMPLE accumulators may delete themselves
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250 # => iterate over list not generator
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251
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252 for acc in list(self.accumulators.values()):
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253 if acc.use_row(row):
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254 acc.update(row, self)
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255
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256 def get_bindings(self):
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257 """calculate and set last values"""
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258 for acc in self.accumulators.values():
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259 acc.set_value(self.bindings)
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260 return self.bindings