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1
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2 from CGData import CGObjectBase
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3
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4 import csv
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5 import types
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6
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7 class TableRow(object):
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8 def __init__(self):
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9 pass
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10
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11 def __str__(self):
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12 return "<" + ",".join( "%s=%s" % (col, getattr(self,col)) for col in self.__format__['columnOrder']) + ">"
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13
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14 class InvalidFormat(Exception):
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15 def __init__(self, txt):
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16 Exception.__init__(self, txt)
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17
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18 class BaseTable(CGObjectBase):
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19 def __init__(self):
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20 super(BaseTable,self).__init__()
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21 self.__row_class__ = type( "TableRow_" + self['cgformat']['name'], (TableRow,), dict(__format__=self.__format__) )
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22 self.free()
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23
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24 def free(self):
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25 self.firstKey = None
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26 self.secondKey = None
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27 self.groupKey = None
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28 self.loaded = False
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29 if 'primaryKey' in self['cgformat']:
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30 self.firstKey = self['cgformat']['primaryKey']
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31 setattr(self, self['cgformat']['primaryKey'] + "_map", {} )
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32 self.groupKey = False
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33
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34 #setup the map for groupKeys
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35 if 'groupKey' in self['cgformat']:
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36 self.firstKey = self['cgformat']['groupKey']
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37 setattr(self, self['cgformat']['groupKey'] + "_map", {} )
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38 self.groupKey = True
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39
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40 if 'secondaryKey' in self['cgformat']:
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41 self.secondKey = self['cgformat']['secondaryKey']
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42
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43 def read(self, handle):
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44 cols = self['cgformat']['columnOrder']
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45 colType = {}
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46 for col in cols:
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47 if 'columnDef' in self['cgformat'] and col in self['cgformat']['columnDef'] and 'type' in self['cgformat']['columnDef'][col]:
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48 if self['cgformat']['columnDef'][col]['type'] == 'float':
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49 colType[col] = float
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50 elif self['cgformat']['columnDef'][col]['type'] == 'int':
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51 colType[col] = int
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52 else:
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53 colType[col] = str
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54 else:
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55 colType[col] = str
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56
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57 read = csv.reader(handle, delimiter="\t")
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58
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59 storeMap = getattr(self, self.firstKey + "_map")
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60 comment = None
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61 if 'comment' in self['cgformat']:
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62 comment = self['cgformat']['comment']
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63 linenum = 0
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64 for row in read:
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65 linenum += 1
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52
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66 if linenum ==1: #ignore header line
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67 continue
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31
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68 r = self.__row_class__()
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50
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69 if (comment is None or not row[0].startswith(comment)) and not row[0].startswith("#"):
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31
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70 for i, col in enumerate(cols):
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52
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71 skip =0
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31
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72 isOptional = False
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73 if 'columnDef' in self['cgformat'] and col in self['cgformat']['columnDef'] and 'optional' in self['cgformat']['columnDef'][col]:
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74 isOptional = self['cgformat']['columnDef'][col]['optional']
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75 if len(row) > i:
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76 try:
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77 setattr(r, col, colType[col](row[i]))
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52
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78 except ValueError:
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31
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79 raise ValueError( "col invalid type %s on line %d" % (row[i], linenum))
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80 else:
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81 if isOptional:
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82 setattr(r, col, None)
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83 else:
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84 print row
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52
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85 skip =1 # ignore bad lines
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86 break
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31
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87 raise InvalidFormat("missing colum " + col)
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52
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88 if skip:
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89 continue
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90
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31
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91 if not self.groupKey:
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92 if self.secondKey is not None:
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93 key1 = getattr(r, self.firstKey )
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94 key2 = getattr(r, self.secondKey )
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95 if key1 not in storeMap:
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96 storeMap[key1] = {}
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97 storeMap[key1][key2] = r
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98 else:
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99 storeMap[ getattr(r, self.firstKey ) ] = r
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100 else:
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101 key1 = getattr(r, self.firstKey )
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102 if self.secondKey is not None:
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103 key2 = getattr(r, self.secondKey )
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104 if key1 not in storeMap:
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105 storeMap[key1] = {}
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106 if key2 not in storeMap[key1]:
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107 storeMap[key1][key2] = []
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108 storeMap[key1][key2].append(r)
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109 else:
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110 if key1 not in storeMap:
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111 storeMap[key1] = []
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112 storeMap[key1].append(r)
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113 self.loaded = True
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114
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115 """
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116 def __getattr__(self, item):
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117 if not self.loaded:
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118 self.load()
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119
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120 if item == "get_" + self.firstKey + "_list":
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121 return self.__get_firstmap__().keys
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122 if item == "get_by_" + self.firstKey:
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123 return self.__get_firstmap__().__getitem__
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124 if item == "get_" + self.firstKey + "_values":
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125 return self.__get_firstmap__().values
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126 if item == "get_" + self.firstKey + "_map":
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127 return self.__get_firstmap__
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128 if item == "has_" + self.firstKey:
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129 return self.__get_firstmap__().__contains__
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130 raise AttributeError(item)
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131 """
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132
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133 def get_key_list(self):
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134 """
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135 List keys
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136 """
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137 if not self.loaded:
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138 self.load()
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139 return self.__get_firstmap__().keys()
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140
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141 def get_by(self, key):
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142 """
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143 get by key
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144 """
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145 if not self.loaded:
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146 self.load()
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147 return self.__get_firstmap__().__getitem__(key)
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148
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149 def get_values(self):
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150 """
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151 get values
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152 """
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153 if not self.loaded:
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154 self.load()
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155 return self.__get_firstmap__().values()
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156
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157 def get_map(self):
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158 """
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159 get key map
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160 """
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161 if not self.loaded:
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162 self.load()
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163 return self.__get_firstmap__()
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164
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165 def has_key(self, key):
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166 """
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167 Does the table have a key
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168 """
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169 if not self.loaded:
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170 self.load()
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171 return self.__get_firstmap__().__contains__(key)
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172 def __get_firstmap__(self):
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173 return getattr(self, self.firstKey + "_map")
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174
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175 def init_blank(self):
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176 self.free()
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177 self['cgdata'] = { 'type' : self['cgformat']['name'] }
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178 self.loaded = True
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179
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180 def insert(self, name, vals):
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181 storeMap = getattr(self, self.firstKey + "_map")
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182 cols = self['cgformat']['columnOrder']
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183 r = self.__row_class__()
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184 for col in cols:
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185 isOptional = False
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186 if 'columnDef' in self['cgformat'] and col in self['cgformat']['columnDef'] and 'optional' in self['cgformat']['columnDef'][col]:
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187 isOptional = self['cgformat']['columnDef'][col]['optional']
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188 if col in vals:
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189 setattr(r, col, vals[col])
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190 else:
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191 if isOptional:
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192 setattr(r, col, None)
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193 else:
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194 raise InvalidFormat("missing colum " + col)
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195
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196 if not self.groupKey:
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197 if self.secondKey is not None:
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198 key1 = getattr(r, self.firstKey )
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199 key2 = getattr(r, self.secondKey )
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200 if key1 not in storeMap:
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201 storeMap[key1] = {}
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202 storeMap[key1][key2] = r
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203 else:
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204 storeMap[ getattr(r, self.firstKey ) ] = r
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205 else:
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206 key1 = getattr(r, self.firstKey )
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207 if self.secondKey is not None:
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208 key2 = getattr(r, self.secondKey )
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209 if key1 not in storeMap:
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210 storeMap[key1] = {}
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211 if key2 not in storeMap[key1]:
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212 storeMap[key1][key2] = []
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213 storeMap[key1][key2].append(r)
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214 else:
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215 if key1 not in storeMap:
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216 storeMap[key1] = []
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217 storeMap[key1].append(r)
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218
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219 def write(self, handle):
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220 writer = csv.writer(handle, delimiter="\t", lineterminator="\n")
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221 for row in self.row_iter():
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222 orow = []
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223 for col in self['cgformat']['columnOrder']:
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224 orow.append( getattr(row, col) )
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225 writer.writerow(orow)
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226
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227
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228 def row_iter(self):
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229 if not self.groupKey:
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230 keyMap = getattr(self, self.firstKey + "_map")
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231 for rowKey in keyMap:
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232 yield keyMap[rowKey]
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233 else:
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234 keyMap = getattr(self, self.firstKey + "_map")
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235 for rowKey in keyMap:
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236 for elem in keyMap[rowKey]:
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237 yield elem
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238
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239 def __get_firstmap__(self):
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240 return getattr(self, self.firstKey + "_map")
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