Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/tools/csv2rdf.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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0
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1 """
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2 A commandline tool for semi-automatically converting CSV to RDF
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3
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4 try: ``csv2rdf --help``
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5
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6 """
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7
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8
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9 import sys
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10 import re
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11 import csv
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12 import getopt
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13 import configparser
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14 import fileinput
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15 import codecs
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16 import time
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17 import datetime
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18 import warnings
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19 import urllib.request, urllib.error, urllib.parse
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20
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21 import rdflib
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22
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23 from rdflib import RDF, RDFS
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24 from rdflib.namespace import split_uri
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25
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26 __all__ = [ 'CSV2RDF' ]
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27
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28 HELP = """
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29 csv2rdf.py \
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30 -b <instance-base> \
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31 -p <property-base> \
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32 [-c <classname>] \
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33 [-i <identity column(s)>] \
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34 [-l <label columns>] \
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35 [-s <N>] [-o <output>] \
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36 [-f configfile] \
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37 [--col<N> <colspec>] \
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38 [--prop<N> <property>] \
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39 <[-d <delim>] \
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40 [-C] [files...]"
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41
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42 Reads csv files from stdin or given files
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43 if -d is given, use this delimiter
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44 if -s is given, skips N lines at the start
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45 Creates a URI from the columns given to -i, or automatically by numbering if
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46 none is given
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47 Outputs RDFS labels from the columns given to -l
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48 if -c is given adds a type triple with the given classname
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49 if -C is given, the class is defined as rdfs:Class
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50 Outputs one RDF triple per column in each row.
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51 Output is in n3 format.
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52 Output is stdout, unless -o is specified
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53
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54 Long options also supported: \
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55 --base, \
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56 --propbase, \
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57 --ident, \
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58 --class, \
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59 --label, \
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60 --out, \
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61 --defineclass
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62
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63 Long options --col0, --col1, ...
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64 can be used to specify conversion for columns.
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65 Conversions can be:
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66 float(), int(), split(sep, [more]), uri(base, [class]), date(format)
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67
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68 Long options --prop0, --prop1, ...
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69 can be used to use specific properties, rather than ones auto-generated
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70 from the headers
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71
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72 -f says to read config from a .ini/config file - the file must contain one
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73 section called csv2rdf, with keys like the long options, i.e.:
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74
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75 [csv2rdf]
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76 out=output.n3
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77 base=http://example.org/
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78 col0=split(";")
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79 col1=split(";", uri("http://example.org/things/",
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80 "http://xmlns.com/foaf/0.1/Person"))
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81 col2=float()
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82 col3=int()
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83 col4=date("%Y-%b-%d %H:%M:%S")
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84
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85 """
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86
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87 # bah - ugly global
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88 uris = {}
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89
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90
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91 def toProperty(label):
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92 """
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93 CamelCase + lowercase inital a string
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94
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95
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96 FIRST_NM => firstNm
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97
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98 firstNm => firstNm
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99
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100 """
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101 label = re.sub("[^\w]", " ", label)
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102 label = re.sub("([a-z])([A-Z])", "\\1 \\2", label)
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103 label = label.split(" ")
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104 return "".join([label[0].lower()] + [x.capitalize() for x in label[1:]])
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105
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106
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107 def toPropertyLabel(label):
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108 if not label[1:2].isupper():
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109 return label[0:1].lower() + label[1:]
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110 return label
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111
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112
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113 def index(l, i):
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114 """return a set of indexes from a list
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115 >>> index([1,2,3],(0,2))
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116 (1, 3)
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117 """
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118 return tuple([l[x] for x in i])
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119
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120
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121 def csv_reader(csv_data, dialect=csv.excel, **kwargs):
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122
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123 csv_reader = csv.reader(csv_data,
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124 dialect=dialect, **kwargs)
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125 for row in csv_reader:
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126 # decode UTF-8 back to Unicode, cell by cell:
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127 yield [str(cell, 'utf-8', errors='replace') for cell in row]
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128
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129
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130 def prefixuri(x, prefix, class_=None):
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131 if prefix:
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132 r = rdflib.URIRef(
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133 prefix + urllib.parse.quote(
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134 x.encode("utf8").replace(" ", "_"), safe=""))
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135 else:
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136 r = rdflib.URIRef(x)
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137 uris[x] = (r, class_)
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138 return r
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139
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140 # meta-language for config
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141
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142
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143 class NodeMaker(object):
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144 def range(self):
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145 return rdflib.RDFS.Literal
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146
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147 def __call__(self, x):
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148 return rdflib.Literal(x)
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149
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150
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151 class NodeUri(NodeMaker):
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152 def __init__(self, prefix, class_):
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153 self.prefix = prefix
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154 if class_:
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155 self.class_ = rdflib.URIRef(class_)
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156 else:
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157 self.class_ = None
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158
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159 def __call__(self, x):
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160 return prefixuri(x, self.prefix, self.class_)
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161
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162 def range(self):
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163 return self.class_ or rdflib.RDF.Resource
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164
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165
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166 class NodeLiteral(NodeMaker):
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167 def __init__(self, f=None):
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168 self.f = f
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169
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170
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171 class NodeFloat(NodeLiteral):
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172 def __call__(self, x):
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173 if not self.f:
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174 return rdflib.Literal(float(x))
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175 if callable(self.f):
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176 return rdflib.Literal(float(self.f(x)))
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177 raise Exception("Function passed to float is not callable")
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178
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179 def range(self):
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180 return rdflib.XSD.double
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181
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182
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183 class NodeInt(NodeLiteral):
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184 def __call__(self, x):
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185 if not self.f:
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186 return rdflib.Literal(int(x))
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187 if callable(self.f):
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188 return rdflib.Literal(int(self.f(x)))
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189 raise Exception("Function passed to int is not callable")
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190
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191 def range(self):
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192 return rdflib.XSD.int
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193
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194
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195 class NodeReplace(NodeMaker):
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196 def __init__(self, a, b):
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197 self.a = a
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198 self.b = b
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199
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200 def __call__(self, x):
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201 return x.replace(self.a, self.b)
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202
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203
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204 class NodeDate(NodeLiteral):
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205 def __call__(self, x):
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206 return rdflib.Literal(datetime.datetime.strptime(x, self.f))
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207
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208 def range(self):
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209 return rdflib.XSD.dateTime
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210
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211
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212 class NodeSplit(NodeMaker):
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213 def __init__(self, sep, f):
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214 self.sep = sep
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215 self.f = f
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216
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217 def __call__(self, x):
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218 if not self.f:
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219 self.f = rdflib.Literal
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220 if not callable(self.f):
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221 raise Exception("Function passed to split is not callable!")
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222 return [
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223 self.f(y.strip()) for y in x.split(self.sep) if y.strip() != ""]
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224
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225 def range(self):
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226 if self.f and isinstance(self.f, NodeMaker):
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227 return self.f.range()
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228 return NodeMaker.range(self)
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229
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230 default_node_make = NodeMaker()
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231
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232
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233 def _config_ignore(*args, **kwargs):
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234 return "ignore"
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235
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236
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237 def _config_uri(prefix=None, class_=None):
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238 return NodeUri(prefix, class_)
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239
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240
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241 def _config_literal():
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242 return NodeLiteral
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243
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244
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245 def _config_float(f=None):
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246 return NodeFloat(f)
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247
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248
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249 def _config_replace(a, b):
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250 return NodeReplace(a, b)
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251
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252
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253 def _config_int(f=None):
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254 return NodeInt(f)
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255
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256
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257 def _config_date(format_):
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258 return NodeDate(format_)
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259
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260
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261 def _config_split(sep=None, f=None):
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262 return NodeSplit(sep, f)
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263
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264 config_functions = {"ignore": _config_ignore,
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265 "uri": _config_uri,
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266 "literal": _config_literal,
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267 "float": _config_float,
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268 "int": _config_int,
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269 "date": _config_date,
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270 "split": _config_split,
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271 "replace": _config_replace
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272 }
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273
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274
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275 def column(v):
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276 """Return a function for column mapping"""
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277
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278 return eval(v, config_functions)
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279
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280
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281 class CSV2RDF(object):
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282 def __init__(self):
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283
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284 self.CLASS = None
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285 self.BASE = None
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286 self.PROPBASE = None
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287 self.IDENT = 'auto'
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288 self.LABEL = None
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289 self.DEFINECLASS = False
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290 self.SKIP = 0
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291 self.DELIM = ","
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292
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293 self.COLUMNS = {}
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294 self.PROPS = {}
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295
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296 self.OUT = codecs.getwriter("utf-8")(sys.stdout, errors='replace')
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297
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298 self.triples = 0
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299
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300 def triple(self, s, p, o):
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301 self.OUT.write("%s %s %s .\n" % (s.n3(), p.n3(), o.n3()))
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302 self.triples += 1
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303
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304 def convert(self, csvreader):
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305
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306 start = time.time()
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307
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308 if self.OUT:
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309 sys.stderr.write("Output to %s\n" % self.OUT.name)
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310
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311 if self.IDENT != "auto" and not isinstance(self.IDENT, tuple):
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312 self.IDENT = (self.IDENT,)
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313
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314 if not self.BASE:
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315 warnings.warn("No base given, using http://example.org/instances/")
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316 self.BASE = rdflib.Namespace("http://example.org/instances/")
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317
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318 if not self.PROPBASE:
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319 warnings.warn(
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320 "No property base given, using http://example.org/property/")
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321 self.PROPBASE = rdflib.Namespace("http://example.org/props/")
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322
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323 # skip lines at the start
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324 for x in range(self.SKIP):
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325 next(csvreader)
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326
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327 # read header line
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328 header_labels = list(next(csvreader))
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329 headers = dict(
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330 enumerate([self.PROPBASE[toProperty(x)] for x in header_labels]))
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331 # override header properties if some are given
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332 for k, v in self.PROPS.items():
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333 headers[k] = v
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334 header_labels[k] = split_uri(v)[1]
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335
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336 if self.DEFINECLASS:
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337 # output class/property definitions
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338 self.triple(self.CLASS, RDF.type, RDFS.Class)
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339 for i in range(len(headers)):
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340 h, l = headers[i], header_labels[i]
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341 if h == "" or l == "":
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342 continue
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343 if self.COLUMNS.get(i) == _config_ignore:
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344 continue
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345 self.triple(h, RDF.type, RDF.Property)
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346 self.triple(h, RDFS.label, rdflib.Literal(toPropertyLabel(l)))
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347 self.triple(h, RDFS.domain, self.CLASS)
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348 self.triple(h, RDFS.range,
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parents:
diff changeset
349 self.COLUMNS.get(i, default_node_make).range())
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350
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351 rows = 0
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352 for l in csvreader:
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parents:
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353 try:
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parents:
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354 if self.IDENT == 'auto':
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355 uri = self.BASE["%d" % rows]
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parents:
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356 else:
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parents:
diff changeset
357 uri = self.BASE["_".join([urllib.parse.quote(x.encode(
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parents:
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358 "utf8").replace(" ", "_"), safe="")
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parents:
diff changeset
359 for x in index(l, self.IDENT)])]
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parents:
diff changeset
360
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parents:
diff changeset
361 if self.LABEL:
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parents:
diff changeset
362 self.triple(uri, RDFS.label, rdflib.Literal(
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parents:
diff changeset
363 " ".join(index(l, self.LABEL))))
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parents:
diff changeset
364
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parents:
diff changeset
365 if self.CLASS:
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diff changeset
366 # type triple
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parents:
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367 self.triple(uri, RDF.type, self.CLASS)
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parents:
diff changeset
368
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parents:
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369 for i, x in enumerate(l):
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parents:
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370 x = x.strip()
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parents:
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371 if x != '':
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parents:
diff changeset
372 if self.COLUMNS.get(i) == _config_ignore:
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parents:
diff changeset
373 continue
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parents:
diff changeset
374 try:
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parents:
diff changeset
375 o = self.COLUMNS.get(i, rdflib.Literal)(x)
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parents:
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376 if isinstance(o, list):
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parents:
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377 for _o in o:
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parents:
diff changeset
378 self.triple(uri, headers[i], _o)
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parents:
diff changeset
379 else:
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parents:
diff changeset
380 self.triple(uri, headers[i], o)
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parents:
diff changeset
381
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parents:
diff changeset
382 except Exception as e:
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parents:
diff changeset
383 warnings.warn(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
384 "Could not process value for column " +
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parents:
diff changeset
385 "%d:%s in row %d, ignoring: %s " % (
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shellac
parents:
diff changeset
386 i, headers[i], rows, e.message))
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parents:
diff changeset
387
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shellac
parents:
diff changeset
388 rows += 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
389 if rows % 100000 == 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
390 sys.stderr.write(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
391 "%d rows, %d triples, elapsed %.2fs.\n" % (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
392 rows, self.triples, time.time() - start))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
393 except:
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parents:
diff changeset
394 sys.stderr.write("Error processing line: %d\n" % rows)
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395 raise
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396
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397 # output types/labels for generated URIs
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398 classes = set()
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399 for l, x in uris.items():
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400 u, c = x
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401 self.triple(u, RDFS.label, rdflib.Literal(l))
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402 if c:
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403 c = rdflib.URIRef(c)
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404 classes.add(c)
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405 self.triple(u, RDF.type, c)
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406
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407 for c in classes:
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408 self.triple(c, RDF.type, RDFS.Class)
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409
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410 self.OUT.close()
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411 sys.stderr.write(
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412 "Converted %d rows into %d triples.\n" % (rows, self.triples))
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413 sys.stderr.write("Took %.2f seconds.\n" % (time.time() - start))
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414
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415
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416 def main():
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417 csv2rdf = CSV2RDF()
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418
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419 opts, files = getopt.getopt(
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420 sys.argv[1:],
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421 "hc:b:p:i:o:Cf:l:s:d:",
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422 ["out=", "base=", "delim=", "propbase=", "class=",
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423 "ident=", "label=", "skip=", "defineclass", "help"])
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424 opts = dict(opts)
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425
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426 if "-h" in opts or "--help" in opts:
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427 print(HELP)
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428 sys.exit(-1)
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429
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430 if "-f" in opts:
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431 config = configparser.ConfigParser()
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432 config.readfp(open(opts["-f"]))
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433 for k, v in config.items("csv2rdf"):
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434 if k == "out":
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435 csv2rdf.OUT = codecs.open(v, "w", "utf-8")
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436 elif k == "base":
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437 csv2rdf.BASE = rdflib.Namespace(v)
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438 elif k == "propbase":
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439 csv2rdf.PROPBASE = rdflib.Namespace(v)
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440 elif k == "class":
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441 csv2rdf.CLASS = rdflib.URIRef(v)
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442 elif k == "defineclass":
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443 csv2rdf.DEFINECLASS = bool(v)
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444 elif k == "ident":
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445 csv2rdf.IDENT = eval(v)
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446 elif k == "label":
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447 csv2rdf.LABEL = eval(v)
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448 elif k == "delim":
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449 csv2rdf.DELIM = v
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450 elif k == "skip":
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451 csv2rdf.SKIP = int(v)
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452 elif k.startswith("col"):
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453 csv2rdf.COLUMNS[int(k[3:])] = column(v)
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454 elif k.startswith("prop"):
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455 csv2rdf.PROPS[int(k[4:])] = rdflib.URIRef(v)
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456
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457 if "-o" in opts:
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458 csv2rdf.OUT = codecs.open(opts["-o"], "w", "utf-8")
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459 if "--out" in opts:
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460 csv2rdf.OUT = codecs.open(opts["--out"], "w", "utf-8")
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461
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462 if "-b" in opts:
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463 csv2rdf.BASE = rdflib.Namespace(opts["-b"])
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464 if "--base" in opts:
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465 csv2rdf.BASE = rdflib.Namespace(opts["--base"])
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466
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467 if "-d" in opts:
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468 csv2rdf.DELIM = opts["-d"]
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469 if "--delim" in opts:
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470 csv2rdf.DELIM = opts["--delim"]
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471
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472 if "-p" in opts:
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473 csv2rdf.PROPBASE = rdflib.Namespace(opts["-p"])
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474 if "--propbase" in opts:
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475 csv2rdf.PROPBASE = rdflib.Namespace(opts["--propbase"])
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476
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477 if "-l" in opts:
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478 csv2rdf.LABEL = eval(opts["-l"])
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479 if "--label" in opts:
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480 csv2rdf.LABEL = eval(opts["--label"])
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481
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482 if "-i" in opts:
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483 csv2rdf.IDENT = eval(opts["-i"])
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484 if "--ident" in opts:
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485 csv2rdf.IDENT = eval(opts["--ident"])
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486
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487 if "-s" in opts:
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488 csv2rdf.SKIP = int(opts["-s"])
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489 if "--skip" in opts:
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490 csv2rdf.SKIP = int(opts["--skip"])
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491
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492 if "-c" in opts:
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493 csv2rdf.CLASS = rdflib.URIRef(opts["-c"])
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494 if "--class" in opts:
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495 csv2rdf.CLASS = rdflib.URIRef(opts["--class"])
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496
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497 for k, v in opts.items():
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498 if k.startswith("--col"):
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diff changeset
499 csv2rdf.COLUMNS[int(k[5:])] = column(v)
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500 elif k.startswith("--prop"):
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501 csv2rdf.PROPS[int(k[6:])] = rdflib.URIRef(v)
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502
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503 if csv2rdf.CLASS and ("-C" in opts or "--defineclass" in opts):
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504 csv2rdf.DEFINECLASS = True
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505
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506 csv2rdf.convert(
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507 csv_reader(fileinput.input(files), delimiter=csv2rdf.DELIM))
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508
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509
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510 if __name__ == '__main__':
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511 main()