Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/void.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 import collections
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2
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3 from rdflib import URIRef, Graph, Literal
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4 from rdflib.namespace import VOID, RDF
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5
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6
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7 def generateVoID(g, dataset=None, res=None, distinctForPartitions=True):
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8 """
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9 Returns a new graph with a VoID description of the passed dataset
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10
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11 For more info on Vocabulary of Interlinked Datasets (VoID), see:
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12 http://vocab.deri.ie/void
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13
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14 This only makes two passes through the triples (once to detect the types
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15 of things)
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16
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17 The tradeoff is that lots of temporary structures are built up in memory
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18 meaning lots of memory may be consumed :)
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19 I imagine at least a few copies of your original graph.
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20
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21 the distinctForPartitions parameter controls whether
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22 distinctSubjects/objects are tracked for each class/propertyPartition
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23 this requires more memory again
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24
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25 """
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26
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27 typeMap = collections.defaultdict(set)
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28 classes = collections.defaultdict(set)
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29 for e, c in g.subject_objects(RDF.type):
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30 classes[c].add(e)
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31 typeMap[e].add(c)
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32
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33 triples = 0
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34 subjects = set()
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35 objects = set()
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36 properties = set()
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37 classCount = collections.defaultdict(int)
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38 propCount = collections.defaultdict(int)
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39
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40 classProps = collections.defaultdict(set)
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41 classObjects = collections.defaultdict(set)
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42 propSubjects = collections.defaultdict(set)
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43 propObjects = collections.defaultdict(set)
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44
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45 for s, p, o in g:
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46
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47 triples += 1
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48 subjects.add(s)
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49 properties.add(p)
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50 objects.add(o)
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51
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52 # class partitions
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53 if s in typeMap:
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54 for c in typeMap[s]:
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55 classCount[c] += 1
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56 if distinctForPartitions:
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57 classObjects[c].add(o)
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58 classProps[c].add(p)
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59
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60 # property partitions
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61 propCount[p] += 1
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62 if distinctForPartitions:
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63 propObjects[p].add(o)
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64 propSubjects[p].add(s)
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65
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66 if not dataset:
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67 dataset = URIRef("http://example.org/Dataset")
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68
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69 if not res:
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70 res = Graph()
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71
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72 res.add((dataset, RDF.type, VOID.Dataset))
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73
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74 # basic stats
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75 res.add((dataset, VOID.triples, Literal(triples)))
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76 res.add((dataset, VOID.classes, Literal(len(classes))))
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77
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78 res.add((dataset, VOID.distinctObjects, Literal(len(objects))))
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79 res.add((dataset, VOID.distinctSubjects, Literal(len(subjects))))
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80 res.add((dataset, VOID.properties, Literal(len(properties))))
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81
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82 for i, c in enumerate(classes):
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83 part = URIRef(dataset + "_class%d" % i)
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84 res.add((dataset, VOID.classPartition, part))
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85 res.add((part, RDF.type, VOID.Dataset))
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86
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87 res.add((part, VOID.triples, Literal(classCount[c])))
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88 res.add((part, VOID.classes, Literal(1)))
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89
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90 res.add((part, VOID["class"], c))
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91
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92 res.add((part, VOID.entities, Literal(len(classes[c]))))
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93 res.add((part, VOID.distinctSubjects, Literal(len(classes[c]))))
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94
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95 if distinctForPartitions:
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96 res.add(
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97 (part, VOID.properties, Literal(len(classProps[c]))))
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98 res.add((part, VOID.distinctObjects,
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99 Literal(len(classObjects[c]))))
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100
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101 for i, p in enumerate(properties):
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102 part = URIRef(dataset + "_property%d" % i)
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103 res.add((dataset, VOID.propertyPartition, part))
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104 res.add((part, RDF.type, VOID.Dataset))
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105
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106 res.add((part, VOID.triples, Literal(propCount[p])))
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107 res.add((part, VOID.properties, Literal(1)))
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108
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109 res.add((part, VOID.property, p))
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110
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111 if distinctForPartitions:
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112
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113 entities = 0
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114 propClasses = set()
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115 for s in propSubjects[p]:
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116 if s in typeMap:
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117 entities += 1
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118 for c in typeMap[s]:
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119 propClasses.add(c)
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120
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121 res.add((part, VOID.entities, Literal(entities)))
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122 res.add((part, VOID.classes, Literal(len(propClasses))))
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123
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124 res.add((part, VOID.distinctSubjects,
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125 Literal(len(propSubjects[p]))))
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126 res.add((part, VOID.distinctObjects,
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127 Literal(len(propObjects[p]))))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
128
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
129 return res, dataset