Mercurial > hg > drupalISMI

annotate importFromOpenMind/importer/model2neo4j_client.py @ 48:6625019a0c96

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old model2neo4j renamed to model2neo4j_restclient. new model2neo4j_client and model2neo4j_import. fixed ismixml2model and compare_models.
author casties
date Tue, 07 Feb 2017 21:06:13 +0100
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6625019a0c96 old model2neo4j renamed to model2neo4j_restclient. new model2neo4j_client and model2neo4j_import. fixed ismixml2model and compare_models.
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1 import networkx as nx
6625019a0c96 old model2neo4j renamed to model2neo4j_restclient. new model2neo4j_client and model2neo4j_import. fixed ismixml2model and compare_models.
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2 from neo4j.v1 import GraphDatabase, basic_auth
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3 import sys
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4
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5 ## configure behaviour
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6
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7 # metworkx graph file
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8 input_fn = 'ismi_graph.gpickle'
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9
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10 # label added to all nodes
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11 project_label = '_ismi'
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12
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13 # neo4j base URL
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14 neo4jBaseURL = "bolt://localhost:7687"
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16 # name of type attribute
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17 node_type_attribute = '_type'
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18 rel_type_attribute = '_type'
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21 ## setup
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23 n4j_nodes = {}
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24 n4j_relations = {}
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25
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26 # active log levels for logging
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27 logLevels = {'DEBUG', 'INFO', 'WARNING', 'ERROR', 'SYSMSG'}
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28 #logLevels = {'INFO', 'WARNING', 'ERROR', 'SYSMSG'}
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29 #logLevels = {'INFO', 'ERROR', 'SYSMSG'}
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30
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31 def log(level, message):
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32 if level in logLevels:
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33 print("%s: %s"%(level, message))
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34
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35
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36 def createIndices(nx_graph, n4j_graph):
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37 """create indices for nodes from nx_graph in n4j_graph"""
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38
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39 log('INFO', "Creating node indices in Neo4J")
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40 cnt = 0
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41 ismi_types = set()
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42 # collect types of all nodes
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43 for node_id in nx.nodes_iter(nx_graph):
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44 attrs = nx_graph.node[node_id]
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45 # get entity type
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46 ismi_types.add(attrs[node_type_attribute])
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47
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48 # create constraints for all types
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49 for ismi_type in ismi_types:
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50 query = "CREATE CONSTRAINT ON (n:%s) ASSERT n.ismi_id IS UNIQUE"%ismi_type
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51 n4j_graph.run(query)
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52
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53
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54 def copyNodes(nx_graph, n4j_graph):
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55 """copy all nodes from nx_graph to n4j_graph"""
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56
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57 log('INFO', "Copying nodes to Neo4J")
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58 cnt = 0
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59 for node_id in nx.nodes_iter(nx_graph):
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60 attrs = nx_graph.node[node_id]
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61 # get entity type
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62 ntype = attrs[node_type_attribute]
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63 # get ismi_id
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64 ismi_id = attrs['ismi_id']
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65 att_qs = ", ".join(["%s: {%s}"%(k, k) for k in attrs.keys()])
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66 # query to create node with attributes (parameter names are attribute keys)
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67 cypher = "CREATE (n:%s {%s})"%(ntype, att_qs)
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68 # run query
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69 n4j_graph.run(cypher, parameters=attrs)
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70 # save node id
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71 n4j_nodes[ismi_id] = attrs
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72
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73 cnt += 1
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74 if cnt % 100 == 0:
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75 log('INFO', "%s nodes"%cnt)
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76
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77 log('INFO', "%s nodes copied"%cnt)
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78
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79
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80 def copyRelations(nx_graph, n4j_graph):
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81 """copy all relations from nx_graph to n4j_graph"""
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82
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83 print("Copying relations to Neo4J")
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84 cnt = 0
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85 for nx_edge in nx.edges_iter(nx_graph):
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86 (nx_src, nx_tar) = nx_edge
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87 # get attributes of edge
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88 attrs = nx_graph.edge[nx_src][nx_tar][0]
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89 # get relation type
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90 rtype = attrs[rel_type_attribute]
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91 # get ismi_id of source and target nodes
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92 src_id = nx_graph.node[nx_src]['ismi_id']
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93 tar_id = nx_graph.node[nx_tar]['ismi_id']
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94 # get Neo4J nodes
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95 src = n4j_nodes.get(src_id, None)
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96 if src is None:
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97 print("ERROR: src node %s missing!"%src_id)
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98 break
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99
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100 tar = n4j_nodes.get(tar_id, None)
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101 if tar is None:
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102 print("ERROR: tar node %s missing!"%tar_id)
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103 break
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104
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105 src_type = src[node_type_attribute]
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106 tar_type = tar[node_type_attribute]
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107
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108 att_qs = ", ".join(["%s: {%s}"%(k, k) for k in attrs.keys()])
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109 # query to create a relation with attributes
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110 cypher = "MATCH (n1:%s),(n2:%s) WHERE n1.ismi_id = %s AND n2.ismi_id = %s CREATE (n1)-[r:%s {%s}]->(n2)"%(src_type, tar_type, src_id, tar_id, rtype, att_qs)
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111 # run query
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112 n4j_graph.run(cypher, attrs)
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113
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114 cnt += 1
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115 if cnt % 100 == 0:
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116 log('INFO', "%s relations"%cnt)
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117
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118 log('INFO', "%s relations copied"%cnt)
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119 ## main
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120
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121 print("Copy graph from networkx to Neo4J")
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122
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123 # read commandline parameters
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124 if len(sys.argv) > 1:
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125 input_fn = sys.argv[1]
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126
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127 # read networkx graph from pickle
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128 print("Reading graph from %s"%input_fn)
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129 nx_graph = nx.read_gpickle(input_fn)
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130 print("Graph info: %s"%nx.info(nx_graph))
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131
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132 # open neo4j graph db
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133 print("Opening Neo4J db at %s"%neo4jBaseURL)
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134 n4j_driver = GraphDatabase.driver(neo4jBaseURL, auth=basic_auth("neo4j", "neo5j"))
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135 # get session to pass to functions
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136 n4j_graph = n4j_driver.session()
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137
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138 createIndices(nx_graph, n4j_graph)
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139
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140 copyNodes(nx_graph, n4j_graph)
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141
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142 copyRelations(nx_graph, n4j_graph)
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143
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144 print("Done.")