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schema_config_generation.py
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188
schema_config_generation.py
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#!/usr/bin/env python
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# coding: utf-8
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from pathlib import Path
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#import networkx as nx
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import yaml
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from collections import defaultdict
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#extract all node types and generate basic yaml config part for nodes
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def write_automated_schema(graph, filePath, mSchemaPath):
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schemaData = {
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'nodes': {},
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'edges': {}
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}
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if Path(filePath).exists():
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schemaData = loadManualSchema(filePath)
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elif mSchemaPath:
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print("using the manual schema")
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schemaData = loadManualSchema(mSchemaPath)
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for node in graph.nodes():
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label = graph.nodes[node].get('label')
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if label == 'resource':
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label = graph.nodes[node].get('resourceType')
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label = label.capitalize()
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if not label in schemaData['nodes']:
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schemaData['nodes'][label] = {}
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if not 'properties' in schemaData['nodes'][label]:
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schemaData['nodes'][label]['properties'] = {}
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for k in graph.nodes[node].keys():
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#print(k, '----- ', graph.nodes[node][k])
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#if k != 'label':
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schemaData['nodes'][label]['properties'][k] = 'str'
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#schemaData['nodes'][label]['properties'].update(graph.nodes[node].keys())
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file=open(filePath, 'w')
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for n in schemaData['nodes']:
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temp = n+':\n'
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if 'is_a' in schemaData['nodes'][n]:
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temp += ' is_a: ' + schemaData['nodes'][n]['is_a'] + '\n'
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else:
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temp += ' is_a: named thing\n'
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if 'represented_as' in schemaData['nodes'][n]:
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temp += ' represented_as: ' + schemaData['nodes'][n]['represented_as'] + '\n'
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else:
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temp += ' represented_as: node\n'
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if 'label_in_input' in schemaData['nodes'][n]:
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temp += ' label_in_input: ' + schemaData['nodes'][n]['label_in_input'] + '\n'
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if 'preferred_id' in schemaData['nodes'][n]:
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temp += ' preferred_id: ' + schemaData['nodes'][n]['preferred_id'] + '\n'
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else:
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temp += ' preferred_id: fhir_id\n'
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temp += ' label_in_input: ' + n + '\n'
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temp += ' properties:\n'
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# get property values from schemaData if exists
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for pKey in schemaData['nodes'][n]['properties']:
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temp += ' ' + pKey + ': ' + schemaData['nodes'][n]['properties'][pKey] + '\n'
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#elif schemaData['nodes']['properties']:
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#print("----> ", schemaData['nodes']['properties'])
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""" else:
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for attr in schemaData['nodes'][n]:
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temp += ' ' + attr + ': str\n' """
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temp += '\n'
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file.write(temp)
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file.write('\n')
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#extract all relationship types and generate basic yaml config part for relationships
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#if not edgeTypes: edgeTypes = set()
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for u, v, a in graph.edges(data=True):
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#edge_label = graph[u][v].get('edge_type', '')
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source_label = graph.nodes[u].get('label')
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target_label = graph.nodes[v].get('label')
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if source_label == 'resource':
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source_label = graph.nodes[u].get('resourceType', str(u))
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if target_label == 'resource':
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target_label = graph.nodes[v].get('resourceType', str(v))
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source_label = source_label.capitalize()
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#target_label = target_label.capitalize()
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if source_label + ' to ' + target_label + ' association' in schemaData['edges']:
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# add missing attributes
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continue
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elif source_label + ' derived from ' + target_label + ' association' in schemaData['edges']:
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continue
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elif source_label + ' has member ' + target_label + ' association' in schemaData['edges']:
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continue
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elif source_label + ' reasoned by ' + target_label + ' association' in schemaData['edges']:
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continue
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elif source_label + ' is ' + target_label + ' association' in schemaData['edges']:
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continue
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else:
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#schemaData['edges'][source_label + ' to ' + target_label + ' association'] = set()
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schemaData['edges'][source_label + ' to ' + target_label + ' association'] = {
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'is_a': 'association',
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'represented_as': 'edge',
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'label_in_input': source_label + '_to_' + target_label,
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'properties': a
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}
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for label in schemaData['edges']:
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temp = '' + label + ':\n'
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for key in schemaData['edges'][label]:
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if key == 'properties':
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temp += ' properties:\n'
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for prop in schemaData['edges'][label][key]:
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temp += ' ' + prop + ': ' + schemaData['edges'][label][key][prop] + '\n'
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else:
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temp+= ' ' + key + ': ' + schemaData['edges'][label][key] + '\n'
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temp += '\n'
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file.write(temp)
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file.close()
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def loadManualSchema(path):
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schemaData = {
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'nodes': {},
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'edges': {}
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}
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edgeTypes = set()
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with open(path, 'r') as file:
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# Load YAML with comments stripped
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data = yaml.safe_load(file)
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for label, attrs in data.items():
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cLabel = label.capitalize()
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if not label == 'Title':
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if attrs["represented_as"] == 'node':
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if not hasattr(schemaData['nodes'], cLabel):
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schemaData['nodes'][cLabel] = set()
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#assuming uniqueness in schema file here. If the same node type exits twice, it will be overwritten.
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schemaData['nodes'][cLabel] = attrs
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#for a in attrs:
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#print(v)
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""" for k, v in attrs:
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if not k == ''
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schemaData['nodes'][label][k] = v """
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else:
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if not hasattr(schemaData['edges'], cLabel):
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schemaData['edges'][cLabel] = set()
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#assuming uniqueness in schema file here. If the same node type exits twice, it will be overwritten.
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schemaData['edges'][cLabel] = attrs
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return schemaData
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