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json_to_csv.py
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json_to_csv.py
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import json
import csv
import os
import logging
import bz2
logging.basicConfig(level=logging.INFO)
DATA_DIR = 'csv/data'
CYPHER_DIR = 'csv/cypher'
JSON_FILE = 'hetionet-v1.0.json.bz2'
META_JSON_FILE = 'hetionet-v1.0-metagraph.json'
def create_directories():
for dir_name in [DATA_DIR, CYPHER_DIR]:
os.makedirs(dir_name, exist_ok=True)
def determine_type(value):
type_map = {
bool: 'toBoolean',
int: 'toInteger',
float: 'toFloat',
list: 'toArray',
}
return type_map.get(type(value), 'toString')
def load_json(filename):
if filename.endswith('.bz2'):
with bz2.open(filename, 'rt', encoding='utf-8') as f:
return json.load(f)
else:
with open(filename, 'r') as f:
return json.load(f)
def initialize_csv_writer(filename, fieldnames):
csv_file = open(f'{DATA_DIR}/{filename}', 'w', newline='')
csv_writer = csv.DictWriter(csv_file, fieldnames=fieldnames)
csv_writer.writeheader()
logging.info(f"Created node file: {filename}")
return csv_file, csv_writer
def initialize_cypher_file(label, filename, set_statements):
cypher_file = open(f'{CYPHER_DIR}/{filename.replace(".csv", "")}.cypher', 'w')
cypher_file.write(f"CREATE INDEX identifier_index_{label} FOR (n:{label}) ON (n.identifier);\n")
cypher_file.write(f"LOAD CSV WITH HEADERS FROM 'file:///{filename}' AS row\n")
cypher_file.write(f"CREATE (n:{label}) SET {', '.join(set_statements)};\n")
logging.info(f"Created cypher file: {filename.replace('.csv', '')}.cypher")
return cypher_file
def update_csv_and_cypher_files(label, filename, node, csv_writer, csv_file, cypher_file, set_statements):
new_fields = set(node['data'].keys()) - set(csv_writer.fieldnames)
if new_fields:
csv_writer.fieldnames.extend(new_fields)
csv_writer.fieldnames = sorted(csv_writer.fieldnames)
csv_file.seek(0)
csv_file.truncate()
csv_writer.writeheader()
cypher_file.seek(0)
cypher_file.truncate()
cypher_file.write(f"CREATE INDEX identifier_index_{label} FOR (n:{label}) ON (n.identifier);\n")
cypher_file.write(f"LOAD CSV WITH HEADERS FROM 'file:///{filename}' AS row\n")
for new_field in new_fields:
data_type = determine_type(node['data'][new_field])
if data_type == 'toArray':
set_statements.append(f"r.{new_field} = split(replace(replace(replace(row.{new_field}, '[', ''), ']', ''), \"'\", ''), ',')")
else:
set_statements.append(f"n.{new_field} = {data_type}(row.{new_field})")
sorted_set_statements = sorted(set_statements)
cypher_file.write(f"CREATE (n:{label}) SET {', '.join(sorted_set_statements)};\n")
def write_csv_row(node, csv_writer):
row = {'identifier': node['identifier'], 'name': node['name']}
row.update(node['data'])
csv_writer.writerow(row)
def close_files(files):
for file in files.values():
file.close()
def process_nodes(nodes):
node_files = {}
node_writers = {}
node_cypher_files = {}
node_set_statements_dict = {}
for node in nodes:
label = node['kind'].replace(" ", "")
filename = f"node_{label}.csv"
if filename not in node_files:
node_files[filename], node_writers[filename] = initialize_csv_writer(filename, ['identifier', 'name'])
node_set_statements_dict[filename] = [f"n.identifier = {determine_type(node['identifier'])}(row.identifier)", "n.name = row.name"]
node_cypher_files[filename] = initialize_cypher_file(label, filename, node_set_statements_dict[filename])
update_csv_and_cypher_files(label, filename, node, node_writers[filename], node_files[filename], node_cypher_files[filename], node_set_statements_dict[filename])
write_csv_row(node, node_writers[filename])
close_files(node_files)
close_files(node_cypher_files)
def initialize_edge_files(filename, source_label):
fieldnames = ['source_id', 'target_id']
edge_file, edge_writer = initialize_csv_writer(filename, fieldnames)
edge_set_statements = []
edge_cypher_file = initialize_cypher_file(source_label, filename, edge_set_statements)
logging.info(f"Created edge file: {filename}")
return edge_file, edge_writer, edge_cypher_file, edge_set_statements
def update_edge_files_and_cypher_files(filename, edge, edge_writer, edge_file, edge_cypher_file, edge_set_statements, source_label, target_label, rel_type_formatted):
new_fields = set(edge['data'].keys()) - set(edge_writer.fieldnames)
if new_fields:
edge_writer.fieldnames.extend(new_fields)
edge_writer.fieldnames = sorted(edge_writer.fieldnames)
edge_file.seek(0)
edge_file.truncate()
edge_writer.writeheader()
edge_cypher_file.seek(0)
edge_cypher_file.truncate()
edge_cypher_file.write(f"LOAD CSV WITH HEADERS FROM 'file:///{filename}' AS row\n")
edge_cypher_file.write(f"MATCH (a:{source_label} {{identifier: {determine_type(edge['source_id'][1])}(row.source_id)}}), (b:{target_label} {{identifier: {determine_type(edge['target_id'][1])}(row.target_id)}})\n")
edge_cypher_file.write(f"CREATE (a)-[r:{rel_type_formatted}]->(b)\n")
for new_field in new_fields:
data_type = determine_type(edge['data'][new_field])
if data_type == 'toArray':
edge_set_statements.append(f"r.{new_field} = split(replace(replace(replace(row.{new_field}, '[', ''), ']', ''), \"'\", ''), ',')")
else:
edge_set_statements.append(f"r.{new_field} = {data_type}(row.{new_field})")
sorted_set_statements = sorted(edge_set_statements)
edge_cypher_file.write("SET ")
edge_cypher_file.write(",\n ".join(sorted_set_statements))
edge_cypher_file.write(";\n")
def write_edge_row(edge, edge_writer):
row = {'source_id': edge['source_id'][1], 'target_id': edge['target_id'][1]}
row.update(edge['data'])
edge_writer.writerow(row)
def process_edges(edges, kind_to_abbrev):
edge_files = {}
edge_writers = {}
edge_cypher_files = {}
edge_set_statements_dict = {}
for edge in edges:
source_label = edge['source_id'][0].replace(" ", "")
target_label = edge['target_id'][0].replace(" ", "")
rel_type = edge['kind'].replace(" ", "")
filename = f"edge_{source_label}_{rel_type}_{target_label}.csv"
source_abbrev = kind_to_abbrev.get(source_label, source_label)
target_abbrev = kind_to_abbrev.get(target_label, target_label)
rel_type_abbrev = kind_to_abbrev.get(rel_type, rel_type)
rel_type_formatted = f"{rel_type.upper()}_{source_abbrev}{rel_type_abbrev}{target_abbrev}"
if filename not in edge_files:
edge_files[filename], edge_writers[filename], edge_cypher_files[filename], edge_set_statements_dict[filename] = initialize_edge_files(filename, source_label)
update_edge_files_and_cypher_files(filename, edge, edge_writers[filename], edge_files[filename], edge_cypher_files[filename], edge_set_statements_dict[filename], source_label, target_label, rel_type_formatted)
write_edge_row(edge, edge_writers[filename])
close_files(edge_files)
close_files(edge_cypher_files)
if __name__ == "__main__":
create_directories()
data = load_json(JSON_FILE)
meta_data = load_json(META_JSON_FILE)
kind_to_abbrev = {key.replace(" ", ""): value for key, value in meta_data['kind_to_abbrev'].items()}
nodes = data['nodes']
edges = data['edges']
process_nodes(nodes)
process_edges(edges, kind_to_abbrev)