127 lines
5.4 KiB
Python
127 lines
5.4 KiB
Python
from dotenv import load_dotenv, find_dotenv
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load_dotenv(find_dotenv())
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import os
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import modules.logger_tool as logger
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log_name = 'api_modules_database_tools_neontology_tools'
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log_dir = os.getenv("LOG_PATH", "/logs") # Default path as fallback
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logging = logger.get_logger(
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name=log_name,
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log_level=os.getenv("LOG_LEVEL", "DEBUG"),
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log_path=log_dir,
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log_file=log_name,
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runtime=True,
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log_format='default'
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)
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from modules.database.tools.neontology.graphconnection import init_neontology, close_neontology
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from modules.database.tools.neontology.basenode import BaseNode
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from modules.database.tools.neontology.baserelationship import BaseRelationship
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from pydantic import ValidationError
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import os
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import neo4j
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# Initialize Neontology with the Neo4j database details
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def init_neontology_connection(uri=None, user=None, password=None):
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uri = uri or os.getenv("APP_BOLT_URL")
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user = user or os.getenv("USER_NEO4J") # Add default value
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password = password or os.getenv("PASSWORD_NEO4J")
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if not all([uri, user, password]):
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raise ValueError("Missing required Neo4j connection parameters")
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try:
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logging.info(f"Initializing Neontology with URI: {uri}")
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init_neontology(
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neo4j_uri=uri,
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neo4j_username=user,
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neo4j_password=password
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)
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logging.info(f"Neontology connection initialized with URI: {uri}, user: {user}")
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except Exception as e:
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raise ValueError(f"Failed to initialize Neontology connection: {str(e)}")
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def close_neontology_connection():
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logging.debug(f"Attempting to terminate Neontology connection")
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close_neontology()
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logging.info(f"Neontology connection terminated")
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# Terminates the Neo4j connection
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def close_neo4j_connection():
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logging.debug(f"Attempting to terminate Neo4j connection")
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neo4j.close()
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logging.info(f"Neo4j connection terminated")
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# Create a Neontology node in the Neo4j database
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def create_or_merge_neontology_node(node: BaseNode, database: str = 'neo4j', operation: str = "merge"):
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"""
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Create or merge a Neontology node in the Neo4j database.
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Args:
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node (BaseNode): A Neontology node object.
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operation (str): The operation to perform ('create' or 'merge'). Defaults to 'merge'.
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"""
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try:
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logging.debug(f"Creating/merging node: {node.__class__.__name__} with label '{node.__primarylabel__}' in database '{database}'")
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logging.debug(f"Node data: {node.to_dict()}")
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if operation == "create":
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result = node.create(database=database)
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logging.debug(f"Create result: {result}")
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elif operation == "merge":
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result = node.merge(database=database)
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logging.debug(f"Merge result: {result}")
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else:
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logging.error(f"Invalid operation: {operation}")
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except Exception as e:
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logging.error(f"Error in processing node: {e}")
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raise # Re-raise to see the actual error
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# Create or merge a Neontology node in the Neo4j database. If a ValidationError occurs
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# due to a NaN value, replace it with a default value and retry.
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def create_or_merge_neontology_node_with_default(driver, node: BaseNode, database: str = 'neo4j', operation: str = "merge", default_values: dict = {}):
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"""
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Create or merge a Neontology node in the Neo4j database. If a ValidationError occurs
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due to a NaN value, replace it with a default value and retry.
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Args:
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node (BaseNode): A Neontology node object.
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operation (str): The operation to perform ('create' or 'merge'). Defaults to 'merge'.
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default_values (dict): A dictionary of default values for fields that might contain NaN.
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"""
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try:
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# Attempt to create or merge the node
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if operation == "create":
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node.create(database=database)
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else: # "merge" by default
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node.merge(database=database)
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except ValidationError as e:
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# Handle ValidationError due to NaN value
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for field, error in e.errors():
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if field in default_values and 'type' in error and error['type'] == 'value_error.nan':
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setattr(node, field, default_values[field])
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logging.warning(f"Warning: Replacing NaN in {field} with default value '{default_values[field]}' and retrying.")
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create_or_merge_neontology_node_with_default(driver, node, database, operation, default_values)
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break
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else:
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# If the error is not due to a NaN value or field not in default_values, re-raise the error
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logging.error(f"Error in processing node: {e}")
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raise
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except Exception as e:
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logging.error(f"Error in processing node: {e}")
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def create_or_merge_neontology_relationship(relationship: BaseRelationship, database: str = 'neo4j', operation: str = "merge"):
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"""
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Create or merge a Neontology relationship in the Neo4j database.
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Args:
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relationship (BaseRelationship): A Neontology relationship object.
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operation (str): The operation to perform ('create' or 'merge'). Defaults to 'merge'.
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"""
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try:
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if operation == "create":
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relationship.create(database=database)
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elif operation == "merge":
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relationship.merge(database=database)
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else:
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logging.error(f"Invalid operation: {operation}")
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except Exception as e:
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logging.error(f"Error in processing relationship: {e}") |