Initial commit

modules/database/tools/neontology_tools.py

@@ -0,0 +1,121 @@
+from dotenv import load_dotenv, find_dotenv
+load_dotenv(find_dotenv())
+import os
+import modules.logger_tool as logger
+log_name = 'api_modules_database_tools_neontology_tools'
+log_dir = os.getenv("LOG_PATH", "/logs")  # Default path as fallback
+logging = logger.get_logger(
+    name=log_name,
+    log_level=os.getenv("LOG_LEVEL", "DEBUG"),
+    log_path=log_dir,
+    log_file=log_name,
+    runtime=True,
+    log_format='default'
+)
+from modules.database.tools.neontology.graphconnection import init_neontology, close_neontology
+from modules.database.tools.neontology.basenode import BaseNode
+from modules.database.tools.neontology.baserelationship import BaseRelationship
+from pydantic import ValidationError
+import os
+import neo4j
+
+# Initialize Neontology with the Neo4j database details
+def init_neontology_connection(uri=None, user=None, password=None):
+    uri = uri or os.getenv("APP_BOLT_URL")
+    user = user or os.getenv("USER_NEO4J")  # Add default value
+    password = password or os.getenv("PASSWORD_NEO4J")
+
+    if not all([uri, user, password]):
+        raise ValueError("Missing required Neo4j connection parameters")
+
+    try:
+        logging.info(f"Initializing Neontology with URI: {uri}")
+        init_neontology(
+            neo4j_uri=uri,
+            neo4j_username=user,
+            neo4j_password=password
+        )
+        logging.info(f"Neontology connection initialized with URI: {uri}, user: {user}")
+    except Exception as e:
+        raise ValueError(f"Failed to initialize Neontology connection: {str(e)}")
+    
+def close_neontology_connection():
+    logging.debug(f"Attempting to terminate Neontology connection")
+    close_neontology()
+    logging.info(f"Neontology connection terminated")
+
+# Terminates the Neo4j connection
+def close_neo4j_connection():
+    logging.debug(f"Attempting to terminate Neo4j connection")
+    neo4j.close()
+    logging.info(f"Neo4j connection terminated")
+
+# Create a Neontology node in the Neo4j database
+def create_or_merge_neontology_node(node: BaseNode, database: str = 'neo4j', operation: str = "merge"):
+    """
+    Create or merge a Neontology node in the Neo4j database.
+
+    Args:
+        node (BaseNode): A Neontology node object.
+        operation (str): The operation to perform ('create' or 'merge'). Defaults to 'merge'.
+    """
+    try:
+        if operation == "create":
+            node.create(database=database)
+        elif operation == "merge":
+            node.merge(database=database)
+        else:
+            logging.error(f"Invalid operation: {operation}")
+    except Exception as e:
+        logging.error(f"Error in processing node: {e}")
+
+# Create or merge a Neontology node in the Neo4j database. If a ValidationError occurs
+# due to a NaN value, replace it with a default value and retry.
+def create_or_merge_neontology_node_with_default(driver, node: BaseNode, database: str = 'neo4j', operation: str = "merge", default_values: dict = {}):
+    """
+    Create or merge a Neontology node in the Neo4j database. If a ValidationError occurs
+    due to a NaN value, replace it with a default value and retry.
+
+    Args:
+        node (BaseNode): A Neontology node object.
+        operation (str): The operation to perform ('create' or 'merge'). Defaults to 'merge'.
+        default_values (dict): A dictionary of default values for fields that might contain NaN.
+    """
+    try:
+        # Attempt to create or merge the node
+        if operation == "create":
+            node.create(database=database)
+        else:  # "merge" by default
+            node.merge(database=database)
+    except ValidationError as e:
+        # Handle ValidationError due to NaN value
+        for field, error in e.errors():
+            if field in default_values and 'type' in error and error['type'] == 'value_error.nan':
+                setattr(node, field, default_values[field])
+                logging.warning(f"Warning: Replacing NaN in {field} with default value '{default_values[field]}' and retrying.")
+                create_or_merge_neontology_node_with_default(driver, node, database, operation, default_values)
+                break
+        else:
+            # If the error is not due to a NaN value or field not in default_values, re-raise the error
+            logging.error(f"Error in processing node: {e}")
+            raise
+    except Exception as e:
+        logging.error(f"Error in processing node: {e}")
+
+def create_or_merge_neontology_relationship(relationship: BaseRelationship, database: str = 'neo4j', operation: str = "merge"):
+    """
+    Create or merge a Neontology relationship in the Neo4j database.
+
+    Args:
+        relationship (BaseRelationship): A Neontology relationship object.
+        operation (str): The operation to perform ('create' or 'merge'). Defaults to 'merge'.
+    """
+    try:
+        if operation == "create":
+            relationship.create(database=database)
+        elif operation == "merge":
+            relationship.merge(database=database)
+        else:
+            logging.error(f"Invalid operation: {operation}")
+    except Exception as e:
+        logging.error(f"Error in processing relationship: {e}")