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Retrieves a single LIMS_Pathogens node from a Neo4j graph database by its unique identifier.

Purpose

This function queries a Neo4j database to fetch a specific LIMS_Pathogens node using its ID. It's designed for Laboratory Information Management System (LIMS) applications that track pathogen data in a graph database. The function returns the first matching node or None if no match is found, making it useful for retrieving detailed pathogen information by identifier.

Source Code

def get_lims_pathogens_by_id(id):
    """Get a LIMS_Pathogens node by its ID"""
    query = """
    MATCH (n:LIMS_Pathogens {id: $id})
    RETURN n
    """
    result = run_query(query, {"id": id})
    return result[0] if result else None

Parameters

Parameter Details

id: The unique identifier of the LIMS_Pathogens node to retrieve. Expected to be a string or integer that matches the 'id' property of a node in the Neo4j database. This should correspond to a valid pathogen record identifier in the LIMS system.

Return Value

Returns a dictionary-like object representing the LIMS_Pathogens node if found, containing all properties of the node (e.g., pathogen name, classification, metadata). Returns None if no node with the specified ID exists. The exact structure depends on the properties stored in the Neo4j node.

Dependencies

• neo4j

Required Imports

from neo4j import GraphDatabase

Usage Example

# Assuming run_query is defined and Neo4j connection is configured
from neo4j import GraphDatabase

# Example usage
pathogen_id = "PATH-12345"
pathogen_node = get_lims_pathogens_by_id(pathogen_id)

if pathogen_node:
    print(f"Found pathogen: {pathogen_node}")
    # Access node properties
    # print(f"Name: {pathogen_node['n']['name']}")
else:
    print(f"No pathogen found with ID: {pathogen_id}")

Best Practices

• Ensure the run_query function is properly defined with error handling for database connection issues
• Validate the id parameter before passing it to prevent injection attacks, even though parameterized queries are used
• Consider adding type hints to the function signature for better code documentation
• Handle the None return value appropriately in calling code to avoid AttributeError
• Implement proper connection pooling and session management in the run_query function
• Consider adding logging for debugging database queries
• The function assumes run_query returns a list; ensure this contract is maintained

Tags

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