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function get_lims_sampletypetests_with_references_sampletypes_lims_sampletypes

Maturity: 42

Queries a Neo4j graph database to retrieve LIMS_SampleTypes nodes that are connected to a specific LIMS_SampleTypeTests node through a REFERENCES_SAMPLETYPES relationship.

File:
/tf/active/vicechatdev/neo4j_schema/neo4j_python_snippets.py
Lines:
1353 - 1360
Complexity:
simple

Purpose

This function is designed to traverse a Laboratory Information Management System (LIMS) graph database to find sample types associated with a particular sample type test. It's useful for understanding which sample types are valid or applicable for a given test configuration, enabling validation of test-sample compatibility and exploration of LIMS data relationships.

Source Code

def get_lims_sampletypetests_with_references_sampletypes_lims_sampletypes(source_id, limit=100):
    """Get LIMS_SampleTypes nodes connected to a LIMS_SampleTypeTests via REFERENCES_SAMPLETYPES"""
    query = """
    MATCH (source:LIMS_SampleTypeTests {id: $source_id})-[r:REFERENCES_SAMPLETYPES]->(target:LIMS_SampleTypes)
    RETURN target
    LIMIT $limit
    """
    return run_query(query, {"source_id": source_id, "limit": limit})

Parameters

Name Type Default Kind
source_id - - positional_or_keyword
limit - 100 positional_or_keyword

Parameter Details

source_id: The unique identifier (id property) of the LIMS_SampleTypeTests node from which to start the traversal. This should be a string or value that matches the 'id' property of a node in the Neo4j database.

limit: Maximum number of LIMS_SampleTypes nodes to return. Defaults to 100. This parameter prevents excessive data retrieval and controls query performance. Must be a positive integer.

Return Value

Returns the result of the run_query function, which typically contains a list or collection of Neo4j records representing LIMS_SampleTypes nodes. Each record contains the 'target' node with all its properties. The exact return type depends on the run_query implementation, but it's likely a list of dictionaries or Neo4j Record objects. Returns an empty collection if no matching relationships are found or if the source_id doesn't exist.

Dependencies

  • neo4j

Required Imports

from neo4j import GraphDatabase

Usage Example

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

# Define or import run_query function
def run_query(query, params):
    driver = GraphDatabase.driver('bolt://localhost:7687', auth=('neo4j', 'password'))
    with driver.session() as session:
        result = session.run(query, params)
        return [record['target'] for record in result]
    driver.close()

# Get sample types for a specific test
test_id = 'TEST_001'
sample_types = get_lims_sampletypetests_with_references_sampletypes_lims_sampletypes(test_id, limit=50)

# Process results
for sample_type in sample_types:
    print(f"Sample Type ID: {sample_type['id']}, Name: {sample_type.get('name', 'N/A')}")

Best Practices

  • Ensure the run_query function properly handles database connections and closes them after use to prevent connection leaks
  • Validate that source_id exists before calling this function to avoid unnecessary database queries
  • Consider adjusting the limit parameter based on expected data volume and performance requirements
  • Handle cases where the function returns empty results (no matching relationships found)
  • Implement proper error handling around this function to catch Neo4j connection errors or query failures
  • Use parameterized queries (as done here) to prevent Cypher injection attacks
  • Consider adding pagination if working with large datasets instead of relying solely on the limit parameter
  • Ensure proper indexing on the 'id' property of LIMS_SampleTypeTests nodes for optimal query performance

Tags

neo4j graph-database lims laboratory sample-types database-query cypher relationship-traversal data-retrieval

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