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"""
Neo4j Database Manager
Handle graph database connections and operations
"""
from neo4j import GraphDatabase
from typing import Dict, List, Optional, Any
import yaml
import logging
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
class DatabaseManager:
"""Manage Neo4j database connections and schema"""
def __init__(self, config_path: str = "config.yml"):
with open(config_path, 'r') as f:
self.config = yaml.safe_load(f)['neo4j']
self.driver = GraphDatabase.driver(
self.config['uri'],
auth=(self.config['username'], self.config['password'])
)
logger.info(f"Connected to Neo4j at {self.config['uri']}")
def close(self):
"""Close database connection"""
self.driver.close()
def __enter__(self):
return self
def __exit__(self, exc_type, exc_val, exc_tb):
self.close()
def execute_query(self, query: str, parameters: Optional[Dict] = None) -> List[Dict]:
"""Execute a Cypher query and return results"""
with self.driver.session() as session:
result = session.run(query, parameters or {})
return [record.data() for record in result]
def initialize_schema(self):
"""Initialize database schema with constraints and indexes"""
queries = [
# Constraints
"CREATE CONSTRAINT gene_id IF NOT EXISTS FOR (g:Gene) REQUIRE g.gene_id IS UNIQUE",
"CREATE CONSTRAINT mutation_id IF NOT EXISTS FOR (m:Mutation) REQUIRE m.mutation_id IS UNIQUE",
"CREATE CONSTRAINT patient_id IF NOT EXISTS FOR (p:Patient) REQUIRE p.patient_id IS UNIQUE",
"CREATE CONSTRAINT cancer_type_id IF NOT EXISTS FOR (c:CancerType) REQUIRE c.cancer_type_id IS UNIQUE",
# Indexes
"CREATE INDEX gene_symbol IF NOT EXISTS FOR (g:Gene) ON (g.symbol)",
"CREATE INDEX mutation_position IF NOT EXISTS FOR (m:Mutation) ON (m.chromosome, m.position)",
"CREATE INDEX patient_project IF NOT EXISTS FOR (p:Patient) ON (p.project_id)",
]
with self.driver.session() as session:
for query in queries:
try:
session.run(query)
logger.info(f"Executed: {query[:50]}...")
except Exception as e:
logger.warning(f"Schema query failed (may already exist): {e}")
logger.info("Database schema initialized")
def clear_database(self):
"""Clear all nodes and relationships (use with caution!)"""
query = "MATCH (n) DETACH DELETE n"
with self.driver.session() as session:
session.run(query)
logger.info("Database cleared")
class GeneRepository:
"""Repository for Gene nodes"""
def __init__(self, db_manager: DatabaseManager):
self.db = db_manager
def create_gene(self, gene_data: Dict) -> Dict:
"""Create a Gene node"""
query = """
MERGE (g:Gene {gene_id: $gene_id})
SET g.symbol = $symbol,
g.name = $name,
g.chromosome = $chromosome,
g.start_position = $start_position,
g.end_position = $end_position,
g.strand = $strand,
g.gene_type = $gene_type
RETURN g
"""
result = self.db.execute_query(query, gene_data)
return result[0]['g'] if result else {}
def get_gene_by_symbol(self, symbol: str) -> Optional[Dict]:
"""Find gene by symbol"""
query = """
MATCH (g:Gene {symbol: $symbol})
RETURN g
"""
result = self.db.execute_query(query, {'symbol': symbol})
return result[0]['g'] if result else None
def get_gene_mutations(self, gene_id: str) -> List[Dict]:
"""Get all mutations for a gene"""
query = """
MATCH (g:Gene {gene_id: $gene_id})<-[:AFFECTS]-(m:Mutation)
RETURN m
ORDER BY m.position
"""
result = self.db.execute_query(query, {'gene_id': gene_id})
return [r['m'] for r in result]
class MutationRepository:
"""Repository for Mutation nodes"""
def __init__(self, db_manager: DatabaseManager):
self.db = db_manager
def create_mutation(self, mutation_data: Dict, gene_id: str) -> Dict:
"""Create a Mutation node and link to Gene"""
query = """
MATCH (g:Gene {gene_id: $gene_id})
MERGE (m:Mutation {mutation_id: $mutation_id})
SET m.chromosome = $chromosome,
m.position = $position,
m.reference = $reference,
m.alternate = $alternate,
m.consequence = $consequence,
m.variant_type = $variant_type,
m.quality = $quality
MERGE (m)-[:AFFECTS]->(g)
RETURN m
"""
params = {**mutation_data, 'gene_id': gene_id}
result = self.db.execute_query(query, params)
return result[0]['m'] if result else {}
def link_mutation_to_patient(self, mutation_id: str, patient_id: str, properties: Optional[Dict] = None):
"""Create HAS_MUTATION relationship"""
query = """
MATCH (p:Patient {patient_id: $patient_id})
MATCH (m:Mutation {mutation_id: $mutation_id})
MERGE (p)-[r:HAS_MUTATION]->(m)
SET r.allele_frequency = $allele_frequency,
r.depth = $depth
RETURN r
"""
params = {
'patient_id': patient_id,
'mutation_id': mutation_id,
'allele_frequency': properties.get('allele_frequency', 0) if properties else 0,
'depth': properties.get('depth', 0) if properties else 0
}
self.db.execute_query(query, params)
def get_mutation_frequency(self, mutation_id: str) -> Dict:
"""Calculate mutation frequency across patients"""
query = """
MATCH (m:Mutation {mutation_id: $mutation_id})
MATCH (p:Patient)-[:HAS_MUTATION]->(m)
OPTIONAL MATCH (all:Patient)
WITH m, count(DISTINCT p) as patients_with_mutation, count(DISTINCT all) as total_patients
RETURN m.mutation_id as mutation_id,
patients_with_mutation,
total_patients,
toFloat(patients_with_mutation) / total_patients as frequency
"""
result = self.db.execute_query(query, {'mutation_id': mutation_id})
return result[0] if result else {}
class PatientRepository:
"""Repository for Patient nodes"""
def __init__(self, db_manager: DatabaseManager):
self.db = db_manager
def create_patient(self, patient_data: Dict) -> Dict:
"""Create a Patient node"""
query = """
MERGE (p:Patient {patient_id: $patient_id})
SET p.project_id = $project_id,
p.age = $age,
p.gender = $gender,
p.race = $race,
p.ethnicity = $ethnicity,
p.vital_status = $vital_status
RETURN p
"""
result = self.db.execute_query(query, patient_data)
return result[0]['p'] if result else {}
def link_patient_to_cancer_type(self, patient_id: str, cancer_type_id: str, properties: Optional[Dict] = None):
"""Create DIAGNOSED_WITH relationship"""
query = """
MATCH (p:Patient {patient_id: $patient_id})
MATCH (c:CancerType {cancer_type_id: $cancer_type_id})
MERGE (p)-[r:DIAGNOSED_WITH]->(c)
SET r.stage = $stage,
r.grade = $grade,
r.diagnosis_date = $diagnosis_date
RETURN r
"""
params = {
'patient_id': patient_id,
'cancer_type_id': cancer_type_id,
'stage': properties.get('stage') if properties else None,
'grade': properties.get('grade') if properties else None,
'diagnosis_date': properties.get('diagnosis_date') if properties else None
}
self.db.execute_query(query, params)
def get_patient_mutations(self, patient_id: str) -> List[Dict]:
"""Get all mutations for a patient"""
query = """
MATCH (p:Patient {patient_id: $patient_id})-[r:HAS_MUTATION]->(m:Mutation)-[:AFFECTS]->(g:Gene)
RETURN m, g, r.allele_frequency as allele_frequency, r.depth as depth
ORDER BY g.symbol
"""
result = self.db.execute_query(query, {'patient_id': patient_id})
return result
class CancerTypeRepository:
"""Repository for CancerType nodes"""
def __init__(self, db_manager: DatabaseManager):
self.db = db_manager
def create_cancer_type(self, cancer_data: Dict) -> Dict:
"""Create a CancerType node"""
query = """
MERGE (c:CancerType {cancer_type_id: $cancer_type_id})
SET c.name = $name,
c.tissue = $tissue,
c.disease_type = $disease_type
RETURN c
"""
result = self.db.execute_query(query, cancer_data)
return result[0]['c'] if result else {}
def get_common_mutations(self, cancer_type_id: str, limit: int = 10) -> List[Dict]:
"""Get most common mutations for a cancer type"""
query = """
MATCH (c:CancerType {cancer_type_id: $cancer_type_id})<-[:DIAGNOSED_WITH]-(p:Patient)
MATCH (p)-[:HAS_MUTATION]->(m:Mutation)-[:AFFECTS]->(g:Gene)
WITH m, g, count(DISTINCT p) as patient_count
RETURN m, g, patient_count
ORDER BY patient_count DESC
LIMIT $limit
"""
result = self.db.execute_query(query, {'cancer_type_id': cancer_type_id, 'limit': limit})
return result
def get_statistics(self, cancer_type_id: str) -> Dict:
"""Get statistics for a cancer type"""
query = """
MATCH (c:CancerType {cancer_type_id: $cancer_type_id})<-[:DIAGNOSED_WITH]-(p:Patient)
OPTIONAL MATCH (p)-[:HAS_MUTATION]->(m:Mutation)
WITH c, count(DISTINCT p) as total_patients, count(DISTINCT m) as total_mutations
RETURN c.name as cancer_type,
total_patients,
total_mutations,
CASE WHEN total_patients > 0
THEN toFloat(total_mutations) / total_patients
ELSE 0
END as avg_mutations_per_patient
"""
result = self.db.execute_query(query, {'cancer_type_id': cancer_type_id})
return result[0] if result else {}
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