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Phase 2.3: EHR/FHIR Integration Module
Provides FHIR-compliant APIs, HL7 messaging support, and real patient data
integration with Electronic Health Record systems.
"""
import json
import logging
from datetime import datetime
from typing import Optional, Dict, Any, List
from enum import Enum
import hashlib
from core.safe_logging import safe_log_info, safe_log_warning, log_exception_safe, mask_identifier
try:
from fhir.resources.R4B.bundle import Bundle
from fhir.resources.R4B.bundle import BundleEntry
from fhir.resources.R4B.patient import Patient
from fhir.resources.R4B.condition import Condition
from fhir.resources.R4B.observation import Observation
from fhir.resources.R4B.goal import Goal
from fhir.resources.R4B.careplan import CarePlan
FHIR_AVAILABLE = True
except ImportError:
FHIR_AVAILABLE = False
logger = logging.getLogger(__name__)
class FHIRResourceType(str, Enum):
"""FHIR Resource Types supported by the system."""
PATIENT = "Patient"
CONDITION = "Condition"
OBSERVATION = "Observation"
GOAL = "Goal"
CARE_PLAN = "CarePlan"
MEDICATION = "Medication"
PROCEDURE = "Procedure"
APPOINTMENT = "Appointment"
BUNDLE = "Bundle"
class FHIRAPIClient:
"""FHIR API Client for interacting with EHR systems."""
def __init__(self, base_url: str, api_key: Optional[str] = None):
"""
Initialize FHIR API client.
Args:
base_url: FHIR server base URL (e.g., https://fhir.example.com)
api_key: Optional API key for authentication
"""
self.base_url = base_url.rstrip("/")
self.api_key = api_key
self.headers = {
"Content-Type": "application/fhir+json",
"Accept": "application/fhir+json",
}
if api_key:
self.headers["Authorization"] = f"Bearer {api_key}"
logger.info(f"FHIR API client initialized for {base_url}")
def _safe_patient_id_for_log(self, patient_id: str) -> str:
"""
Return a non-reversible, shortened representation of a patient ID
suitable for logging without exposing the raw identifier.
"""
if not patient_id:
return "pid:unknown"
digest = hashlib.sha256(patient_id.encode("utf-8")).hexdigest()
# Truncate to reduce log size while remaining collision-resistant for debugging.
return f"pid:{digest[:8]}"
def get_patient(self, patient_id: str) -> Optional[Dict[str, Any]]:
"""
Retrieve a patient resource from the FHIR server.
Args:
patient_id: FHIR patient ID
Returns:
Patient resource as dictionary
"""
try:
import requests
url = f"{self.base_url}/Patient/{patient_id}"
response = requests.get(url, headers=self.headers, timeout=10)
if response.status_code == 200:
safe_log_info(
logger,
"Retrieved patient",
patient_id=(patient_id, "pat"),
)
return response.json()
else:
safe_log_warning(
logger,
"Failed to retrieve patient {patient_id}: {status_code}",
patient_id=(patient_id, "pat"),
status_code=response.status_code,
)
return None
except Exception as e:
log_exception_safe(logger, "Error retrieving patient", e)
return None
def get_patient_conditions(self, patient_id: str) -> List[Dict[str, Any]]:
"""
Retrieve all conditions for a patient.
Args:
patient_id: FHIR patient ID
Returns:
List of Condition resources
"""
try:
import requests
url = f"{self.base_url}/Condition?subject=Patient/{patient_id}"
response = requests.get(url, headers=self.headers, timeout=10)
if response.status_code == 200:
bundle = response.json()
entries = bundle.get("entry", [])
conditions = [entry["resource"] for entry in entries]
safe_log_info(
logger,
"Retrieved {count} conditions for patient {patient_id}",
count=len(conditions),
patient_id=(patient_id, "pat"),
)
return conditions
else:
safe_log_warning(
logger,
"Failed to retrieve conditions for patient {patient_id}: {status_code}",
patient_id=(patient_id, "pat"),
status_code=response.status_code,
)
return []
except Exception as e:
log_exception_safe(logger, "Error retrieving conditions", e)
return []
def get_patient_observations(
self, patient_id: str, observation_type: Optional[str] = None
) -> List[Dict[str, Any]]:
"""
Retrieve observations (vital signs, labs) for a patient.
Args:
patient_id: FHIR patient ID
observation_type: Optional filter by code
Returns:
List of Observation resources
"""
try:
import requests
query = f"subject=Patient/{patient_id}"
if observation_type:
query += f"&code={observation_type}"
url = f"{self.base_url}/Observation?{query}"
response = requests.get(url, headers=self.headers, timeout=10)
if response.status_code == 200:
bundle = response.json()
entries = bundle.get("entry", [])
observations = [entry["resource"] for entry in entries]
logger.info(
f"Retrieved {len(observations)} observations for patient "
f"{patient_id}"
)
return observations
else:
logger.warning(
f"Failed to retrieve observations: {response.status_code}"
)
return []
except Exception as e:
log_exception_safe(logger, "Error retrieving observations", e)
return []
def get_patient_care_plans(self, patient_id: str) -> List[Dict[str, Any]]:
"""
Retrieve care plans for a patient.
Args:
patient_id: FHIR patient ID
Returns:
List of CarePlan resources
"""
try:
import requests
url = f"{self.base_url}/CarePlan?subject=Patient/{patient_id}"
response = requests.get(url, headers=self.headers, timeout=10)
if response.status_code == 200:
bundle = response.json()
entries = bundle.get("entry", [])
care_plans = [entry["resource"] for entry in entries]
logger.info(
f"Retrieved {len(care_plans)} care plans for patient "
f"{patient_id}"
)
return care_plans
else:
logger.warning(
f"Failed to retrieve care plans: {response.status_code}"
)
return []
except Exception as e:
log_exception_safe(logger, "Error retrieving care plans", e)
return []
def get_patient_goals(self, patient_id: str) -> List[Dict[str, Any]]:
"""
Retrieve goals for a patient.
Args:
patient_id: FHIR patient ID
Returns:
List of Goal resources
"""
try:
import requests
url = f"{self.base_url}/Goal?subject=Patient/{patient_id}"
response = requests.get(url, headers=self.headers, timeout=10)
if response.status_code == 200:
bundle = response.json()
entries = bundle.get("entry", [])
goals = [entry["resource"] for entry in entries]
logger.info(
f"Retrieved {len(goals)} goals for patient {patient_id}"
)
return goals
else:
logger.warning(f"Failed to retrieve goals: {response.status_code}")
return []
except Exception as e:
log_exception_safe(logger, "Error retrieving goals", e)
return []
def create_observation(self, patient_id: str, data: Dict[str, Any]) -> Optional[str]:
"""
Create a new observation for a patient.
Args:
patient_id: FHIR patient ID
data: Observation data
Returns:
New resource ID or None on failure
"""
try:
import requests
observation = {
"resourceType": "Observation",
"status": "final",
"subject": {"reference": f"Patient/{patient_id}"},
"effectiveDateTime": datetime.utcnow().isoformat(),
**data,
}
url = f"{self.base_url}/Observation"
response = requests.post(
url, json=observation, headers=self.headers, timeout=10
)
if response.status_code in [200, 201]:
new_id = response.headers.get(
"Location", ""
).split("/")[-1]
logger.info(
f"Created observation for patient {patient_id}: {new_id}"
)
return new_id
else:
logger.warning(
f"Failed to create observation: {response.status_code}"
)
return None
except Exception as e:
log_exception_safe(logger, "Error creating observation", e)
return None
def update_care_plan(
self, care_plan_id: str, data: Dict[str, Any]
) -> bool:
"""
Update a care plan.
Args:
care_plan_id: FHIR CarePlan ID
data: Updated data
Returns:
True on success, False otherwise
"""
try:
import requests
url = f"{self.base_url}/CarePlan/{care_plan_id}"
response = requests.put(
url, json=data, headers=self.headers, timeout=10
)
if response.status_code in [200, 204]:
logger.info(f"Updated care plan: {care_plan_id}")
return True
else:
logger.warning(
f"Failed to update care plan: {response.status_code}"
)
return False
except Exception as e:
log_exception_safe(logger, "Error updating care plan", e)
return False
class HL7Parser:
"""HL7 v2 message parser for EHR interoperability."""
@staticmethod
def parse_hl7_message(message: str) -> Dict[str, Any]:
"""
Parse HL7 v2 message into structured data.
Args:
message: HL7 v2 message string
Returns:
Parsed message as dictionary
"""
try:
lines = message.strip().split("\r")
parsed = {}
for line in lines:
segments = line.split("|")
segment_type = segments[0]
if segment_type == "PID":
parsed["patient"] = {
"id": segments[3],
"name": segments[5],
"dob": segments[7],
"gender": segments[8],
}
elif segment_type == "OBX":
if "observations" not in parsed:
parsed["observations"] = []
parsed["observations"].append(
{
"type": segments[2],
"value": segments[5],
"units": segments[6],
}
)
elif segment_type == "ORC":
parsed["order"] = {
"control_id": segments[1],
"status": segments[2],
}
logger.info("Parsed HL7 message successfully")
return parsed
except Exception as e:
log_exception_safe(logger, "Error parsing HL7 message", e)
return {}
@staticmethod
def create_hl7_message(
message_type: str, data: Dict[str, Any]
) -> str:
"""
Create an HL7 v2 message.
Args:
message_type: Type of message (e.g., ADT, ORM)
data: Message data
Returns:
HL7 v2 formatted message
"""
try:
segments = []
# MSH segment (header)
segments.append(f"MSH|^~\\&|{data.get('sending_app', 'APP')}|"
f"{data.get('sending_facility', 'FAC')}|"
f"{data.get('receiving_app', 'APP')}|"
f"{data.get('receiving_facility', 'FAC')}|"
f"{datetime.utcnow().isoformat()}|||")
# PID segment (patient)
if "patient" in data:
segments.append(
f"PID|||{data['patient'].get('id', '')}||"
f"{data['patient'].get('name', '')}||"
f"{data['patient'].get('dob', '')}|"
f"{data['patient'].get('gender', '')}"
)
message = "\r".join(segments)
logger.info(f"Created HL7 {message_type} message")
return message
except Exception as e:
log_exception_safe(logger, "Error creating HL7 message", e)
return ""
class FHIRResourceBuilder:
"""Builder for creating FHIR resources."""
@staticmethod
def build_condition(
patient_id: str,
code: str,
display: str,
onset_date: Optional[str] = None,
) -> Dict[str, Any]:
"""
Build a FHIR Condition resource.
Args:
patient_id: Patient ID
code: Condition code (SNOMED/ICD)
display: Condition display name
onset_date: Date condition started
Returns:
FHIR Condition resource
"""
return {
"resourceType": "Condition",
"subject": {"reference": f"Patient/{patient_id}"},
"code": {"coding": [{"code": code, "display": display}]},
"onsetDateTime": onset_date or datetime.utcnow().isoformat(),
"recordedDate": datetime.utcnow().isoformat(),
}
@staticmethod
def build_observation(
patient_id: str,
code: str,
value: float,
unit: str,
reference_range: Optional[tuple] = None,
) -> Dict[str, Any]:
"""
Build a FHIR Observation resource.
Args:
patient_id: Patient ID
code: Observation code
value: Measured value
unit: Unit of measurement
reference_range: Optional (low, high) tuple
Returns:
FHIR Observation resource
"""
obs = {
"resourceType": "Observation",
"status": "final",
"subject": {"reference": f"Patient/{patient_id}"},
"code": {"coding": [{"code": code}]},
"valueQuantity": {"value": value, "unit": unit},
"effectiveDateTime": datetime.utcnow().isoformat(),
}
if reference_range:
obs["referenceRange"] = [
{
"low": {"value": reference_range[0]},
"high": {"value": reference_range[1]},
}
]
return obs
@staticmethod
def build_goal(
patient_id: str,
description: str,
status: str = "proposed",
target_date: Optional[str] = None,
) -> Dict[str, Any]:
"""
Build a FHIR Goal resource.
Args:
patient_id: Patient ID
description: Goal description
status: Goal status (proposed, accepted, in-progress, achieved, etc.)
target_date: Target date for achievement
Returns:
FHIR Goal resource
"""
return {
"resourceType": "Goal",
"subject": {"reference": f"Patient/{patient_id}"},
"description": {
"text": description,
},
"status": status,
"targetDate": target_date or datetime.utcnow().isoformat(),
}
class EHRIntegrationManager:
"""Manager for EHR system integration."""
def __init__(self, fhir_url: str, api_key: Optional[str] = None):
"""Initialize EHR integration."""
self.fhir_client = FHIRAPIClient(fhir_url, api_key)
self.hl7_parser = HL7Parser()
self.resource_builder = FHIRResourceBuilder()
logger.info("EHR Integration Manager initialized")
def sync_patient_data(self, patient_id: str) -> Dict[str, Any]:
"""
Sync all patient data from EHR system.
Args:
patient_id: Patient ID
Returns:
Complete patient record
"""
try:
patient_data = {
"patient": self.fhir_client.get_patient(patient_id),
"conditions": self.fhir_client.get_patient_conditions(patient_id),
"observations": self.fhir_client.get_patient_observations(
patient_id
),
"care_plans": self.fhir_client.get_patient_care_plans(
patient_id
),
"goals": self.fhir_client.get_patient_goals(patient_id),
}
logger.info(f"Synced patient data for {mask_identifier(patient_id, 'pat')}")
logger.info("Synced patient data successfully")
return patient_data
except Exception as e:
log_exception_safe(logger, "Error syncing patient data", e)
return {}
def send_observation_to_ehr(
self, patient_id: str, observation: Dict[str, Any]
) -> Optional[str]:
"""
Send observation data to EHR system.
Args:
patient_id: Patient ID
observation: Observation data
Returns:
Observation ID or None
"""
try:
obs_id = self.fhir_client.create_observation(
patient_id, observation
)
logger.info(f"Sent observation to EHR: {obs_id}")
return obs_id
except Exception as e:
log_exception_safe(logger, "Error sending observation", e)
return None
def process_hl7_message(self, message: str) -> Dict[str, Any]:
"""
Process incoming HL7 message from EHR.
Args:
message: HL7 v2 message
Returns:
Parsed message data
"""
try:
parsed = self.hl7_parser.parse_hl7_message(message)
logger.info("Processed HL7 message successfully")
return parsed
except Exception as e:
log_exception_safe(logger, "Error processing HL7 message", e)
return {}
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