NORM/FHIR_OCR_POC/fhir_module/fhir_repository.py

import os
import json
import uuid
import datetime
import logging
from typing import Dict, Any, List, Optional, Union
from pathlib import Path
from fhir.resources.resource import Resource
from fhir.resources.patient import Patient
from fhir.resources.observation import Observation

class FHIRRepository:
    """
    Local storage repository for FHIR resources.
    This is a simplified implementation for the POC, using file storage.
    In production, this would be replaced with a database.
    """
    
    def __init__(self, storage_dir: str = 'fhir_storage'):
        """
        Initialize the FHIR repository.
        
        Args:
            storage_dir: Directory to store FHIR resources
        """
        self.storage_dir = storage_dir
        self.logger = logging.getLogger(__name__)
        
        # Create storage directory if it doesn't exist
        try:
            os.makedirs(os.path.join(storage_dir, 'Patient'), exist_ok=True)
            os.makedirs(os.path.join(storage_dir, 'Observation'), exist_ok=True)
            self.logger.info(f"FHIR storage directories created in {storage_dir}")
        except Exception as e:
            self.logger.error(f"Error creating storage directories: {str(e)}")
            raise
    
    def _get_resource_path(self, resource_type: str, resource_id: str) -> str:
        """
        Get the file path for a resource.
        
        Args:
            resource_type: Type of resource
            resource_id: ID of the resource
            
        Returns:
            Path to the resource file
        """
        return os.path.join(self.storage_dir, resource_type, f"{resource_id}.json")
    
    def _read_resource_file(self, file_path: str) -> Dict[str, Any]:
        """
        Read a resource file.
        
        Args:
            file_path: Path to the resource file
            
        Returns:
            Resource data as a dictionary
        """
        try:
            with open(file_path, 'r') as f:
                return json.load(f)
        except Exception as e:
            self.logger.error(f"Error reading resource file: {str(e)}")
            raise
    
    def _write_resource_file(self, file_path: str, data: Dict[str, Any]) -> None:
        """
        Write a resource file.
        
        Args:
            file_path: Path to the resource file
            data: Resource data
        """
        try:
            with open(file_path, 'w') as f:
                json.dump(data, f, indent=2)
        except Exception as e:
            self.logger.error(f"Error writing resource file: {str(e)}")
            raise
    
    def create_resource(self, resource: Resource) -> Dict[str, Any]:
        """
        Create a new FHIR resource.
        
        Args:
            resource: FHIR resource to create
            
        Returns:
            Created resource data
        """
        resource_type = resource.resource_type
        
        # Ensure resource has an ID
        if not resource.id:
            resource.id = str(uuid.uuid4())
        
        # Convert resource to dictionary
        resource_data = json.loads(resource.json())
        
        # Add metadata
        resource_data['meta'] = resource_data.get('meta', {})
        resource_data['meta']['lastUpdated'] = datetime.datetime.utcnow().isoformat()
        
        # Save resource to file
        file_path = self._get_resource_path(resource_type, resource.id)
        self._write_resource_file(file_path, resource_data)
        
        self.logger.info(f"Created {resource_type} resource with ID {resource.id}")
        return resource_data
    
    def read_resource(self, resource_type: str, resource_id: str) -> Dict[str, Any]:
        """
        Read a FHIR resource by ID.
        
        Args:
            resource_type: Type of resource
            resource_id: ID of the resource
            
        Returns:
            Resource data
        """
        file_path = self._get_resource_path(resource_type, resource_id)
        
        if not os.path.exists(file_path):
            self.logger.error(f"Resource not found: {resource_type}/{resource_id}")
            raise FileNotFoundError(f"Resource not found: {resource_type}/{resource_id}")
        
        resource_data = self._read_resource_file(file_path)
        self.logger.debug(f"Read {resource_type} resource with ID {resource_id}")
        return resource_data
    
    def update_resource(self, resource: Resource) -> Dict[str, Any]:
        """
        Update an existing FHIR resource.
        
        Args:
            resource: FHIR resource to update
            
        Returns:
            Updated resource data
        """
        resource_type = resource.resource_type
        resource_id = resource.id
        
        if not resource_id:
            self.logger.error("Cannot update resource without ID")
            raise ValueError("Resource must have an ID for update")
        
        # Check if resource exists
        file_path = self._get_resource_path(resource_type, resource_id)
        if not os.path.exists(file_path):
            self.logger.error(f"Resource not found for update: {resource_type}/{resource_id}")
            raise FileNotFoundError(f"Resource not found for update: {resource_type}/{resource_id}")
        
        # Convert resource to dictionary
        resource_data = json.loads(resource.json())
        
        # Update metadata
        resource_data['meta'] = resource_data.get('meta', {})
        resource_data['meta']['lastUpdated'] = datetime.datetime.utcnow().isoformat()
        
        # Save updated resource
        self._write_resource_file(file_path, resource_data)
        
        self.logger.info(f"Updated {resource_type} resource with ID {resource_id}")
        return resource_data
    
    def delete_resource(self, resource_type: str, resource_id: str) -> bool:
        """
        Delete a FHIR resource.
        
        Args:
            resource_type: Type of resource
            resource_id: ID of the resource
            
        Returns:
            True if deletion was successful
        """
        file_path = self._get_resource_path(resource_type, resource_id)
        
        if not os.path.exists(file_path):
            self.logger.error(f"Resource not found for deletion: {resource_type}/{resource_id}")
            return False
        
        try:
            os.remove(file_path)
            self.logger.info(f"Deleted {resource_type} resource with ID {resource_id}")
            return True
        except Exception as e:
            self.logger.error(f"Error deleting resource: {str(e)}")
            return False
    
    def search_resources(self, resource_type: str, params: Dict[str, Any] = None) -> List[Dict[str, Any]]:
        """
        Search for FHIR resources.
        
        Args:
            resource_type: Type of resource to search for
            params: Search parameters
            
        Returns:
            List of matching resources
        """
        # Check if resource type directory exists
        resource_dir = os.path.join(self.storage_dir, resource_type)
        if not os.path.exists(resource_dir):
            self.logger.error(f"Resource type directory not found: {resource_type}")
            return []
        
        # Get all resource files of the specified type
        resources = []
        for file_name in os.listdir(resource_dir):
            if file_name.endswith('.json'):
                file_path = os.path.join(resource_dir, file_name)
                resource = self._read_resource_file(file_path)
                
                # Filter by parameters if provided
                if params:
                    matches_all_params = True
                    for key, value in params.items():
                        # Handle nested properties with dot notation (e.g., "name.family")
                        parts = key.split('.')
                        resource_value = resource
                        for part in parts:
                            if isinstance(resource_value, dict) and part in resource_value:
                                resource_value = resource_value[part]
                            else:
                                resource_value = None
                                break
                        
                        # Check if value matches
                        if resource_value != value:
                            matches_all_params = False
                            break
                    
                    if not matches_all_params:
                        continue
                
                resources.append(resource)
        
        self.logger.debug(f"Found {len(resources)} {resource_type} resources matching search criteria")
        return resources