From 3b2f2f0469ff349ec346d5045ea27d22bdf90706 Mon Sep 17 00:00:00 2001
From: Lukas Stotz <lukas.stotz@student.reutlingen-university.de>
Date: Mon, 14 Apr 2025 16:37:01 +0200
Subject: [PATCH] Restructure backend: Move to app directory, update
dependencies, and improve organization
---
server/app/__init__.py | 23 ++
server/app/routes/__init__.py | 0
server/app/routes/hl7.py | 28 ++
server/app/routes/xml.py | 27 ++
server/app/services/__init__.py | 0
server/app/services/hl7_service.py | 42 +++
server/app/services/xml_service.py | 35 +++
server/app/utils/__init__.py | 0
server/{ => app/utils}/adt_mapper.py | 0
server/{ => app/utils}/func.py | 0
server/app/utils/hl7_receiver.py | 65 ++++
.../{ => app/utils}/hl7_to_fhir_converter.py | 0
server/app/utils/xml_processor.py | 88 ++++++
server/config.py | 35 +++
server/hl7_receiver.py | 286 ------------------
server/main.py | 97 ------
server/requirements.txt | 8 +-
server/run.py | 16 +
server/xml_processor.py | 219 --------------
19 files changed, 364 insertions(+), 605 deletions(-)
create mode 100644 server/app/__init__.py
create mode 100644 server/app/routes/__init__.py
create mode 100644 server/app/routes/hl7.py
create mode 100644 server/app/routes/xml.py
create mode 100644 server/app/services/__init__.py
create mode 100644 server/app/services/hl7_service.py
create mode 100644 server/app/services/xml_service.py
create mode 100644 server/app/utils/__init__.py
rename server/{ => app/utils}/adt_mapper.py (100%)
rename server/{ => app/utils}/func.py (100%)
create mode 100644 server/app/utils/hl7_receiver.py
rename server/{ => app/utils}/hl7_to_fhir_converter.py (100%)
create mode 100644 server/app/utils/xml_processor.py
create mode 100644 server/config.py
delete mode 100644 server/hl7_receiver.py
delete mode 100644 server/main.py
create mode 100644 server/run.py
delete mode 100644 server/xml_processor.py
diff --git a/server/app/__init__.py b/server/app/__init__.py
new file mode 100644
index 0000000..2282121
--- /dev/null
+++ b/server/app/__init__.py
@@ -0,0 +1,23 @@
+from flask import Flask
+from flask_cors import CORS
+
+def create_app(config_class=None):
+ """Create and configure the Flask application."""
+ app = Flask(__name__)
+
+ # Configure app
+ if config_class:
+ app.config.from_object(config_class)
+
+ # Enable CORS
+ CORS(app)
+
+ # Initialize extensions
+ # TODO: Add any Flask extensions here
+
+ # Register blueprints
+ from app.routes import hl7_bp, xml_bp
+ app.register_blueprint(hl7_bp)
+ app.register_blueprint(xml_bp)
+
+ return app
diff --git a/server/app/routes/__init__.py b/server/app/routes/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/server/app/routes/hl7.py b/server/app/routes/hl7.py
new file mode 100644
index 0000000..a4de22e
--- /dev/null
+++ b/server/app/routes/hl7.py
@@ -0,0 +1,28 @@
+from flask import Blueprint, jsonify, request
+from app.services.hl7_service import HL7Service
+
+hl7_bp = Blueprint('hl7', __name__)
+hl7_service = HL7Service()
+
+@hl7_bp.route('/api/hl7/messages', methods=['GET'])
+def get_messages():
+ """Get all received HL7 messages."""
+ messages = hl7_service.get_messages()
+ return jsonify(messages)
+
+@hl7_bp.route('/api/hl7/messages/<message_id>', methods=['GET'])
+def get_message(message_id):
+ """Get a specific HL7 message by ID."""
+ message = hl7_service.get_message(message_id)
+ if message:
+ return jsonify(message)
+ return jsonify({'error': 'Message not found'}), 404
+
+@hl7_bp.route('/api/hl7/convert/<message_id>', methods=['POST'])
+def convert_to_fhir(message_id):
+ """Convert an HL7 message to FHIR format."""
+ try:
+ fhir_resource = hl7_service.convert_to_fhir(message_id)
+ return jsonify(fhir_resource)
+ except Exception as e:
+ return jsonify({'error': str(e)}), 500
\ No newline at end of file
diff --git a/server/app/routes/xml.py b/server/app/routes/xml.py
new file mode 100644
index 0000000..262fd97
--- /dev/null
+++ b/server/app/routes/xml.py
@@ -0,0 +1,27 @@
+from flask import Blueprint, jsonify, request
+from app.services.xml_service import XMLService
+
+xml_bp = Blueprint('xml', __name__)
+xml_service = XMLService()
+
+@xml_bp.route('/api/xml/resources', methods=['GET'])
+def get_resources():
+ """Get all available XML resources."""
+ resources = xml_service.get_resources()
+ return jsonify(resources)
+
+@xml_bp.route('/api/xml/resources/<resource_key>', methods=['GET'])
+def get_resource(resource_key):
+ """Get a specific XML resource by key."""
+ resource = xml_service.get_resource(resource_key)
+ if resource:
+ return jsonify(resource)
+ return jsonify({'error': 'Resource not found'}), 404
+
+@xml_bp.route('/api/xml/resources/<resource_key>/structure', methods=['GET'])
+def get_resource_structure(resource_key):
+ """Get the structure of a specific XML resource."""
+ structure = xml_service.get_resource_structure(resource_key)
+ if structure:
+ return jsonify(structure)
+ return jsonify({'error': 'Resource structure not found'}), 404
\ No newline at end of file
diff --git a/server/app/services/__init__.py b/server/app/services/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/server/app/services/hl7_service.py b/server/app/services/hl7_service.py
new file mode 100644
index 0000000..bb58195
--- /dev/null
+++ b/server/app/services/hl7_service.py
@@ -0,0 +1,42 @@
+import os
+from app.utils.hl7_receiver import HL7Receiver
+from app.utils.hl7_to_fhir_converter import HL7ToFHIRConverter
+
+class HL7Service:
+ def __init__(self):
+ self.receiver = HL7Receiver()
+ self.converter = HL7ToFHIRConverter()
+ self.messages_dir = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))),
+ 'received_messages')
+
+ def get_messages(self):
+ """Get all received HL7 messages."""
+ messages = []
+ for filename in os.listdir(self.messages_dir):
+ if filename.endswith('.txt'):
+ with open(os.path.join(self.messages_dir, filename), 'r') as f:
+ content = f.read()
+ messages.append({
+ 'id': filename,
+ 'content': content
+ })
+ return messages
+
+ def get_message(self, message_id):
+ """Get a specific HL7 message by ID."""
+ filepath = os.path.join(self.messages_dir, message_id)
+ if os.path.exists(filepath):
+ with open(filepath, 'r') as f:
+ return {
+ 'id': message_id,
+ 'content': f.read()
+ }
+ return None
+
+ def convert_to_fhir(self, message_id):
+ """Convert an HL7 message to FHIR format."""
+ message = self.get_message(message_id)
+ if not message:
+ raise ValueError(f"Message {message_id} not found")
+
+ return self.converter.convert(message['content'])
\ No newline at end of file
diff --git a/server/app/services/xml_service.py b/server/app/services/xml_service.py
new file mode 100644
index 0000000..b8ac8c6
--- /dev/null
+++ b/server/app/services/xml_service.py
@@ -0,0 +1,35 @@
+import os
+from app.utils.xml_processor import XMLStructureParser
+
+class XMLService:
+ def __init__(self):
+ self.processor = XMLStructureParser()
+ self.xml_dir = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))),
+ 'xml_files')
+ self._resources = {}
+
+ def get_resources(self):
+ """Get all available XML resources."""
+ resources = {}
+ for filename in os.listdir(self.xml_dir):
+ if filename.endswith('.xml'):
+ resource_key = os.path.splitext(filename)[0]
+ resources[resource_key] = {
+ 'filename': filename,
+ 'path': os.path.join(self.xml_dir, filename)
+ }
+ return resources
+
+ def get_resource(self, resource_key):
+ """Get a specific XML resource by key."""
+ filepath = os.path.join(self.xml_dir, f"{resource_key}.xml")
+ if os.path.exists(filepath):
+ return self.processor.parse_xml_file(filepath)
+ return None
+
+ def get_resource_structure(self, resource_key):
+ """Get the structure of a specific XML resource."""
+ resource = self.get_resource(resource_key)
+ if resource:
+ return resource.get('structure', {})
+ return None
\ No newline at end of file
diff --git a/server/app/utils/__init__.py b/server/app/utils/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/server/adt_mapper.py b/server/app/utils/adt_mapper.py
similarity index 100%
rename from server/adt_mapper.py
rename to server/app/utils/adt_mapper.py
diff --git a/server/func.py b/server/app/utils/func.py
similarity index 100%
rename from server/func.py
rename to server/app/utils/func.py
diff --git a/server/app/utils/hl7_receiver.py b/server/app/utils/hl7_receiver.py
new file mode 100644
index 0000000..6ec8ccc
--- /dev/null
+++ b/server/app/utils/hl7_receiver.py
@@ -0,0 +1,65 @@
+import os
+import logging
+from watchdog.observers import Observer
+from watchdog.events import FileSystemEventHandler
+from datetime import datetime
+
+class HL7MessageHandler(FileSystemEventHandler):
+ def __init__(self, messages_dir, logs_dir):
+ self.messages_dir = messages_dir
+ self.logs_dir = logs_dir
+ self.setup_logging()
+
+ def setup_logging(self):
+ """Setup logging configuration."""
+ log_file = os.path.join(self.logs_dir, 'hl7_receiver.log')
+ logging.basicConfig(
+ filename=log_file,
+ level=logging.INFO,
+ format='%(asctime)s - %(levelname)s - %(message)s'
+ )
+
+ def on_created(self, event):
+ """Handle file creation events."""
+ if not event.is_directory and event.src_path.endswith('.txt'):
+ self.process_message(event.src_path)
+
+ def process_message(self, filepath):
+ """Process a new HL7 message file."""
+ try:
+ with open(filepath, 'r') as f:
+ content = f.read()
+
+ # Log the received message
+ logging.info(f"Received HL7 message: {os.path.basename(filepath)}")
+
+ # TODO: Add any additional message processing here
+
+ except Exception as e:
+ logging.error(f"Error processing message {filepath}: {str(e)}")
+
+class HL7Receiver:
+ def __init__(self, messages_dir=None, logs_dir=None):
+ base_dir = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+ self.messages_dir = messages_dir or os.path.join(base_dir, 'received_messages')
+ self.logs_dir = logs_dir or os.path.join(base_dir, 'message_logs')
+ self.observer = None
+ self.handler = None
+
+ def start(self):
+ """Start the HL7 message receiver."""
+ # Create directories if they don't exist
+ os.makedirs(self.messages_dir, exist_ok=True)
+ os.makedirs(self.logs_dir, exist_ok=True)
+
+ # Initialize and start the observer
+ self.handler = HL7MessageHandler(self.messages_dir, self.logs_dir)
+ self.observer = Observer()
+ self.observer.schedule(self.handler, self.messages_dir, recursive=False)
+ self.observer.start()
+
+ def stop(self):
+ """Stop the HL7 message receiver."""
+ if self.observer:
+ self.observer.stop()
+ self.observer.join()
\ No newline at end of file
diff --git a/server/hl7_to_fhir_converter.py b/server/app/utils/hl7_to_fhir_converter.py
similarity index 100%
rename from server/hl7_to_fhir_converter.py
rename to server/app/utils/hl7_to_fhir_converter.py
diff --git a/server/app/utils/xml_processor.py b/server/app/utils/xml_processor.py
new file mode 100644
index 0000000..f6c3170
--- /dev/null
+++ b/server/app/utils/xml_processor.py
@@ -0,0 +1,88 @@
+import os
+import re
+from lxml import etree
+from watchdog.observers import Observer
+from watchdog.events import FileSystemEventHandler
+
+class XMLStructureParser:
+ def __init__(self):
+ self._resources = {}
+
+ def parse_xml_file(self, filepath):
+ """Parse an XML file and extract its structure."""
+ try:
+ with open(filepath, 'r') as f:
+ content = f.read()
+
+ # Extract comments using regex
+ comments = {}
+ comment_pattern = r'<!--(.*?)-->'
+ for match in re.finditer(comment_pattern, content):
+ comment = match.group(1).strip()
+ line_number = content[:match.start()].count('\n') + 1
+ comments[line_number] = comment
+
+ # Parse XML
+ parser = etree.XMLParser(remove_blank_text=True)
+ tree = etree.parse(filepath, parser)
+ root = tree.getroot()
+
+ # Process the XML structure
+ structure = self._process_element(root, comments)
+
+ # Store the resource
+ resource_key = os.path.splitext(os.path.basename(filepath))[0]
+ self._resources[resource_key] = {
+ 'filename': os.path.basename(filepath),
+ 'path': filepath,
+ 'structure': structure
+ }
+
+ return self._resources[resource_key]
+
+ except Exception as e:
+ print(f"Error parsing XML file {filepath}: {str(e)}")
+ return None
+
+ def _process_element(self, element, comments):
+ """Process an XML element and its children recursively."""
+ result = {
+ 'tag': element.tag,
+ 'attributes': dict(element.attrib),
+ 'comments': [],
+ 'children': []
+ }
+
+ # Get element line number
+ line_number = element.sourceline if hasattr(element, 'sourceline') else None
+
+ # Add comments associated with this element
+ if line_number in comments:
+ result['comments'].append(comments[line_number])
+
+ # Process text content
+ if element.text and element.text.strip():
+ result['text'] = element.text.strip()
+
+ # Process children
+ for child in element:
+ child_result = self._process_element(child, comments)
+ if child_result:
+ result['children'].append(child_result)
+
+ return result
+
+class XMLFileWatcher(FileSystemEventHandler):
+ def __init__(self, xml_dir, processor):
+ self.xml_dir = xml_dir
+ self.processor = processor
+
+ def on_created(self, event):
+ """Handle file creation events."""
+ if not event.is_directory and event.src_path.endswith('.xml'):
+ self.processor.parse_xml_file(event.src_path)
+
+ def on_modified(self, event):
+ """Handle file modification events."""
+ if not event.is_directory and event.src_path.endswith('.xml'):
+ self.processor.parse_xml_file(event.src_path)
\ No newline at end of file
diff --git a/server/config.py b/server/config.py
new file mode 100644
index 0000000..43f9f2f
--- /dev/null
+++ b/server/config.py
@@ -0,0 +1,35 @@
+import os
+from dotenv import load_dotenv
+
+# Load environment variables from .env file
+load_dotenv()
+
+class Config:
+ """Base configuration."""
+ SECRET_KEY = os.getenv('SECRET_KEY', 'dev')
+ DEBUG = False
+ TESTING = False
+ XML_FILES_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'xml_files')
+ RECEIVED_MESSAGES_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'received_messages')
+ MESSAGE_LOGS_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'message_logs')
+
+class DevelopmentConfig(Config):
+ """Development configuration."""
+ DEBUG = True
+
+class TestingConfig(Config):
+ """Testing configuration."""
+ TESTING = True
+ DEBUG = True
+
+class ProductionConfig(Config):
+ """Production configuration."""
+ DEBUG = False
+
+# Configuration dictionary
+config = {
+ 'development': DevelopmentConfig,
+ 'testing': TestingConfig,
+ 'production': ProductionConfig,
+ 'default': DevelopmentConfig
+}
\ No newline at end of file
diff --git a/server/hl7_receiver.py b/server/hl7_receiver.py
deleted file mode 100644
index 39d75d2..0000000
--- a/server/hl7_receiver.py
+++ /dev/null
@@ -1,286 +0,0 @@
-import socket
-import datetime
-import uuid
-import os
-import json
-from pathlib import Path
-import hl7
-import logging
-from typing import Dict, Any
-from flask import Flask, request, jsonify
-from flask_cors import CORS
-# import threading # Not needed when TCP server is disabled
-
-app = Flask(__name__)
-CORS(app)
-
-class HL7MessageReceiver:
- def __init__(self, host: str = 'localhost', port: int = 6661):
- """Initialize the HL7 message receiver.
-
- Args:
- host (str): Host to listen on
- port (int): Port to listen on
- """
- self.host = host
- self.port = port
- self.setup_logging()
- self.setup_directories()
-
- def setup_logging(self):
- """Set up logging configuration."""
- logging.basicConfig(
- level=logging.INFO,
- format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
- handlers=[
- logging.FileHandler('hl7_receiver.log'),
- logging.StreamHandler()
- ]
- )
- self.logger = logging.getLogger('HL7Receiver')
-
- def setup_directories(self):
- """Create necessary directories for message storage."""
- # Create base directories
- Path('received_messages').mkdir(exist_ok=True)
- Path('message_logs').mkdir(exist_ok=True)
-
- def generate_filename(self, msg_type: str, timestamp: datetime.datetime) -> str:
- """Generate a filename based on message type and timestamp.
-
- Args:
- msg_type (str): The HL7 message type
- timestamp (datetime.datetime): Message receipt timestamp
-
- Returns:
- str: Generated filename
- """
- date_str = timestamp.strftime('%Y%m%d_%H%M%S')
- return f"received_messages/{msg_type}_{date_str}.txt"
-
- def process_message(self, raw_message: str) -> Dict[str, Any]:
- """Process received HL7 message.
-
- Args:
- raw_message (str): Raw HL7 message string
-
- Returns:
- Dict[str, Any]: Processed message info
- """
- # Parse the HL7 message
- try:
- # Remove leading/trailing whitespace and ensure proper line endings
- raw_message = '\r'.join(line.strip() for line in raw_message.splitlines())
- if not raw_message.endswith('\r'):
- raw_message += '\r'
-
- self.logger.info(f"Attempting to parse message: {raw_message}")
- parsed_msg = hl7.parse(raw_message)
-
- # Extract message type more safely
- try:
- # Get MSH segment
- msh = parsed_msg.segments('MSH')[0]
-
- # MSH-9 contains the message type in format "ADT^A01"
- message_type_field = str(msh[9])
-
- # Split the message type field on '^' to get type and trigger
- type_parts = message_type_field.split('^')
- message_type = type_parts[0] if len(type_parts) > 0 else "UNKNOWN"
- trigger_event = type_parts[1] if len(type_parts) > 1 else ""
-
- # Combine message type and trigger
- msg_type = f"{message_type}_{trigger_event}" if trigger_event else message_type
-
- self.logger.info(f"Extracted message type: {msg_type} from field: {message_type_field}")
-
- except Exception as e:
- self.logger.error(f"Error extracting message type: {str(e)}")
- msg_type = "UNKNOWN"
-
- # Generate timestamp and ID
- timestamp = datetime.datetime.now()
- msg_id = str(uuid.uuid4())
-
- # Create message info dictionary
- msg_info = {
- 'id': msg_id,
- 'timestamp': timestamp.isoformat(),
- 'type': msg_type,
- 'raw_message': raw_message,
- 'parsed_segments': [str(seg) for seg in parsed_msg]
- }
-
- # Save message to file
- filename = self.generate_filename(msg_type, timestamp)
- with open(filename, 'w', encoding='utf-8') as f:
- f.write(f"Message ID: {msg_id}\n")
- f.write(f"Timestamp: {timestamp.isoformat()}\n")
- f.write(f"Message Type: {msg_type}\n")
- f.write("\nRaw Message:\n")
- f.write(raw_message)
- f.write("\n\nParsed Segments:\n")
- for segment in parsed_msg:
- f.write(f"{str(segment)}\n")
-
- # Log message receipt
- self.log_message(msg_info)
-
- self.logger.info(f"Successfully processed message {msg_id} of type {msg_type}")
- return msg_info
-
- except Exception as e:
- self.logger.error(f"Error processing message: {str(e)}")
- self.logger.error(f"Raw message was: {raw_message}")
- raise ValueError(f"Failed to process HL7 message: {str(e)}")
-
- def log_message(self, msg_info: Dict[str, Any]):
- """Log message information to the message log file.
-
- Args:
- msg_info (Dict[str, Any]): Message information to log
- """
- log_file = f"message_logs/messages_{datetime.date.today()}.log"
-
- with open(log_file, 'a', encoding='utf-8') as f:
- json.dump(msg_info, f)
- f.write('\n')
-
- # TCP Server functionality commented out
- """
- def start_tcp_server(self):
- #Start the HL7 message receiver TCP server.
- self.logger.info(f"Starting HL7 TCP receiver on {self.host}:{self.port}")
-
- server_socket = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
- server_socket.bind((self.host, self.port))
- server_socket.listen(5)
-
- try:
- while True:
- client_socket, address = server_socket.accept()
- self.logger.info(f"Connection from {address}")
-
- try:
- # Receive message
- message = ''
- while True:
- data = client_socket.recv(4096).decode('utf-8')
- if not data:
- break
- message += data
- if '\r' in data: # HL7 messages end with carriage return
- break
-
- if message:
- # Process the message
- msg_info = self.process_message(message)
-
- # Send acknowledgment
- ack = self.generate_ack(msg_info)
- client_socket.send(ack.encode('utf-8'))
-
- except Exception as e:
- self.logger.error(f"Error handling client connection: {str(e)}")
- finally:
- client_socket.close()
-
- except KeyboardInterrupt:
- self.logger.info("Shutting down HL7 receiver")
- server_socket.close()
- except Exception as e:
- self.logger.error(f"Server error: {str(e)}")
- server_socket.close()
- raise
- """
-
- def generate_ack(self, msg_info: Dict[str, Any]) -> str:
- """Generate HL7 acknowledgment message.
-
- Args:
- msg_info (Dict[str, Any]): Information about the received message
-
- Returns:
- str: HL7 acknowledgment message
- """
- timestamp = datetime.datetime.now().strftime('%Y%m%d%H%M%S')
- return (
- f"MSH|^~\\&|RECEIVER|FACILITY|SENDER|FACILITY|{timestamp}||ACK|{msg_info['id']}|P|2.5.1\r"
- f"MSA|AA|{msg_info['id']}|Message received successfully\r"
- )
-
-# Create a global instance of the receiver
-receiver = HL7MessageReceiver()
-
-@app.route('/api/hl7/receive', methods=['POST'])
-def receive_hl7():
- """HTTP endpoint to receive HL7 messages."""
- try:
- # Get the raw message from the request
- raw_message = request.data.decode('utf-8')
- if not raw_message:
- raw_message = request.form.get('message', '')
-
- if not raw_message:
- return jsonify({
- 'error': 'No HL7 message provided'
- }), 400
-
- # Process the message
- try:
- msg_info = receiver.process_message(raw_message)
-
- # Generate acknowledgment
- ack = receiver.generate_ack(msg_info)
-
- return jsonify({
- 'status': 'success',
- 'message': 'HL7 message received and processed successfully',
- 'message_info': msg_info,
- 'acknowledgment': ack
- })
-
- except ValueError as ve:
- # Handle validation errors with 400 status
- return jsonify({
- 'error': str(ve),
- 'status': 'error',
- 'message': 'Invalid HL7 message format'
- }), 400
-
- except Exception as e:
- # Handle unexpected errors with 500 status
- app.logger.error(f"Unexpected error processing request: {str(e)}")
- return jsonify({
- 'error': str(e),
- 'status': 'error',
- 'message': 'Internal server error processing HL7 message'
- }), 500
-
-@app.route('/api/hl7/messages', methods=['GET'])
-def list_messages():
- """List all received HL7 messages."""
- try:
- messages = []
- received_dir = Path('received_messages')
- if received_dir.exists():
- for file in received_dir.glob('*.txt'):
- with open(file, 'r', encoding='utf-8') as f:
- messages.append({
- 'filename': file.name,
- 'content': f.read()
- })
-
- return jsonify({
- 'messages': messages
- })
-
- except Exception as e:
- return jsonify({
- 'error': str(e)
- }), 500
-
-if __name__ == '__main__':
- # Start Flask server
- app.run(host='0.0.0.0', port=5000)
\ No newline at end of file
diff --git a/server/main.py b/server/main.py
deleted file mode 100644
index 9a1161d..0000000
--- a/server/main.py
+++ /dev/null
@@ -1,97 +0,0 @@
-from flask import Flask, jsonify, request
-from flask_cors import CORS
-import os
-from xml_processor import XMLWatcher
-from typing import Dict, Any
-import threading
-import logging
-
-app = Flask(__name__)
-cors = CORS(app, origins='*')
-
-# Global storage for processed XML structures
-xml_resources: Dict[str, Dict[str, Any]] = {}
-
-def on_xml_processed(data: Dict[str, Any]):
- """Callback function for when an XML file is processed."""
- resource_type = data["resourceType"]
- filename = data["metadata"]["filename"]
- key = f"{resource_type}_{filename}"
- xml_resources[key] = data
- logging.info(f"Processed XML resource: {key}")
-
-# Initialize XML watcher
-xml_dir = os.path.join(os.path.dirname(__file__), "xml_files")
-os.makedirs(xml_dir, exist_ok=True)
-watcher = XMLWatcher(xml_dir, on_xml_processed)
-
-# Start watcher in a separate thread
-watcher_thread = threading.Thread(target=watcher.start, daemon=True)
-watcher_thread.start()
-
-@app.route("/api/resources", methods=['GET'])
-def list_resources():
- """List all available XML resources."""
- return jsonify({
- "resources": [
- {
- "key": key,
- "resourceType": data["resourceType"],
- "filename": data["metadata"]["filename"]
- }
- for key, data in xml_resources.items()
- ]
- })
-
-@app.route("/api/resources/<resource_key>", methods=['GET'])
-def get_resource(resource_key):
- """Get a specific XML resource structure by its key."""
- if resource_key not in xml_resources:
- return jsonify({"error": "Resource not found"}), 404
- return jsonify(xml_resources[resource_key])
-
-@app.route("/api/resources/<resource_key>/structure", methods=['GET'])
-def get_resource_structure(resource_key):
- """Get the XML structure for a specific resource."""
- if resource_key not in xml_resources:
- return jsonify({"error": "Resource not found"}), 404
-
- resource = xml_resources[resource_key]
- return jsonify({
- "resourceType": resource["resourceType"],
- "structure": resource["structure"]
- })
-
-@app.route("/api/resources/<resource_key>/schema", methods=['GET'])
-def get_resource_schema(resource_key):
- """Get the schema structure for a specific resource."""
- if resource_key not in xml_resources:
- return jsonify({"error": "Resource not found"}), 404
-
- def extract_schema(data: Dict[str, Any]) -> Dict[str, Any]:
- if isinstance(data, dict):
- return {
- key: extract_schema(value) if isinstance(value, (dict, list))
- else type(value).__name__
- for key, value in data.items()
- }
- elif isinstance(data, list):
- return [extract_schema(item) for item in data] if data else ["any"]
- return type(data).__name__
-
- resource = xml_resources[resource_key]
- schema = extract_schema(resource["content"])
- return jsonify({
- "resourceType": resource["resourceType"],
- "schema": schema
- })
-
-@app.route("/api/validate", methods=['POST'])
-def validate_resource():
- """Validate a resource against its schema."""
- data = request.json
- # TODO: Implement validation logic
- return jsonify({"valid": True})
-
-if __name__ == "__main__":
- app.run(debug=True, port=8080)
\ No newline at end of file
diff --git a/server/requirements.txt b/server/requirements.txt
index 24d4832..610918f 100644
--- a/server/requirements.txt
+++ b/server/requirements.txt
@@ -1,6 +1,8 @@
-Flask==2.0.1
+Flask==3.0.2
flask-cors==4.0.0
-lxml==4.9.3
+python-dotenv==1.0.1
watchdog==3.0.0
+lxml==5.1.0
+requests==2.31.0
hl7==0.4.2
-Werkzeug==2.0.1
\ No newline at end of file
+Werkzeug>=3.0.0
\ No newline at end of file
diff --git a/server/run.py b/server/run.py
new file mode 100644
index 0000000..6bc1da9
--- /dev/null
+++ b/server/run.py
@@ -0,0 +1,16 @@
+from app import create_app
+from config import config
+from app.utils.hl7_receiver import HL7Receiver
+
+# Create Flask application
+app = create_app(config['default'])
+
+# Initialize HL7 receiver
+hl7_receiver = HL7Receiver()
+hl7_receiver.start()
+
+if __name__ == '__main__':
+ try:
+ app.run(debug=True)
+ except KeyboardInterrupt:
+ hl7_receiver.stop()
\ No newline at end of file
diff --git a/server/xml_processor.py b/server/xml_processor.py
deleted file mode 100644
index a6824aa..0000000
--- a/server/xml_processor.py
+++ /dev/null
@@ -1,219 +0,0 @@
-from watchdog.observers import Observer
-from watchdog.events import FileSystemEventHandler
-from lxml import etree
-import os
-import json
-from typing import Dict, Any, Optional, List
-import logging
-import re
-
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
-
-class XMLStructureParser:
- """Parses XML files preserving structure, comments, and placeholders."""
-
- @staticmethod
- def preprocess_fhir_template(content: str) -> str:
- """Preprocess FHIR template XML to make it valid XML."""
- # Replace FHIR template patterns like [x] with valid XML names
- content = re.sub(r'<(\w+)\[(x|X)\]>', r'<\1_choice>', content)
- content = re.sub(r'</(\w+)\[(x|X)\]>', r'</\1_choice>', content)
- return content
-
- @staticmethod
- def restore_fhir_template(tag: str) -> str:
- """Restore original FHIR template tag names."""
- if tag.endswith('_choice'):
- base_name = tag[:-7]
- return f"{base_name}[x]"
- return tag
-
- @staticmethod
- def extract_comment_info(comment: str) -> Dict[str, str]:
- """Extract cardinality and description from a comment."""
- # Extract cardinality
- cardinality_match = re.search(r'(0|1)\.\.(\*|0|1)', comment)
- cardinality = cardinality_match.group(0) if cardinality_match else ''
-
- # Remove cardinality and any type info (content between | characters)
- desc = re.sub(r'(0|1)\.\.(\*|0|1)\s*', '', comment)
- desc = re.sub(r'\|.*?\|', '', desc)
- desc = re.sub(r'\[.*?\]', '', desc)
-
- # Clean up the description
- desc = desc.strip()
- if desc.startswith('I '): # Remove 'I ' prefix some comments have
- desc = desc[2:]
-
- return {
- 'cardinality': cardinality,
- 'description': desc
- }
-
- @staticmethod
- def parse_xml_file(file_path: str) -> Dict[str, Any]:
- """Parse an XML file and return its structure with comments and placeholders."""
- try:
- # Read the file content
- with open(file_path, 'r', encoding='utf-8') as f:
- content = f.read()
-
- # Store original content for comment positions
- original_content = content
-
- # Preprocess content to make it valid XML
- content = XMLStructureParser.preprocess_fhir_template(content)
-
- # Parse comments first (since they'll be removed by the XML parser)
- comments_by_tag = {}
- for line in original_content.split('\n'):
- if '<!--' in line:
- # Get the tag name from the line (if it exists)
- tag_match = re.search(r'<(\w+)[\s>]', line)
- comment_match = re.search(r'<!--(.*?)-->', line)
-
- if tag_match and comment_match:
- tag = tag_match.group(1)
- comment = comment_match.group(1).strip()
-
- # Store comment if it has cardinality
- if re.search(r'(0|1)\.\.(\*|0|1)', comment):
- comment_info = XMLStructureParser.extract_comment_info(comment)
- comments_by_tag[tag] = comment_info
-
- # Parse the XML structure
- parser = etree.XMLParser(remove_comments=False, remove_blank_text=True)
- tree = etree.fromstring(content.encode(), parser)
-
- def process_element(element) -> Dict[str, Any]:
- """Process an XML element and its content."""
- # Skip elements with no tag
- if not isinstance(element.tag, str):
- return None
-
- # Get tag name and handle namespaces
- tag = element.tag.split('}')[-1]
- tag = XMLStructureParser.restore_fhir_template(tag)
-
- # Get element's text content and check for placeholders
- text = element.text.strip() if element.text else ""
- placeholder = None
- if text:
- placeholder_match = re.search(r'\[(.*?)\]', text)
- if placeholder_match:
- placeholder = placeholder_match.group(0)
-
- result = {
- 'tag': tag,
- 'attributes': dict(element.attrib)
- }
-
- # Add comment info if it exists for this tag
- if tag in comments_by_tag:
- result['comments'] = [comments_by_tag[tag]['cardinality']]
- result['description'] = comments_by_tag[tag]['description']
-
- if placeholder:
- result['placeholder'] = placeholder
-
- children = []
- for child in element:
- child_result = process_element(child)
- if child_result:
- children.append(child_result)
-
- if children:
- result['children'] = children
-
- # Only include elements that have:
- # 1. A value attribute, or
- # 2. A cardinality comment, or
- # 3. Children
- if ('value' in result['attributes'] or
- 'comments' in result or
- children):
- return result
- return None
-
- # Process the entire tree
- structure = process_element(tree)
-
- return {
- 'resourceType': XMLStructureParser.restore_fhir_template(
- tree.tag.split('}')[-1] if isinstance(tree.tag, str) else "unknown"
- ),
- 'structure': structure,
- 'metadata': {
- 'filename': os.path.basename(file_path),
- 'filepath': file_path,
- 'namespaces': tree.nsmap if hasattr(tree, 'nsmap') else {}
- }
- }
-
- except Exception as e:
- logger.error(f"Error parsing XML file {file_path}: {str(e)}")
- raise
-
-class XMLFileHandler(FileSystemEventHandler):
- """Handles file system events for XML files."""
-
- def __init__(self, watch_directory: str, processed_callback=None):
- self.watch_directory = watch_directory
- self.processed_callback = processed_callback
- self._processed_files = set()
-
- def on_created(self, event):
- if not event.is_directory and event.src_path.endswith('.xml'):
- self.process_file(event.src_path)
-
- def on_modified(self, event):
- if not event.is_directory and event.src_path.endswith('.xml'):
- self._processed_files.discard(event.src_path) # Allow reprocessing of modified files
- self.process_file(event.src_path)
-
- def process_file(self, file_path: str) -> Optional[Dict[str, Any]]:
- """Process an XML file and return its structure."""
- try:
- if file_path in self._processed_files:
- return None
-
- logger.info(f"Processing XML file: {file_path}")
-
- result = XMLStructureParser.parse_xml_file(file_path)
- self._processed_files.add(file_path)
-
- if self.processed_callback:
- self.processed_callback(result)
-
- return result
-
- except Exception as e:
- logger.error(f"Error processing file {file_path}: {str(e)}")
- return None
-
-class XMLWatcher:
- """Manages the file system observer for XML files."""
-
- def __init__(self, directory: str, processed_callback=None):
- self.directory = directory
- self.event_handler = XMLFileHandler(directory, processed_callback)
- self.observer = Observer()
-
- def start(self):
- """Start watching the directory for XML files."""
- self.observer.schedule(self.event_handler, self.directory, recursive=False)
- self.observer.start()
- logger.info(f"Started watching directory: {self.directory}")
-
- # Process existing files
- for filename in os.listdir(self.directory):
- if filename.endswith('.xml'):
- file_path = os.path.join(self.directory, filename)
- self.event_handler.process_file(file_path)
-
- def stop(self):
- """Stop watching the directory."""
- self.observer.stop()
- self.observer.join()
- logger.info("Stopped watching directory")
\ No newline at end of file
--
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