Compare commits
2 Commits
| Author | SHA1 | Date | |
|---|---|---|---|
|
54f29f2a88 | ||
|
3850aa103d |
@@ -1,180 +0,0 @@
|
|||||||
# DICOM Migration REST API
|
|
||||||
|
|
||||||
A simple REST API that triggers DICOM study migration for a specific Accession Number.
|
|
||||||
|
|
||||||
## How to Run
|
|
||||||
|
|
||||||
```bash
|
|
||||||
# Start the server on default port 8000
|
|
||||||
python run.py
|
|
||||||
|
|
||||||
# Custom port
|
|
||||||
python run.py --port 9000
|
|
||||||
|
|
||||||
# Custom token
|
|
||||||
python run.py --token your-secure-token
|
|
||||||
|
|
||||||
# Development mode with auto-reload
|
|
||||||
python run.py --reload
|
|
||||||
```
|
|
||||||
|
|
||||||
## How to Use
|
|
||||||
|
|
||||||
### Make a Request
|
|
||||||
|
|
||||||
```bash
|
|
||||||
# Using curl
|
|
||||||
curl -X POST "http://localhost:8000/migrate/R.20240401.0138" \
|
|
||||||
-H "Authorization: Bearer token-his2-untuk-hit-api-migrasi-clarity" \
|
|
||||||
-H "Content-Type: application/json"
|
|
||||||
```
|
|
||||||
|
|
||||||
### Response Success Example
|
|
||||||
|
|
||||||
```json
|
|
||||||
{
|
|
||||||
"success":true,
|
|
||||||
"message":"Berhasil migrasi file DICOM Accession Number: R.20240401.0138",
|
|
||||||
"details":
|
|
||||||
{
|
|
||||||
"accession_number":"R.20240401.0138",
|
|
||||||
"process_start_time":"2025-07-11 15:27:26",
|
|
||||||
"steps_completed":[
|
|
||||||
"study_found","study_retrieved","study_sent","log_created","his_api_success","cleanup_success"
|
|
||||||
],
|
|
||||||
"study_uid":"1.2.826.1.3680043.9.5282.150415.544835.202404010138",
|
|
||||||
"patient_id":"00544835",
|
|
||||||
"study_description":"A103 - Thorax PA",
|
|
||||||
"instances_retrieved":4,
|
|
||||||
"files_sent":2,
|
|
||||||
"total_files":2,
|
|
||||||
"c_store_success":true,
|
|
||||||
"series_count":4,
|
|
||||||
"his_api_status_code":200,
|
|
||||||
"his_integration_success":true,
|
|
||||||
"cleanup_success":true,
|
|
||||||
"process_end_time":"2025-07-11 15:27:46"
|
|
||||||
}
|
|
||||||
}
|
|
||||||
```
|
|
||||||
|
|
||||||
### Response Failed Example
|
|
||||||
Kalau sudah ada di tabel HIS:
|
|
||||||
|
|
||||||
```json
|
|
||||||
{
|
|
||||||
"success":true,
|
|
||||||
"message":"Berhasil migrasi file DICOM tetapi gagal update HIS: ERR: Accession No. R.20240401.0142 sudah ada ke table `pacs_order_mwl`!",
|
|
||||||
"details":{
|
|
||||||
"accession_number":"R.20240401.0142",
|
|
||||||
"process_start_time":"2025-07-11 16:05:10",
|
|
||||||
"steps_completed":[
|
|
||||||
"study_found","study_retrieved","study_sent","log_created","his_api_failed","cleanup_success"
|
|
||||||
],
|
|
||||||
"study_uid":"1.2.826.1.3680043.9.5282.150415.204342.202404010142",
|
|
||||||
"patient_id":"00204342",
|
|
||||||
"study_description":"A103 - Thorax PA",
|
|
||||||
"instances_retrieved":4,
|
|
||||||
"files_sent":2,
|
|
||||||
"total_files":2,
|
|
||||||
"c_store_success":true,
|
|
||||||
"series_count":4,
|
|
||||||
"his_api_status_code":406,
|
|
||||||
"his_integration_success":false,
|
|
||||||
"his_error":"ERR: Accession No. R.20240401.0142 sudah ada ke table `pacs_order_mwl`!","cleanup_success":true,
|
|
||||||
"process_end_time":"2025-07-11 16:05:12"
|
|
||||||
}
|
|
||||||
}
|
|
||||||
```
|
|
||||||
|
|
||||||
|
|
||||||
## Logs
|
|
||||||
|
|
||||||
- Main API logs: `logs/api.log`
|
|
||||||
- Process details: `logs/api_process.log`
|
|
||||||
|
|
||||||
## Simple Workflow
|
|
||||||
|
|
||||||
1. API receives request with accession number
|
|
||||||
2. Finds study UID using C-FIND
|
|
||||||
3. Downloads DICOM files using C-GET
|
|
||||||
4. Uploads files to destination PACS using C-STORE
|
|
||||||
5. Updates HIS system via API call
|
|
||||||
6. Cleans up all temporary DICOM files
|
|
||||||
7. Returns success/failure response
|
|
||||||
|
|
||||||
## Troubleshooting Tips
|
|
||||||
|
|
||||||
- Check PACS connectivity in `config/settings.py`
|
|
||||||
- Verify the accession number exists in source PACS
|
|
||||||
- Ensure permissions for log directories
|
|
||||||
- Check both log files for detailed error messages
|
|
||||||
- Verify HIS API connectivity for end-to-end success
|
|
||||||
|
|
||||||
## Quick Test
|
|
||||||
|
|
||||||
1. Start the server:
|
|
||||||
```bash
|
|
||||||
python run.py
|
|
||||||
```
|
|
||||||
|
|
||||||
2. In another terminal, test the root endpoint:
|
|
||||||
```bash
|
|
||||||
curl http://localhost:8000/
|
|
||||||
```
|
|
||||||
|
|
||||||
3. Test migration with a valid accession number:
|
|
||||||
```bash
|
|
||||||
curl -X POST "http://localhost:8000/migrate/R.20240401.0138" \
|
|
||||||
-H "Authorization: Bearer token-his2-untuk-hit-api-migrasi-clarity"
|
|
||||||
```
|
|
||||||
|
|
||||||
## Deploy Systemd Service
|
|
||||||
|
|
||||||
1. Create a service file:
|
|
||||||
```bash
|
|
||||||
sudo nano /etc/systemd/system/api-pydicom-migrasi.service
|
|
||||||
```
|
|
||||||
2. Add the following content:
|
|
||||||
```ini
|
|
||||||
[Unit]
|
|
||||||
Description=DICOM Migration API Service
|
|
||||||
After=network.target
|
|
||||||
|
|
||||||
[Service]
|
|
||||||
User=pacs
|
|
||||||
Group=pacs
|
|
||||||
WorkingDirectory=/home/pacs/pydicom-migrasi-clarity
|
|
||||||
Environment="PATH=/home/pacs/pydicom-migrasi-clarity/venv/bin"
|
|
||||||
Environment="API_TOKEN=$2y$05$o1Sfikmwynq76PmuBkJeROpS2WcD.Sh4lgrjohMicnlhBlGAt8UAq"
|
|
||||||
ExecStart=/home/pacs/pydicom-migrasi-clarity/venv/bin/python /home/pacs/pydicom-migrasi-clarity/api-app/run.py --host 0.0.0.0 --port 8000
|
|
||||||
Restart=on-failure
|
|
||||||
RestartSec=5s
|
|
||||||
|
|
||||||
[Install]
|
|
||||||
WantedBy=multi-user.target
|
|
||||||
```
|
|
||||||
|
|
||||||
3. Reload systemd and enable the service:
|
|
||||||
```bash
|
|
||||||
# Reload the systemd configuration
|
|
||||||
sudo systemctl daemon-reload
|
|
||||||
|
|
||||||
# Enable the service to start on boot
|
|
||||||
sudo systemctl enable api-pydicom-migrasi.service
|
|
||||||
|
|
||||||
# Start the service
|
|
||||||
sudo systemctl start api-pydicom-migrasi.service
|
|
||||||
|
|
||||||
# Check the status
|
|
||||||
sudo systemctl status api-pydicom-migrasi.service
|
|
||||||
```
|
|
||||||
|
|
||||||
4. Monitor logs:
|
|
||||||
```bash
|
|
||||||
# View all logs
|
|
||||||
sudo journalctl -u api-pydicom-migrasi.service
|
|
||||||
|
|
||||||
# Follow logs in real-time
|
|
||||||
sudo journalctl -u api-pydicom-migrasi.service -f
|
|
||||||
```
|
|
||||||
@@ -1,25 +0,0 @@
|
|||||||
"""
|
|
||||||
Custom cleanup utilities for the API application.
|
|
||||||
This module provides customized cleanup functions that are more compatible with FastAPI.
|
|
||||||
"""
|
|
||||||
import os
|
|
||||||
import sys
|
|
||||||
import shutil
|
|
||||||
import atexit
|
|
||||||
from config import settings
|
|
||||||
from utils.logger import setup_logger
|
|
||||||
from utils.cleanup import _cleanup_dirs, cleanup_dicom_files
|
|
||||||
|
|
||||||
# Create API cleanup logger
|
|
||||||
cleanup_logger = setup_logger("api_cleanup", "logs/api_cleanup.log")
|
|
||||||
|
|
||||||
def register_api_cleanup():
|
|
||||||
"""
|
|
||||||
Register cleanup handlers for the API application.
|
|
||||||
This avoids registering signal handlers which can conflict with FastAPI.
|
|
||||||
"""
|
|
||||||
# Only register the atexit handler, not signal handlers
|
|
||||||
atexit.register(cleanup_dicom_files)
|
|
||||||
cleanup_logger.info("Registered API cleanup handler for exit")
|
|
||||||
|
|
||||||
return True
|
|
||||||
134
api-app/main.py
134
api-app/main.py
@@ -1,134 +0,0 @@
|
|||||||
#!/usr/bin/env python3
|
|
||||||
"""
|
|
||||||
FastAPI application for DICOM migration service.
|
|
||||||
"""
|
|
||||||
import sys
|
|
||||||
import os
|
|
||||||
import json
|
|
||||||
from typing import Dict, Any, Optional
|
|
||||||
from fastapi import FastAPI, HTTPException, Depends, status
|
|
||||||
from fastapi.security import HTTPBearer, HTTPAuthorizationCredentials
|
|
||||||
from pydantic import BaseModel
|
|
||||||
|
|
||||||
# Add parent directory to sys.path to allow importing from the main project
|
|
||||||
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
|
|
||||||
|
|
||||||
# Import the process module for API-specific processing
|
|
||||||
from process import process_study_by_accession
|
|
||||||
from utils.logger import setup_logger
|
|
||||||
from utils.dicom_utils import create_directory_if_not_exists
|
|
||||||
from api_cleanup import register_api_cleanup
|
|
||||||
|
|
||||||
# Create API logger
|
|
||||||
api_logger = setup_logger("api", "logs/api.log")
|
|
||||||
|
|
||||||
# Initialize FastAPI app
|
|
||||||
app = FastAPI(
|
|
||||||
title="DICOM Migration API",
|
|
||||||
description="API for migrating DICOM studies by accession number",
|
|
||||||
version="1.0.0"
|
|
||||||
)
|
|
||||||
|
|
||||||
# Security scheme for Bearer token authentication
|
|
||||||
security = HTTPBearer()
|
|
||||||
|
|
||||||
# Environment variable for API key (use a secure method in production)
|
|
||||||
API_TOKEN = os.environ.get("API_TOKEN", "$2y$05$o1Sfikmwynq76PmuBkJeROpS2WcD.Sh4lgrjohMicnlhBlGAt8UAq")
|
|
||||||
|
|
||||||
class MigrationResponse(BaseModel):
|
|
||||||
"""Response model for migration endpoints."""
|
|
||||||
success: bool
|
|
||||||
message: str
|
|
||||||
details: Optional[Dict[str, Any]] = None
|
|
||||||
|
|
||||||
def verify_token(credentials: HTTPAuthorizationCredentials = Depends(security)):
|
|
||||||
"""
|
|
||||||
Verify the authentication token.
|
|
||||||
|
|
||||||
Args:
|
|
||||||
credentials: Bearer token credentials
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
bool: True if token is valid
|
|
||||||
|
|
||||||
Raises:
|
|
||||||
HTTPException: If token is invalid
|
|
||||||
"""
|
|
||||||
if credentials.scheme != "Bearer":
|
|
||||||
raise HTTPException(
|
|
||||||
status_code=status.HTTP_401_UNAUTHORIZED,
|
|
||||||
detail="Invalid authentication scheme. Bearer token required."
|
|
||||||
)
|
|
||||||
|
|
||||||
if credentials.credentials != API_TOKEN:
|
|
||||||
raise HTTPException(
|
|
||||||
status_code=status.HTTP_401_UNAUTHORIZED,
|
|
||||||
detail="Invalid token or expired token"
|
|
||||||
)
|
|
||||||
|
|
||||||
return True
|
|
||||||
|
|
||||||
@app.on_event("startup")
|
|
||||||
async def startup_event():
|
|
||||||
"""Initialize resources when the API starts."""
|
|
||||||
# Create necessary directories
|
|
||||||
create_directory_if_not_exists("logs")
|
|
||||||
|
|
||||||
# Use our custom API cleanup registration that avoids signal handlers
|
|
||||||
register_api_cleanup()
|
|
||||||
|
|
||||||
api_logger.info("API started successfully")
|
|
||||||
|
|
||||||
@app.on_event("shutdown")
|
|
||||||
async def shutdown_event():
|
|
||||||
"""Clean up resources when the API shuts down."""
|
|
||||||
api_logger.info("API shutting down, cleaning up resources...")
|
|
||||||
# Perform cleanup operations here
|
|
||||||
from utils.cleanup import cleanup_dicom_files
|
|
||||||
cleanup_dicom_files()
|
|
||||||
api_logger.info("Cleanup complete, API shutdown successful")
|
|
||||||
|
|
||||||
@app.get("/", response_model=MigrationResponse)
|
|
||||||
async def root():
|
|
||||||
"""
|
|
||||||
Root endpoint to check if the API is running.
|
|
||||||
"""
|
|
||||||
return {
|
|
||||||
"success": True,
|
|
||||||
"message": "DICOM Migration API is running",
|
|
||||||
"details": {
|
|
||||||
"version": "1.0.0",
|
|
||||||
"copyright": "PT. Sadhana Abiyasa Sampoerna",
|
|
||||||
"developer": "Mario and FX Padmanto"
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
@app.post("/migrate/{accession_number}", response_model=MigrationResponse)
|
|
||||||
async def migrate_study(
|
|
||||||
accession_number: str,
|
|
||||||
_: bool = Depends(verify_token)
|
|
||||||
):
|
|
||||||
"""
|
|
||||||
Migrate a single study by its accession number.
|
|
||||||
|
|
||||||
Args:
|
|
||||||
accession_number: The accession number of the study to migrate
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
MigrationResponse: The result of the migration operation
|
|
||||||
"""
|
|
||||||
api_logger.info(f"Received migration request for accession number: {accession_number}")
|
|
||||||
|
|
||||||
# Process the study using the specialized API processing module
|
|
||||||
result = process_study_by_accession(accession_number)
|
|
||||||
|
|
||||||
if result['success']:
|
|
||||||
api_logger.info(f"Successfully processed migration for accession number: {accession_number}")
|
|
||||||
else:
|
|
||||||
api_logger.error(f"Failed to process migration for accession number: {accession_number}: {result['message']}")
|
|
||||||
|
|
||||||
return result
|
|
||||||
|
|
||||||
if __name__ == "__main__":
|
|
||||||
import uvicorn
|
|
||||||
uvicorn.run("main:app", host="0.0.0.0", port=8000, reload=True)
|
|
||||||
@@ -1,284 +0,0 @@
|
|||||||
#!/usr/bin/env python3
|
|
||||||
"""
|
|
||||||
Process module for DICOM migration API service.
|
|
||||||
This module contains the core processing logic for migrating DICOM studies through the API.
|
|
||||||
"""
|
|
||||||
import os
|
|
||||||
import sys
|
|
||||||
import json
|
|
||||||
import shutil
|
|
||||||
from datetime import datetime
|
|
||||||
import requests
|
|
||||||
|
|
||||||
# Add parent directory to sys.path to allow importing from the main project
|
|
||||||
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
|
|
||||||
|
|
||||||
from config import settings
|
|
||||||
from services.dicom_finder import DicomFinder
|
|
||||||
from services.dicom_retriever import DicomRetriever
|
|
||||||
from services.dicom_sender import DicomSender
|
|
||||||
from utils.logger import setup_logger
|
|
||||||
from utils.dicom_utils import save_json_data, create_directory_if_not_exists
|
|
||||||
|
|
||||||
# Create API process logger
|
|
||||||
process_logger = setup_logger("api_process", "logs/api_process.log")
|
|
||||||
|
|
||||||
|
|
||||||
def cleanup_study_directory(study_uid):
|
|
||||||
"""
|
|
||||||
Explicitly clean up the DICOM files for a study after processing.
|
|
||||||
|
|
||||||
Args:
|
|
||||||
study_uid: Study Instance UID to clean up
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
bool: True if cleanup was successful, False otherwise
|
|
||||||
"""
|
|
||||||
study_dir = os.path.join(settings.DICOM_STORE_DIR, study_uid)
|
|
||||||
process_logger.info(f"Cleaning up DICOM files for study: {study_uid} at {study_dir}")
|
|
||||||
|
|
||||||
try:
|
|
||||||
if os.path.exists(study_dir):
|
|
||||||
shutil.rmtree(study_dir)
|
|
||||||
process_logger.info(f"Successfully removed study directory: {study_dir}")
|
|
||||||
return True
|
|
||||||
else:
|
|
||||||
process_logger.warning(f"Study directory does not exist: {study_dir}")
|
|
||||||
return True # Return True since there's nothing to clean
|
|
||||||
except Exception as e:
|
|
||||||
process_logger.error(f"Error cleaning up study directory {study_dir}: {str(e)}")
|
|
||||||
return False
|
|
||||||
|
|
||||||
|
|
||||||
def process_study_by_accession(accession_number):
|
|
||||||
"""
|
|
||||||
Process a study by its accession number for the API service.
|
|
||||||
|
|
||||||
This function:
|
|
||||||
1. Finds the study UID based on accession number
|
|
||||||
2. Retrieves DICOM files using C-GET
|
|
||||||
3. Sends DICOM files to destination PACS using C-STORE
|
|
||||||
4. Sends study information to HIS API
|
|
||||||
5. Cleans up temporary DICOM files
|
|
||||||
|
|
||||||
Args:
|
|
||||||
accession_number: The accession number of the study to process
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
dict: Result with success status, message, and details
|
|
||||||
"""
|
|
||||||
process_logger.info(f"Processing study with accession number: {accession_number}")
|
|
||||||
|
|
||||||
# Initialize response data
|
|
||||||
response_data = {
|
|
||||||
"success": False,
|
|
||||||
"message": "",
|
|
||||||
"details": {
|
|
||||||
"accession_number": accession_number,
|
|
||||||
"process_start_time": datetime.now().strftime('%Y-%m-%d %H:%M:%S'),
|
|
||||||
"steps_completed": []
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
try:
|
|
||||||
# STEP 1: Find study by accession number to get the Study UID
|
|
||||||
process_logger.info(f"Finding study with accession number: {accession_number}")
|
|
||||||
finder = DicomFinder()
|
|
||||||
study = finder.find_study_by_accession(accession_number)
|
|
||||||
|
|
||||||
if not study:
|
|
||||||
process_logger.error(f"Study not found for accession number: {accession_number}")
|
|
||||||
response_data["message"] = f"Study not found for accession number: {accession_number}"
|
|
||||||
return response_data
|
|
||||||
|
|
||||||
study_uid = study.StudyInstanceUID
|
|
||||||
patient_id = getattr(study, 'PatientID', '')
|
|
||||||
study_description = getattr(study, 'StudyDescription', '')
|
|
||||||
study_date = getattr(study, 'StudyDate', '')
|
|
||||||
study_time = getattr(study, 'StudyTime', '000000')
|
|
||||||
|
|
||||||
response_data["details"]["study_uid"] = study_uid
|
|
||||||
response_data["details"]["patient_id"] = patient_id
|
|
||||||
response_data["details"]["study_description"] = study_description
|
|
||||||
|
|
||||||
process_logger.info(f"Found study with UID: {study_uid} for accession number: {accession_number}")
|
|
||||||
response_data["details"]["steps_completed"].append("study_found")
|
|
||||||
|
|
||||||
# STEP 2: Retrieve the study using C-GET
|
|
||||||
process_logger.info(f"Retrieving study: {study_uid}")
|
|
||||||
retriever = DicomRetriever()
|
|
||||||
retrieve_result = retriever.retrieve_study(study_uid, accession_number=accession_number)
|
|
||||||
|
|
||||||
if not retrieve_result['success']:
|
|
||||||
process_logger.error(f"Failed to retrieve study {study_uid}: {retrieve_result['status']}")
|
|
||||||
cleanup_study_directory(study_uid) # Clean up any partial files
|
|
||||||
response_data["message"] = f"Failed to retrieve study: {retrieve_result['status']}"
|
|
||||||
return response_data
|
|
||||||
|
|
||||||
process_logger.info(f"Retrieved {retrieve_result['successful_instances']} instances for study {study_uid}")
|
|
||||||
response_data["details"]["instances_retrieved"] = retrieve_result['successful_instances']
|
|
||||||
response_data["details"]["steps_completed"].append("study_retrieved")
|
|
||||||
|
|
||||||
# STEP 3: Send the study to destination PACS using C-STORE
|
|
||||||
process_logger.info(f"Sending study {study_uid} to destination PACS")
|
|
||||||
sender = DicomSender()
|
|
||||||
send_result = sender.send_study(os.path.join(settings.DICOM_STORE_DIR, study_uid))
|
|
||||||
|
|
||||||
response_data["details"]["files_sent"] = send_result['successful_sends']
|
|
||||||
response_data["details"]["total_files"] = send_result['total_files']
|
|
||||||
|
|
||||||
if not send_result['success']:
|
|
||||||
process_logger.error(f"Failed to send study {study_uid}: {send_result.get('error', 'Unknown error')}")
|
|
||||||
# We continue processing even if send fails, to log the details
|
|
||||||
response_data["details"]["c_store_success"] = False
|
|
||||||
response_data["details"]["c_store_error"] = send_result.get('error', 'Unknown error')
|
|
||||||
else:
|
|
||||||
process_logger.info(f"Successfully sent {send_result['successful_sends']} of {send_result['total_files']} files to destination PACS")
|
|
||||||
response_data["details"]["c_store_success"] = True
|
|
||||||
|
|
||||||
response_data["details"]["steps_completed"].append("study_sent")
|
|
||||||
|
|
||||||
# STEP 4: Create detailed log for the study
|
|
||||||
process_logger.info(f"Creating detailed log for study: {study_uid}")
|
|
||||||
series_list = finder.find_series_for_study(study_uid, accession_number=accession_number)
|
|
||||||
|
|
||||||
study_datetime = f"{study_date}{study_time}"
|
|
||||||
|
|
||||||
study_log = {
|
|
||||||
'Study_IUID': study_uid,
|
|
||||||
'AccessionNumber': accession_number,
|
|
||||||
'PatientID': patient_id,
|
|
||||||
'StudyDescription': study_description,
|
|
||||||
'StudyDateTime': study_datetime,
|
|
||||||
'CstoreSuccess': send_result['success'],
|
|
||||||
'Series': []
|
|
||||||
}
|
|
||||||
|
|
||||||
for series in series_list:
|
|
||||||
series_uid = series.SeriesInstanceUID
|
|
||||||
|
|
||||||
# Get first instance for the series
|
|
||||||
instance = finder.find_first_instance_for_series(study_uid, series_uid)
|
|
||||||
|
|
||||||
# Helper function to safely get attributes
|
|
||||||
def safe_get_attr(obj, attr_name, default=''):
|
|
||||||
"""Get attribute value, ensuring None is converted to default."""
|
|
||||||
value = getattr(obj, attr_name, default)
|
|
||||||
return default if value is None else str(value)
|
|
||||||
|
|
||||||
series_info = {
|
|
||||||
'Series_IUID': safe_get_attr(series, 'SeriesInstanceUID'),
|
|
||||||
'SeriesNumber': safe_get_attr(series, 'SeriesNumber'),
|
|
||||||
'SeriesDescription': safe_get_attr(series, 'SeriesDescription'),
|
|
||||||
'NumberOfInstances': safe_get_attr(series, 'NumberOfSeriesRelatedInstances'),
|
|
||||||
'SOP_IUID': safe_get_attr(instance, 'SOPInstanceUID') if instance else ''
|
|
||||||
}
|
|
||||||
|
|
||||||
study_log['Series'].append(series_info)
|
|
||||||
|
|
||||||
response_data["details"]["series_count"] = len(study_log['Series'])
|
|
||||||
response_data["details"]["steps_completed"].append("log_created")
|
|
||||||
|
|
||||||
# STEP 5: Send study_log to HIS API
|
|
||||||
process_logger.info(f"Sending study data to HIS API for accession: {accession_number}")
|
|
||||||
his_url = f"http://{settings.HIS_HOST}{settings.HIS_URL}"
|
|
||||||
|
|
||||||
try:
|
|
||||||
headers = {
|
|
||||||
'id': 'Vmtaa2MySnRUblJTYWtKb1ZucHNNVlZVU2pSaFIwNTBZa1JDYkZaV1NtOWFSV1JIVmxkSmQxSnJUbFpTVlZwRlZsaGpPVkJSUFQwPQ==',
|
|
||||||
'Content-Type': 'application/json'
|
|
||||||
}
|
|
||||||
response = requests.post(his_url, json=study_log, headers=headers)
|
|
||||||
|
|
||||||
# Add response data to the log
|
|
||||||
study_log['HisApiResponse'] = {
|
|
||||||
'StatusCode': response.status_code,
|
|
||||||
'ResponseText': response.text,
|
|
||||||
'Success': False,
|
|
||||||
'Timestamp': datetime.now().strftime('%Y-%m-%d %H:%M:%S')
|
|
||||||
}
|
|
||||||
|
|
||||||
response_data["details"]["his_api_status_code"] = response.status_code
|
|
||||||
|
|
||||||
# Parse the response
|
|
||||||
try:
|
|
||||||
response_data_his = response.json() if response.content else {}
|
|
||||||
study_log['HisApiResponse']['ResponseData'] = response_data_his
|
|
||||||
|
|
||||||
if response.status_code == 200 and response_data_his.get('OK') == "1":
|
|
||||||
study_log['HisApiResponse']['Success'] = True
|
|
||||||
process_logger.info(f"Successfully sent JSON {accession_number} to HIS API")
|
|
||||||
response_data["details"]["his_integration_success"] = True
|
|
||||||
response_data["details"]["steps_completed"].append("his_api_success")
|
|
||||||
else:
|
|
||||||
error_msg = response_data_his.get('MSG', response_data_his.get('message', 'Unknown error'))
|
|
||||||
process_logger.error(f"Failed to send JSON for {accession_number} to HIS API: {error_msg}. Study_IUID: {study_uid}")
|
|
||||||
response_data["details"]["his_integration_success"] = False
|
|
||||||
response_data["details"]["his_error"] = error_msg
|
|
||||||
response_data["details"]["steps_completed"].append("his_api_failed")
|
|
||||||
except ValueError:
|
|
||||||
study_log['HisApiResponse']['ParseError'] = "Invalid JSON response"
|
|
||||||
process_logger.error(f"Failed to parse response for {accession_number}, invalid JSON response. Status code: {response.status_code}")
|
|
||||||
response_data["details"]["his_integration_success"] = False
|
|
||||||
response_data["details"]["his_error"] = "Invalid JSON response from HIS API"
|
|
||||||
response_data["details"]["steps_completed"].append("his_api_failed")
|
|
||||||
|
|
||||||
except Exception as e:
|
|
||||||
study_log['HisApiResponse'] = {
|
|
||||||
'Success': False,
|
|
||||||
'Error': str(e),
|
|
||||||
'Timestamp': datetime.now().strftime('%Y-%m-%d %H:%M:%S')
|
|
||||||
}
|
|
||||||
process_logger.error(f"Error sending study for {accession_number} to HIS API: {str(e)}")
|
|
||||||
response_data["details"]["his_integration_success"] = False
|
|
||||||
response_data["details"]["his_error"] = str(e)
|
|
||||||
response_data["details"]["steps_completed"].append("his_api_error")
|
|
||||||
|
|
||||||
# STEP 6: Clean up DICOM files
|
|
||||||
cleanup_result = cleanup_study_directory(study_uid)
|
|
||||||
if cleanup_result:
|
|
||||||
process_logger.info(f"Successfully cleaned up DICOM files for study: {study_uid}")
|
|
||||||
response_data["details"]["cleanup_success"] = True
|
|
||||||
response_data["details"]["steps_completed"].append("cleanup_success")
|
|
||||||
else:
|
|
||||||
process_logger.warning(f"Failed to clean up DICOM files for study: {study_uid}")
|
|
||||||
response_data["details"]["cleanup_success"] = False
|
|
||||||
response_data["details"]["steps_completed"].append("cleanup_failed")
|
|
||||||
|
|
||||||
# STEP 7: Save the study log for reference
|
|
||||||
log_dir = settings.JSON_OUTPUT_DIR
|
|
||||||
create_directory_if_not_exists(log_dir)
|
|
||||||
log_filename = f"api_{accession_number}.json"
|
|
||||||
save_json_data(study_log, log_filename, log_dir)
|
|
||||||
process_logger.info(f"Saved study log to {os.path.join(log_dir, log_filename)}")
|
|
||||||
|
|
||||||
# Set final response based on C-STORE success (primary success metric)
|
|
||||||
response_data["success"] = send_result['success']
|
|
||||||
|
|
||||||
if send_result['success']:
|
|
||||||
his_success = response_data["details"].get("his_integration_success", False)
|
|
||||||
if his_success:
|
|
||||||
response_data["message"] = f"Berhasil migrasi file DICOM Accession Number: {accession_number}"
|
|
||||||
else:
|
|
||||||
his_error = response_data["details"].get("his_error", "Unknown HIS error")
|
|
||||||
response_data["message"] = f"Berhasil migrasi file DICOM tetapi gagal update HIS: {his_error}"
|
|
||||||
else:
|
|
||||||
response_data["message"] = f"Gagal migrasi file DICOM: {send_result.get('error', 'Unknown error')}"
|
|
||||||
|
|
||||||
process_logger.info(f"Completed processing study with accession number: {accession_number}")
|
|
||||||
response_data["details"]["process_end_time"] = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
|
|
||||||
|
|
||||||
return response_data
|
|
||||||
|
|
||||||
except Exception as e:
|
|
||||||
process_logger.exception(f"Unexpected error processing study {accession_number}: {str(e)}")
|
|
||||||
|
|
||||||
# Try to clean up if we have a study_uid
|
|
||||||
if 'study_uid' in locals():
|
|
||||||
cleanup_study_directory(study_uid)
|
|
||||||
|
|
||||||
response_data["message"] = f"Error during migration: {str(e)}"
|
|
||||||
response_data["details"]["error"] = str(e)
|
|
||||||
response_data["details"]["process_end_time"] = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
|
|
||||||
|
|
||||||
return response_data
|
|
||||||
@@ -1,9 +0,0 @@
|
|||||||
fastapi>=0.95.0
|
|
||||||
uvicorn>=0.22.0
|
|
||||||
pydicom>=2.3.0
|
|
||||||
pynetdicom>=2.0.0
|
|
||||||
python-dateutil>=2.8.2
|
|
||||||
retry==0.9.2
|
|
||||||
requests>=2.28.0
|
|
||||||
python-jose>=3.3.0
|
|
||||||
python-multipart>=0.0.6
|
|
||||||
@@ -1,52 +0,0 @@
|
|||||||
#!/usr/bin/env python3
|
|
||||||
"""
|
|
||||||
Script to run the FastAPI server for DICOM migration service.
|
|
||||||
"""
|
|
||||||
import os
|
|
||||||
import sys
|
|
||||||
import signal
|
|
||||||
import uvicorn
|
|
||||||
import argparse
|
|
||||||
|
|
||||||
def parse_args():
|
|
||||||
"""Parse command-line arguments."""
|
|
||||||
parser = argparse.ArgumentParser(description='DICOM Migration API Server')
|
|
||||||
parser.add_argument('--host', default='0.0.0.0', help='Host to bind to')
|
|
||||||
parser.add_argument('--port', type=int, default=8000, help='Port to bind to')
|
|
||||||
parser.add_argument('--token', help='API token for authentication (overrides environment variable)')
|
|
||||||
parser.add_argument('--reload', action='store_true', help='Enable auto-reload for development')
|
|
||||||
return parser.parse_args()
|
|
||||||
|
|
||||||
def handle_exit(signum, frame):
|
|
||||||
"""Handle exit signals gracefully."""
|
|
||||||
print(f"Received signal {signum}, shutting down gracefully...")
|
|
||||||
# Let uvicorn handle the exit
|
|
||||||
sys.exit(0)
|
|
||||||
|
|
||||||
def main():
|
|
||||||
"""Main function to run the API server."""
|
|
||||||
args = parse_args()
|
|
||||||
|
|
||||||
# Set API token if provided
|
|
||||||
if args.token:
|
|
||||||
os.environ['API_TOKEN'] = args.token
|
|
||||||
|
|
||||||
# Check if API_TOKEN is set
|
|
||||||
if not os.environ.get('API_TOKEN'):
|
|
||||||
print("WARNING: API_TOKEN not set. Using default token '$2y$05$o1Sfikmwynq76PmuBkJeROpS2WcD.Sh4lgrjohMicnlhBlGAt8UAq'.")
|
|
||||||
print("Set environment variable API_TOKEN or use --token argument for better security.")
|
|
||||||
|
|
||||||
# Set up signal handlers for graceful shutdown
|
|
||||||
signal.signal(signal.SIGINT, handle_exit)
|
|
||||||
signal.signal(signal.SIGTERM, handle_exit)
|
|
||||||
|
|
||||||
print(f"Starting DICOM Migration API server on {args.host}:{args.port}")
|
|
||||||
uvicorn.run(
|
|
||||||
"main:app",
|
|
||||||
host=args.host,
|
|
||||||
port=args.port,
|
|
||||||
reload=args.reload
|
|
||||||
)
|
|
||||||
|
|
||||||
if __name__ == "__main__":
|
|
||||||
main()
|
|
||||||
@@ -1,17 +0,0 @@
|
|||||||
@host = http://localhost:8000
|
|
||||||
@token = $2y$05$o1Sfikmwynq76PmuBkJeROpS2WcD.Sh4lgrjohMicnlhBlGAt8UAq
|
|
||||||
|
|
||||||
|
|
||||||
### Healtcheck
|
|
||||||
GET {{host}}/
|
|
||||||
|
|
||||||
|
|
||||||
###
|
|
||||||
POST {{host}}/migrate/R.20240401.0138
|
|
||||||
Authorization: Bearer {{token}}
|
|
||||||
Content-Type: application/json
|
|
||||||
|
|
||||||
####
|
|
||||||
POST {{host}}/migrate/R.20240401.0142
|
|
||||||
Authorization: Bearer {{token}}
|
|
||||||
Content-Type: application/json
|
|
||||||
2
main.py
2
main.py
@@ -532,6 +532,8 @@ def process_workflow(args):
|
|||||||
|
|
||||||
# Create services
|
# Create services
|
||||||
finder = DicomFinder()
|
finder = DicomFinder()
|
||||||
|
retriever = DicomRetriever()
|
||||||
|
sender = DicomSender()
|
||||||
|
|
||||||
# Create directory for logs
|
# Create directory for logs
|
||||||
create_directory_if_not_exists(log_dir)
|
create_directory_if_not_exists(log_dir)
|
||||||
|
|||||||
@@ -348,81 +348,3 @@ class DicomFinder:
|
|||||||
raise DicomQueryError(error_msg)
|
raise DicomQueryError(error_msg)
|
||||||
|
|
||||||
return study
|
return study
|
||||||
|
|
||||||
@dicom_retry(exception_types=(DicomQueryError, ConnectionError))
|
|
||||||
def find_study_by_accession(self, accession_number):
|
|
||||||
"""
|
|
||||||
Find a specific study by its AccessionNumber.
|
|
||||||
|
|
||||||
Args:
|
|
||||||
accession_number (str): AccessionNumber to find
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
Dataset: Study dataset or None if not found
|
|
||||||
"""
|
|
||||||
logger.info(f"Finding study with AccessionNumber: {accession_number}")
|
|
||||||
|
|
||||||
# Create query dataset
|
|
||||||
ds = Dataset()
|
|
||||||
ds.QueryRetrieveLevel = 'STUDY'
|
|
||||||
|
|
||||||
# Set the AccessionNumber filter
|
|
||||||
ds.AccessionNumber = accession_number
|
|
||||||
|
|
||||||
# Required fields (minimal set)
|
|
||||||
ds.StudyInstanceUID = ''
|
|
||||||
ds.StudyDate = ''
|
|
||||||
|
|
||||||
# Additional fields we want to retrieve
|
|
||||||
ds.PatientID = '' # MedrecID
|
|
||||||
ds.StudyDescription = ''
|
|
||||||
ds.StudyTime = ''
|
|
||||||
ds.NumberOfStudyRelatedSeries = ''
|
|
||||||
|
|
||||||
# Create association
|
|
||||||
assoc = self.ae.associate(
|
|
||||||
self.pacs_config['host'],
|
|
||||||
self.pacs_config['port'],
|
|
||||||
ae_title=self.pacs_config['aet']
|
|
||||||
)
|
|
||||||
|
|
||||||
study = None
|
|
||||||
|
|
||||||
if assoc.is_established:
|
|
||||||
try:
|
|
||||||
logger.debug("Association established, sending C-FIND request")
|
|
||||||
|
|
||||||
# Send C-FIND request
|
|
||||||
responses = assoc.send_c_find(
|
|
||||||
ds,
|
|
||||||
StudyRootQueryRetrieveInformationModelFind
|
|
||||||
)
|
|
||||||
|
|
||||||
# Process responses - just get the first one
|
|
||||||
for (status, dataset) in responses:
|
|
||||||
if status and status.Status == 0xFF00: # Pending
|
|
||||||
if dataset:
|
|
||||||
study = dataset
|
|
||||||
logger.debug(f"Found study: {dataset.StudyInstanceUID} for AccessionNumber: {accession_number}")
|
|
||||||
break
|
|
||||||
elif status and status.Status != 0x0000: # Not success
|
|
||||||
logger.error(f"C-FIND error: {status}")
|
|
||||||
|
|
||||||
if study:
|
|
||||||
logger.info(f"Found study with AccessionNumber {accession_number}, StudyUID: {study.StudyInstanceUID}")
|
|
||||||
else:
|
|
||||||
logger.warning(f"No study found with AccessionNumber {accession_number}")
|
|
||||||
|
|
||||||
except Exception as e:
|
|
||||||
logger.error(f"Error during C-FIND by AccessionNumber: {str(e)}")
|
|
||||||
raise DicomQueryError(f"C-FIND operation failed: {str(e)}")
|
|
||||||
finally:
|
|
||||||
# Release the association
|
|
||||||
assoc.release()
|
|
||||||
logger.debug("Association released")
|
|
||||||
else:
|
|
||||||
error_msg = f"Association rejected, aborted or never connected to {self.pacs_config['aet']}"
|
|
||||||
logger.error(error_msg)
|
|
||||||
raise DicomQueryError(error_msg)
|
|
||||||
|
|
||||||
return study
|
|
||||||
@@ -2,7 +2,6 @@
|
|||||||
DICOM file cleanup utility to ensure temporary DICOM files are removed even on script termination.
|
DICOM file cleanup utility to ensure temporary DICOM files are removed even on script termination.
|
||||||
"""
|
"""
|
||||||
import os
|
import os
|
||||||
import sys
|
|
||||||
import shutil
|
import shutil
|
||||||
import atexit
|
import atexit
|
||||||
import signal
|
import signal
|
||||||
@@ -43,36 +42,6 @@ def cleanup_dicom_files():
|
|||||||
# Clear the registry after cleanup
|
# Clear the registry after cleanup
|
||||||
_cleanup_dirs.clear()
|
_cleanup_dirs.clear()
|
||||||
|
|
||||||
def cleanup_study_directory(study_uid):
|
|
||||||
"""
|
|
||||||
Immediately remove the directory for a specific study.
|
|
||||||
|
|
||||||
Args:
|
|
||||||
study_uid (str): Study Instance UID of the study to clean up
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
bool: True if cleanup was successful, False otherwise
|
|
||||||
"""
|
|
||||||
study_dir = os.path.join(settings.DICOM_STORE_DIR, study_uid)
|
|
||||||
|
|
||||||
if not os.path.exists(study_dir):
|
|
||||||
logger.debug(f"Cleanup: Study directory does not exist: {study_dir}")
|
|
||||||
return True
|
|
||||||
|
|
||||||
try:
|
|
||||||
shutil.rmtree(study_dir)
|
|
||||||
logger.info(f"Cleanup: Removed DICOM files from {study_dir}")
|
|
||||||
|
|
||||||
# Also remove from the registry if it's there
|
|
||||||
global _cleanup_dirs
|
|
||||||
if study_dir in _cleanup_dirs:
|
|
||||||
_cleanup_dirs.remove(study_dir)
|
|
||||||
|
|
||||||
return True
|
|
||||||
except Exception as e:
|
|
||||||
logger.error(f"Cleanup: Failed to remove DICOM files from {study_dir}: {str(e)}")
|
|
||||||
return False
|
|
||||||
|
|
||||||
def register_exit_handlers():
|
def register_exit_handlers():
|
||||||
"""
|
"""
|
||||||
Register cleanup handlers for various exit scenarios.
|
Register cleanup handlers for various exit scenarios.
|
||||||
@@ -101,12 +70,4 @@ def signal_handler(sig, frame):
|
|||||||
|
|
||||||
logger.info(f"Received {signal_name}, cleaning up...")
|
logger.info(f"Received {signal_name}, cleaning up...")
|
||||||
cleanup_dicom_files()
|
cleanup_dicom_files()
|
||||||
# Don't call exit() directly in a web application context
|
exit(0)
|
||||||
# Let the calling application handle the exit process
|
|
||||||
# This fix makes it compatible with FastAPI and other web frameworks
|
|
||||||
# Raise SystemExit instead of calling exit() directly
|
|
||||||
if hasattr(frame, '_is_web_app') and frame._is_web_app:
|
|
||||||
return
|
|
||||||
else:
|
|
||||||
# For command-line applications, we can exit directly
|
|
||||||
sys.exit(0)
|
|
||||||
Reference in New Issue
Block a user