- install dependencies
npm install - run the appliaction (server will be running on port 5000)
npm start - Database: MongoDB
- Import sample data into database
npm run initDB
Clinician & Radiologist API PATH
Authentication & User
- POST /api/auth/login ( reqBody = {username, password, remember} )
- POST /api/auth/logout
- GET /api/users/:id ( Get user by id )
Webapp Project
- GET /api/projects/user/:id ( Get all projects by user id )
- GET /api/projects/:project_id ( Get project by id )
Vitals
- POST /api/vitals/records ( Create vitals project and upload medical records, reqBody = {project_name, record_name, user_id, records} )
- GET /api/vitals/ ( Get projects by field, reqQuery = (user_id, project_id) )
- GET /api/vitals/projects/:id/medrec ( Get all records by project id )
- GET /api/vitals/records/ ( Get all records by patient's HN, reqQuery = (HN, project_name) )
- GET /api/vitals/template/:project_id (Get .xlsx template from project's requirements)
- PATCH /api/vitals/records/updaterow (Update selected row in record file, reqBody = {record_id, update_data})
- PATCH /api/vitals/records/deleterow/ (Delete selected row in record file reqBody = {record_id, record_index})
- DELETE /api/vitals/records/deletefile/:id (Delete entire record file by record_id)
Infer & Report
- POST /api/infer (Start inference, reqBody = (accession_no, project_id, record, user_id) )
- POST /api/infer/batch (Start batch inference, reqBody = {project_id, user_id, dicom_info_list: {accession_no, record: {...}}} )
- GET /api/report/:rid (Get report by id)
- GET /api/report/list/project/:project_id (View history by project id)
- PATCH /api/report/ (Update or finalize report, reqBody = ( report_id, note, user_id, label, rating ) )
- DELETE /api/report/delete/:rid (Delete report by id)
Image
- GET /api/image (get image, reqQuery = (result_id, finding, accession_no))
example: /api/image/?accession_no=74 (original file from PACS)
example: /api/image/?result_id=6181884fdb269acd1bf1bd77&finding=Mass (overlay file)
PACS
- GET /api/pacs/ ( Get all patient's data from pacs by HN, reqQuery = (HN, accession_no, start_date, end_date) )
- GET /api/pacs/info/ ( Get patient info by HN, reqQuery = (HN, dir) )
- POST /api/pacs/save/:report_id ( Save report to PACS )
Mask
- PATCH /api/masks/ ( Crete bounding box position, reqBody=(report_id, data: [{label, tool, updated_by, data}, ...]) )
- GET /api/masks/report/:report_id ( Get bounding box position by report id )
Admin API PATH
Webapp Project
- POST /api/projects ( Create new project, reqBody = {name, task, description, predClasses, head} )
- PATCH /api/projects ( Update project, reqBody = {id, name, task, description, predClasses, head} )
- PATCH /api/projects/manage ( Manage project's user list, reqBody = {id, users} )
- GET /api/projects ( Get all projects )
- GET /api/projects/tasks ( Get all AI tasks )
- DELETE /api/projects/delete/:project_id ( Delete project by id )
User
- POST /api/users ( Create new user, reqBody = {username, password, first_name, last_name, role, email} )
- PATCH /api/users ( Update user, reqBody = {id, password, first_name, last_name, role, email, isChulaSSO} )
- GET /api/users ( Get all users )
Docker
- Go to root directory of all three fl servers
- Copy
docker-compose.ymland.envinto root directory and copyinit-mongo.shinto mongo volume directory
docker-compose.yml
version: "3.8"
services:
webapp-front:
container_name: webapp-front
restart: always
build: ./fl-webapp-front
ports:
- '80:3000'
env_file:
- ./.env
webapp-model:
container_name: webapp-model
restart: always
build: ./fl-webapp-model
ports:
- '7000:7000'
- '11112:11112'
volumes:
- /fl-webapp-model/resources:/code/resources
env_file:
- ./.env
mongo:
image: mongo:4.0.3
container_name: mongo
ports:
- '27018:27017' # host_port:container_port
environment:
MONGO_INITDB_ROOT_USERNAME: $ROOT_USER
MONGO_INITDB_ROOT_PASSWORD: $ROOT_PASSWORD
volumes:
- /mongo-test/migrations:/docker-entrypoint-initdb.d # path to init-mongo.sh
- /mongo-test/db:/data/db # can be anywhere
env_file:
- ./.env
webapp-back:
container_name: webapp-back
restart: always
build: ./fl-webapp-back
ports:
- '5000:5000'
volumes:
- /fl-webapp-back/resources:/usr/src/app/resources
env_file:
- ./.env
init-mongo.sh
set -e
mongo <<EOF
use webapp
db.createUser({
user: '$WEB_DB_USER',
pwd: '$DB_PASSWORD',
roles: [{
role: 'readWrite',
db: 'webapp'
}]
})
use vitals
db.createUser({
user: '$VITALS_DB_USER',
pwd: '$DB_PASSWORD',
roles: [{
6753
role: 'readWrite',
db: 'vitals'
}]
})
EOF
.env
# DATABASE URL FOR BACK AND MODEL
webappDB=mongodb://<admin>:<admin>@mongo:27017/webapp?authSource=webapp&w=1
vitalsDB=mongodb://<admin>:<admin>@mongo:27017/vitals?authSource=vitals&w=1
# ROOT DATABASE USERNAME/PASSWORD
ROOT_USER=<root>
ROOT_PASSWORD=<password>
# USER DATABASE USERNAME/PASSWORD
VITALS_DB_USER=<admin>
WEB_DB_USER=<admin>
DB_PASSWORD=<admin> # same for both db
# SECRET
SECRET_TOKEN=oUQF9vv5MB77302BJm6HDKulKKPqfukuiW5zMeamAx2JJU21cJkx23MBShP3GVt
# BACKEND
DeeAppId=DEE_APP_ID
DeeAppSecret=DEE_APP_SECRET
GROUP_SIZE=2
PY_SERVER=http://webapp-model:7000
# FRONTEND
REACT_APP_IP_ADDRESS=localhost
# PYTHON
PACS_ADDR=127.0.0.1
PACS_PORT=11113
- Build docker compose. Frontend, backend, and model will be run at port 80, 5000, and 7000
or
docker-compose up -d --builddocker-compose up -d - Import sample data into the containers
docker exec -it webapp-back bashnpm run initDB - Others
- ดูรายละเอียดของแต่ละ container:
docker ps - เข้าไปดูข้อมูลต่าง ๆ ใน database ของ container ผ่าน MongoDB Compass ได้ทาง url
mongodb://localhost:27018หรือใช้คำสั่งdocker exec -it mongo bashเข้าไปใน container ของ mongo แล้วใช้คำสั่งของ MongoDB Shell ดูข้อมูลใน database ก็ได้