# vindr-lab-deployment **Repository Path**: aiacLab/vindr-lab-deployment ## Basic Information - **Project Name**: vindr-lab-deployment - **Description**: No description available - **Primary Language**: Unknown - **License**: MIT - **Default Branch**: master - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2021-12-02 - **Last Updated**: 2021-12-02 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README

# VinDr Lab Deployment Welcome to the VinDr Lab project. # :wrench: System Properties Our project requires at least 4GB of RAM system for the best performance and experiement. # :rocket: Start it up There are two ways to deploy our project are: **Option 1: Kubernetes** **Option 2: Docker** and the instruction is going to be described below. But we think using Kubernetes will be more interesting. # :ship: Kubernetes ## Prerequisites We use k3s as Kubernetes supporter. Install the k3s at first. ## Run - First, you must initialize the namespace for these deployments by running: `kubectl create namespace vinlab` - Then, go in to the `kubernetes` folder and create the config map: `sh ./create_config_map.sh` - Next step, just run `kubectl apply -f . -n vinlab` - As you can see, in the first commits, we use `ingress-nginx` to load-balance and route endpoints. However, we found out that was inconvenient. So remove it and try another simple solution, a load-balancer service. ## Check To make sure everything is fine, please run `kubectl -n vinlab get pod` and `kubectl -n vinlab get svc` ``` NAME READY STATUS RESTARTS AGE svclb-vinlab-lb-h5tn2 1/1 Running 0 2m8s vinlab-uploader-deployment-785449b44f-wl8wq 1/1 Running 0 2m7s es-deployment-779db4985d-tqzn2 1/1 Running 0 2m8s keycloak-deployment-6dc647c6cc-9fpxq 1/1 Running 0 2m8s apigateway-deployment-d6dcc5d8f-qvb8l 1/1 Running 0 2m8s redis-deployment-756b4b8956-48lpp 1/1 Running 0 2m8s orthanc-deployment-fb799595-kl8vw 1/1 Running 0 2m8s minio-deployment-556459976d-fb6g2 1/1 Running 0 2m8s vinlab-viewer-deployment-59cfd85f6b-mgj6t 1/1 Running 0 2m7s id-generator-deployment-7454b7bf6d-m2pv9 2/2 Running 0 2m8s vinlab-api-deployment-d4fbc5c5f-pctbr 1/1 Running 3 2m8s vinlab-dashboard-deployment-64f679d7b8-b7cqt 1/1 Running 0 2m7s ``` ``` NAME TYPE CLUSTER-IP EXTERNAL-IP PORT(S) AGE nginx ClusterIP 10.43.226.118 80/TCP 4m39s dashboard ClusterIP 10.43.83.174 80/TCP 4m39s es ClusterIP 10.43.27.208 9200/TCP 4m39s id-generator ClusterIP 10.43.103.96 8080/TCP 4m39s keycloak ClusterIP 10.43.220.30 8080/TCP 4m39s minio ClusterIP 10.43.2.239 9000/TCP 4m39s orthanc ClusterIP 10.43.23.53 8042/TCP 4m39s redis ClusterIP 10.43.71.155 6379/TCP 4m39s viewer ClusterIP 10.43.242.203 80/TCP 4m39s vinlab-api ClusterIP 10.43.66.181 8080/TCP 4m39s vinlab-uploader ClusterIP 10.43.61.64 8080/TCP 4m39s vinlab-lb LoadBalancer 10.43.150.40 192.168.1.2 8080:31579/TCP 4m39s ``` # :whale2: Docker ## Prerequisites To deploy using Docker, yes, install `docker` and `docker-compose` first ## Run We've already made it as simple as we can. Just go to the docker directory then run: `./run.sh` file and double check by `docker ps -a` ## Check ``` CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES 153009b8a67a vindr/vinlab-viewer "docker-entrypoint.s…" 59 seconds ago Up 57 seconds 443/tcp, 0.0.0.0:50075->80/tcp vinlab-viewer 3b125d42a158 vindr/vinlab-dashboard "docker-entrypoint.s…" 59 seconds ago Up 55 seconds 0.0.0.0:50076->80/tcp vinlab-dashboard 2fa93511c79a vindr/vinlab-dicom-uploader "./run.sh" 59 seconds ago Up 56 seconds 0.0.0.0:50074->8080/tcp vinlab-uploader 91b58129b11a vindr/vinlab-api "./bin" About a minute ago Up 46 seconds 0.0.0.0:50081->8080/tcp vinlab-api 834ec27d02aa vindr/vinlab-idgen "./bin" About a minute ago Up About a minute 0.0.0.0:50072->8080/tcp vinlab-idgen 446fd95f1dc5 nginx:latest "/docker-entrypoint.…" About a minute ago Up 54 seconds 80/tcp, 0.0.0.0:8080->8080/tcp vinlab-nginx 1163d0f96615 osimis/orthanc "/docker-entrypoint.…" About a minute ago Up About a minute 0.0.0.0:50071->4242/tcp, 0.0.0.0:50070->8042/tcp vinlab-orthanc 06529c0e2267 jboss/keycloak:11.0.2 "/opt/jboss/tools/do…" About a minute ago Up About a minute 8080/tcp, 8443/tcp, 0.0.0.0:50064->9090/tcp vinlab-keycloak 09c3634789a0 rqlite/rqlite:5.10.2 "docker-entrypoint.s…" About a minute ago Up About a minute 0.0.0.0:50069->4001/tcp, 0.0.0.0:50068->4002/tcp vinlab-rqlite 78533dc42a78 docker.elastic.co/elasticsearch/elasticsearch:7.9.2 "/tini -- /usr/local…" About a minute ago Up About a minute 9300/tcp, 0.0.0.0:50067->9200/tcp vinlab-es 5079b39c21d5 redis:latest "docker-entrypoint.s…" About a minute ago Up About a minute 0.0.0.0:50065->6379/tcp vinlab-redis 5494a30718a4 minio/minio "/usr/bin/docker-ent…" About a minute ago Up About a minute 0.0.0.0:50066->9000/tcp vinlab-minio ``` # :paperclip: Relevants ## Keycloak We use Keycloak as an user management system (users, roles, permissions...), please follow [this link](KEYCLOAK.md) to complete the installation But to make it smoother, you now can import through some assets which we provided under the `keycloak_assets` folder. First, create a new `realm` by: Add Realm

Select `vindr-lab-realm-export.json` and hit `Create`. This step will replace steps [Roles](./KEYCLOAK.md#Roles), [Clients](./KEYCLOAK.md#Clients) in [our Keycloak document](KEYCLOAK.md). Then, go to `Clients/vinlab-backend`, choose `Authorization/Settings` tab, click `Import` then open `vindr-lab-backend-authz-config.json` file Add Realm

This step will replace step [Authorizing Permissions](./KEYCLOAK.md#authorizing-permissions) in [our Keycloak document](KEYCLOAK.md). Finally, it seems done however, please create your own user to login the system. Now, you must follow [Users](./KEYCLOAK.md#Users) in our doc. Enjoy! ## MinIO MinIO is being used to store some other things from the API. There is a small setup to do. After launching the whole system, please visit [MinIO url](http://localhost:8080/minio), then login with the keys we provided, feel free to change it to whatever you want but remember that. # :link: Endpoints | Name | Endpoint | | --------- | ------------------------------------- | | Main | `http://localhost:8080` | | Dashboard | `http://localhost:8080/dashboard` | | Backend | `http://localhost:8080/api` | | Orthanc | `http://localhost:8080/dicomweb` | | Keycloak | `http://localhost:8080/auth` | | ES | `http://localhost:8080/elasticsearch` | | MinIO | `http://localhost:8080/minio` | # :pencil2: Note 1. Before using the system, please remember to setup the Keycloak first by [the doc](KEYCLOAK.md) ! 2. As you can see, from the start, you will start at the `http://localhost:8080` endpoint. Normally, the nginx will redirect to `http://localhost:8080/dashboard`. However, the Dashboard endpoint will check what is your current session and permissions, if it is not permitted or not available. The site will redirect to login page of Keycloak. There is one more thing to notice here, when the Dashboard redirect to Keycloak login screen, if you see the error page of Keycloak, please go to the Keycloak enpoint to set it up 3. When you enter the Main site, you may see the 502 Error from Nginx. But do not worry, the system needs a bit of time to warm up and it will ready in some minutes. --- :cookie: Have fun!