infrastructure

Infrastructure as Code

We treat Infrastructure as Code. Here code is used to deploy Consent2Share application in Docker containers.

Prerequisites

• Docker
• Docker Compose

Deployment

Two server deployment options are provided to run Consent2Share application on Linux. Here we use CentOS 7.X as an example to describe the setups.

Consent2Share Docker images will be downloaded from Dockerhub BHITS public registry.

Two Servers Setup

This option is to run Consent2Share services, UIs on an application server and databases on a separated database server.

Configure Database Server

• Get the c2s_config.sh file and run the file. curl https://raw.githubusercontent.com/bhits/consent2share/master/infrastructure/scripts/c2s_config.sh > c2s_config.sh sh c2s_config.sh twoServerDbConfig

• If SELinux is enabled, run the command below to assign the relevant SELinux policy type as a workaround to prevent issues while mounting volumes to the containers from /usr/local/java

  chcon -Rt svirt_sandbox_file_t /usr/local/java

• Re-login to the server in order for the file c2s_env.sh to run automatically during the login

  • Verify by checking any variable mentioned in the file
    Example: echo ${C2S_BASE_PATH} should show the value set in the file

Configure Application Server

• Get the c2s_config.sh file and run the file. curl https://raw.githubusercontent.com/bhits/consent2share/master/infrastructure/scripts/c2s_config.sh > c2s_config.sh sh c2s_config.sh twoServerAppConfig

• If SELinux is enabled, run the command below to assign the relevant SELinux policy type as a workaround to prevent issues while mounting volumes to the containers from /usr/local/java

  chcon -Rt svirt_sandbox_file_t /usr/local/java

• Edge-server security:

  • Create/Obtain a valid SSL certificate

  • Export the public and private keys from the SSL certificate to a JKS formatted keystore file named edge-server.keystore

  • upload the edge-server.keystore file into /usr/local/java/keystore folder

  • Add the following in the /usr/local/java/C2S_PROPS/c2s-config-data/edge-server.yml file.

    spring.profiles: your_app_Server_specific_profile
    server:
      ssl:
        key-store: /java/keystore/edge-server.keystore
        key-store-password: "keystore password"

  • Modify the ENV_APP_PROFILE= your_app_Server_specific_profile in twoServerAppConfig() function in the /etc/profile.d/c2s_env.sh file.

• Modify the following configuration files

  • Set edge server, config server, SMTP variables to the server specific values in the ` file in ‘/etc/profile.d/c2s_env.sh’ folder.

  • Re-login to the server in order for the file c2s_env.sh to run automatically during the login

  • Verify by checking any variable mentioned in the file
    Example: echo ${C2S_BASE_PATH} should show the value set in the file

Compose Containers on Database Server

• Run docker-compose up -d from the usr/local/java folder to start up all databases

• Run docker ps -a to verify all the containers are up running except data-only containers

Compose Containers on Application Server

• Run docker-compose up -d from the usr/local/java folder to start up all Consent2Share services, UIs

• Run docker ps -a to verify all the containers are up running

Populate sample providers

• Login to docker pls database container docker ps | grep pls-db docker exec -it <<pls-db container id>> bash

• Run pls_db_sample.sql from container directory /java/C2S_PROPS/pls. cd /java/C2S_PROPS/pls mysql -p

  enter root pwd(default is admin)

  source pls_db_sample.sql

Development

The docker compose file in Development folder is designed to run Consent2Share application on developer machine. Compared to the deployment one-server option, this one doesn't set any memory constraints on Docker containers because developer's machine may has limited memory on docker-machine. Also, this one uses default c2s-config-data without any addtional setup.

Resolve Deployment Error

If you encounter an error in the deployment:
`ERROR: for dss.c2s.com UnixHTTPConnectionPool(host='localhost', port=None): Read timed out. (read timeout=60)

Follow the steps below to resolve the error:

1. Restart the Docker service: sudo service docker restart

2. Check for all Docker containers that are running: docker ps -a
   If you notice any containers that are exited or down except the data-only containers based on busybox image, follow the next steps

3. For instance, if mysql containers are not running
   a. Go to /usr/local/java and then remove all containers : docker-compose down
   b. Go to /usr/local/java and then remove mysql folder : sudo rm -rf mysql/

4. Start up all containers: Re-run from /usr/local/java folder: docker-compose up -d

UI Urls

• Consent2Share Staff Admin UI: https://<application_server>/staff-ui

  • By default, Consent2Share comes with a staff admin user

  • Login to Consent2Share Admin UI as an admin using username [email protected] and password AAA#aaa1 to create a user patient account

• Consent2Share Patient Portal UI: https://<application_server>/c2s-ui

Scripts

build-all.sh

This script is used to build all consent2share APIs' docker images on local machine.

After clone the this repository under the same parent folder as other Consent2Share project repositories. Run build-all.sh in git bash or terminal/command line after navigate to scripts folder.

Run docker images to check all created docker images.

Reference

For more detail, please refer to README.md file in each repository for Consent2Share.

Report Issues

Please use GitHub Issues page to report issues.