Repository for the free community edition of the sandbox
This document outlines downloading and installing the Logica Sandbox Community Edition and getting it running. It is broken into four sections. An Overview section detailing the prerequisites to getting the system running as well as three installation sections… one each for MacOS, Linux, and Windows installations. Versions of the operating systems used and tested and the versions of any tools will be explicitly stated where appropriate. We recognize tools change over time and the content of this document may be out-of-date by the time you read this. We hope to give you enough information to adjust to new versions as needed. Some of the information in this document may seem remedial but we are including it anyway for those who may not be as familiar with the command line and other tools involved in the setup.
The community edition is currently at HAPI 5.2.0.
WARNING: Follow these instructions VERY carefully. If you miss a step… you will likely get pages and pages of errors.
Running the sandbox locally on any OS requires the following:
- git
- Docker
- MySQL container
- Keycloak server container
- Sandbox containers
- FHIR server containers
- Application containers
In the current configuration there will be a total of 11 containers. These containers listen on specific network TCP ports as described in the next section.
The sandbox makes use of the following TCP ports and may conflict with services already running on your system:
- 3000 - EHR Simulator
- 3001 - http (user interface) server
- 3306 - MySQL 5.7 database server
- 8060 - OAuth server
- 8070 - FHIR R4 server
- 8071 - FHIR R5 server
- 8078 - FHIR DSTU2 server
- 8079 - FHIR STU3 server
- 8080 - Keycloak authentication server
- 8086 - Bilirubin Risk Chart sample app
- 8090 - Static content server
- 8096 - Patient Data Manager sample app
- 12000 - Sandbox Manager server
Stop any current services running on these ports before running the containers. A script to check for anything listening on these ports (check-ports.sh and check-ports.bat) is included in the community edition. Most conflicts will occur when a developer has something running on one of these ports. For example, if you have a MySQL server running you will likely get a conflict on port 3306.
The sandbox also uses a number of internal redirects built into the user interface requiring the following addition to the hosts file (/etc/hosts on macOS and linux):
127.0.0.1 keycloak
127.0.0.1 sandbox-mysql
127.0.0.1 sandbox-manager-api
127.0.0.1 sandbox
127.0.0.1 dstu2
127.0.0.1 stu3
127.0.0.1 r4
127.0.0.1 r5
127.0.0.1 static-content
This tells the web browser on the local machine that, for example, “http://r4/” will be found listening on the local machine… assuming the container is running.
OSX Install (tested under macOS Catalina 10.15.7):
There are two options to install Docker Desktop. Either install it by going to the website, downloading it, and running the dmg file… or install “homebrew” and then use homebrew to install it. For the minimum… just install Docker Desktop. Homebrew is a package manager for installing all sorts of tools and utilities… but you may not want it. If docker is already installed please skip ahead to setting it up to give the containers enough memory.
NOTE: If you want to install docker using homebrew you’ll find installation instructions in the appendix.
Browse to: https://www.docker.com/products/docker-desktop Download and run the installer
Run the Docker Desktop app and set the memory allocation requirements by clicking on the gear in the top right corner of the main dialog… then Resources… then ADVANCED:
Set Memory to a minimum of 8.00 GB:
Now instances will get the memory they require to run correctly. If you are running into memory issues with the containers this is most likely the culprit.
The community edition was tested on Docker Desktop v3.1.0 and docker compose version 1.27.4. The docker version may be checked using the About menu option. The docker compose version may be checked using the command docker compose -v.
- Clone this project
git clone https://github.com/logicahealth/sandbox-community-edition.git
- Change to the new directory
cd sandbox-community-edition
Make sure there are no port conflicts by running check-ports.sh. In the same terminal window or another terminal window run the following:
docker compose upThis will start the services for the sandbox. At first, you will see something like the following
Creating network "sandbox-community-edition_default" with the default driver
Creating sandbox-community-edition_sandbox-mysql_1 ... done
Creating sandbox-community-edition_keycloak_1 ... done
Creating sandbox-community-edition_bilirubin-risk-chart_1 ... done
Creating sandbox-community-edition_static-content_1 ... done
Creating sandbox-community-edition_patient-data-manager_1 ... doneThe output will stay unchanged while the database is being seeded. After the database seeding is completed, you will see other services that depend on the database start up. Images for the containers will be downloaded from docker hub. This process may take a while the first time and produce a lot of logging output. Wait until the logging output stops.
To check if things are running open another terminal window and run:
docker compose psYou should see output like this showing the running instances and the ports they are listening on. All the states should say “Up”:
Name Command State Ports
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
sandbox-community-edition_bilirubin-risk-chart_1 docker-entrypoint.sh npm r ... Up 0.0.0.0:8086->8086/tcp
sandbox-community-edition_dstu2_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8078->8078/tcp
sandbox-community-edition_keycloak_1 /opt/jboss/tools/docker-en ... Up 0.0.0.0:8080->8080/tcp, 8443/tcp
sandbox-community-edition_patient-data-manager_1 docker-entrypoint.sh npm r ... Up 0.0.0.0:8096->8096/tcp
sandbox-community-edition_r4_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8070->8070/tcp
sandbox-community-edition_r5_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8071->8071/tcp
sandbox-community-edition_sandbox-manager-api_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:12000->12000/tcp
sandbox-community-edition_sandbox-mysql_1 docker-entrypoint.sh mysqld Up (healthy) 0.0.0.0:3306->3306/tcp, 33060/tcp
sandbox-community-edition_sandbox_1 /bin/sh -c sh start.sh Up 0.0.0.0:3000->3000/tcp, 0.0.0.0:3001->3001/tcp, 0.0.0.0:8060->8060/tcp
sandbox-community-edition_static-content_1 /docker-entrypoint.sh ngin ... Up 0.0.0.0:8090->80/tcp
sandbox-community-edition_stu3_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8079->8079/tcp
In a web browser (preferably Chrome) go to http://sandbox:3001. You should see a Keycloak login screen like the following. Click on register and fill in your details.
You will be able to use this username and password to login to the sandbox from now on whenever you run it.
NOTE: If you ever lose or forget this password, look in the appendices to find out how to reset it. After logging in, you should see the following screen with no sandboxes. Click the NEW SANDBOX button to create a sandbox.
After you have created a sandbox you will see it listed:
To start the services
docker compose upIn another terminal window show the running services
docker compose psRun the check-ports.sh shell script to see the services listening on ports. If you get an error saying permission is denied, then run the command chmod +x check-ports.sh.
com.docke 811 gopalmenon 91u IPv6 0xf1b6ae35fee19aa7 0t0 TCP *:3000 (LISTEN)
com.docke 811 gopalmenon 92u IPv6 0xf1b6ae35fee18de7 0t0 TCP *:3001 (LISTEN)
com.docke 811 gopalmenon 82u IPv6 0xf1b6ae3606694aa7 0t0 TCP *:3306 (LISTEN)
com.docke 811 gopalmenon 94u IPv6 0xf1b6ae35fee19447 0t0 TCP *:8060 (LISTEN)
com.docke 811 gopalmenon 89u IPv6 0xf1b6ae3608c46447 0t0 TCP *:8070 (LISTEN)
com.docke 811 gopalmenon 88u IPv6 0xf1b6ae3608c46aa7 0t0 TCP *:8078 (LISTEN)
com.docke 811 gopalmenon 87u IPv6 0xf1b6ae35fd26cde7 0t0 TCP *:8079 (LISTEN)
com.docke 811 gopalmenon 85u IPv6 0xf1b6ae360bfaeaa7 0t0 TCP *:8080 (LISTEN)
com.docke 811 gopalmenon 83u IPv6 0xf1b6ae3606695767 0t0 TCP *:8086 (LISTEN)
com.docke 811 gopalmenon 84u IPv6 0xf1b6ae3609554767 0t0 TCP *:8090 (LISTEN)
com.docke 811 gopalmenon 81u IPv6 0xf1b6ae3623986aa7 0t0 TCP *:8096 (LISTEN)
com.docke 811 gopalmenon 90u IPv6 0xf1b6ae3608c45de7 0t0 TCP *:12000 (LISTEN)
Use the following command to stop the services.
docker compose stopYou will see something like this as the containers are stopped:
Stopping sandbox-community-edition_sandbox_1 ... done
Stopping sandbox-community-edition_sandbox-manager-api_1 ... done
Stopping sandbox-community-edition_r4_1 ... done
Stopping sandbox-community-edition_stu3_1 ... done
Stopping sandbox-community-edition_r5_1 ... done
Stopping sandbox-community-edition_dstu2_1 ... done
Stopping sandbox-community-edition_keycloak_1 ... done
Stopping sandbox-community-edition_patient-data-manager_1 ... done
Stopping sandbox-community-edition_static-content_1 ... done
Stopping sandbox-community-edition_bilirubin-risk-chart_1 ... done
Stopping sandbox-community-edition_sandbox-mysql_1 ... done
If you run the check-ports.sh shell script… you will see no output once the containers are stopped.
Running docker compose ps will show something like the following:
Name Command State Ports
----------------------------------------------------------------------------------------------------
sandbox-community-edition_bilirubin-risk-chart_1 docker-entrypoint.sh npm r ... Exit 0
sandbox-community-edition_dstu2_1 sh -c java $JAVA_OPTS -jar ... Exit 137
sandbox-community-edition_keycloak_1 /opt/jboss/tools/docker-en ... Exit 0
sandbox-community-edition_patient-data-manager_1 docker-entrypoint.sh npm r ... Exit 0
sandbox-community-edition_r4_1 sh -c java $JAVA_OPTS -jar ... Exit 137
sandbox-community-edition_r5_1 sh -c java $JAVA_OPTS -jar ... Exit 137
sandbox-community-edition_sandbox-manager-api_1 sh -c java $JAVA_OPTS -jar ... Exit 137
sandbox-community-edition_sandbox-mysql_1 docker-entrypoint.sh mysqld Exit 0
sandbox-community-edition_sandbox_1 /bin/sh -c sh start.sh Exit 137
sandbox-community-edition_static-content_1 /docker-entrypoint.sh ngin ... Exit 0
sandbox-community-edition_stu3_1 sh -c java $JAVA_OPTS -jar ... Exit 137
Install Docker for your distribution of Linux. The community edition was tested on docker compose version 1.26.0. The docker compose version may be checked using the command docker compose -v.
-
Clone this project
git clone https://github.com/logicahealth/sandbox-community-edition.git
-
Change to the new directory
cd sandbox-community-edition -
Add the following rows to the file /etc/hosts using a text editor
127.0.0.1 keycloak 127.0.0.1 sandbox-mysql 127.0.0.1 sandbox-manager-api 127.0.0.1 sandbox 127.0.0.1 dstu2 127.0.0.1 stu3 127.0.0.1 r4 127.0.0.1 r5 127.0.0.1 static-contentHere is an example of using nano to edit
/etc/hostssudo nano /etc/hosts
-
Start the database seeding by running the following command
sudo docker compose up -d sandbox-mysql
-
Run the following command to see a list of docker processes that are running.
sudo docker compose ps
You should see something similar to the screen print below showing the database starting up.
Name Command State Ports ----------------------------------------------------------------------------------------------------------------------------------- sandbox-community-edition_sandbox-mysql_1 docker-entrypoint.sh mysqld Up (health: starting) 0.0.0.0:3306->3306/tcp, 33060/tcpRun the command to see the status of the process. Before changing state to healthy, the process status will be as shown below.
Name Command State Ports ----------------------------------------------------------------------------------------------------------------------------------- sandbox-community-edition_sandbox-mysql_1 docker-entrypoint.sh mysqld Up (unhealthy) 0.0.0.0:3306->3306/tcp, 33060/tcpWait until the process shows up as healthy as shown below. You will need to check by running the command to list out the docker processes.
Name Command State Ports ----------------------------------------------------------------------------------------------------------------------------------- sandbox-community-edition_sandbox-mysql_1 docker-entrypoint.sh mysqld Up (healthy) 0.0.0.0:3306->3306/tcp, 33060/tcp -
Run the following command to bring up the rest of the processes for the sandbox.
sudo docker compose up -
List out the processes and you should see something like the following.
Name Command State Ports ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- sandbox-community-edition_bilirubin-risk-chart_1 docker-entrypoint.sh npm r ... Up 0.0.0.0:8086->8086/tcp sandbox-community-edition_dstu2_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8078->8078/tcp sandbox-community-edition_keycloak_1 /opt/jboss/tools/docker-en ... Up 0.0.0.0:8080->8080/tcp, 8443/tcp sandbox-community-edition_patient-data-manager_1 docker-entrypoint.sh npm r ... Up 0.0.0.0:8096->8096/tcp sandbox-community-edition_r4_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8070->8070/tcp sandbox-community-edition_r5_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8071->8071/tcp sandbox-community-edition_sandbox-manager-api_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:12000->12000/tcp sandbox-community-edition_sandbox-mysql_1 docker-entrypoint.sh mysqld Up (healthy) 0.0.0.0:3306->3306/tcp, 33060/tcp sandbox-community-edition_sandbox_1 /bin/sh -c sh start.sh Up 0.0.0.0:3000->3000/tcp, 0.0.0.0:3001->3001/tcp, 0.0.0.0:8060->8060/tcp sandbox-community-edition_static-content_1 /docker-entrypoint.sh ngin ... Up 0.0.0.0:8090->80/tcp sandbox-community-edition_stu3_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8079->8079/tcp -
Go to http://sandbox:3001 on a browser to go to the sandbox. You will need to register the first time you are there. Save your user and password information.
-
To stop the sandbox
sudo docker compose stop
- After the install, run the following command to start the sandbox
sudo docker compose up - Run this to stop the sandbox
sudo docker compose stop
Windows Install (tested under Windows 10):
Browse to: https://www.docker.com/products/docker-desktop Download and run the installer
The community edition was tested on Docker Desktop v3.1.0 and docker compose version 1.27.4. The docker version may be checked using the About menu option. The docker compose version may be checked using the command docker compose -v.
The command line instructions below should be executed in a console with administrative privileges ("Run as Administrator").
-
Clone this project
git clone https://github.com/logicahealth/sandbox-community-edition.git -
Change to the new directory
cd sandbox-community-edition -
Add the following rows to the file
C:\Windows\System32\drivers\etc\hostsusing a text editor with administrative priviles127.0.0.1 keycloak 127.0.0.1 sandbox-mysql 127.0.0.1 sandbox-manager-api 127.0.0.1 sandbox 127.0.0.1 dstu2 127.0.0.1 stu3 127.0.0.1 r4 127.0.0.1 r5 127.0.0.1 static-contentNote: Restart Docker Desktop after saving the changes above to make sure that it picks up the host substitutions.
-
Start the database seeding by running the following command
docker compose up -d sandbox-mysql -
Run the following command to see a list of docker processes that are running.
docker compose psYou should see something similar to the screen print below showing the database starting up.
Name Command State Ports ----------------------------------------------------------------------------------------------------------------------------------- sandbox-community-edition_sandbox-mysql_1 docker-entrypoint.sh mysqld Up (health: starting) 0.0.0.0:3306->3306/tcp, 33060/tcpRun the command to see the status of the process. Before changing state to healthy, the process status will be as shown below.
Name Command State Ports ----------------------------------------------------------------------------------------------------------------------------------- sandbox-community-edition_sandbox-mysql_1 docker-entrypoint.sh mysqld Up (unhealthy) 0.0.0.0:3306->3306/tcp, 33060/tcpWait until the process shows up as healthy as shown below. You will need to check by running the command to list out the docker processes.
Name Command State Ports ----------------------------------------------------------------------------------------------------------------------------------- sandbox-community-edition_sandbox-mysql_1 docker-entrypoint.sh mysqld Up (healthy) 0.0.0.0:3306->3306/tcp, 33060/tcp -
Run the following command to bring up the rest of the processes for the sandbox.
docker compose upNote: Wait a couple minutes for the containers to stabilize before proceeding (when they stop producing startup output in the cosole log)
-
List out the processes and you should see something like the following.
Name Command State Ports ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- sandbox-community-edition_bilirubin-risk-chart_1 docker-entrypoint.sh npm r ... Up 0.0.0.0:8086->8086/tcp sandbox-community-edition_dstu2_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8078->8078/tcp sandbox-community-edition_keycloak_1 /opt/jboss/tools/docker-en ... Up 0.0.0.0:8080->8080/tcp, 8443/tcp sandbox-community-edition_patient-data-manager_1 docker-entrypoint.sh npm r ... Up 0.0.0.0:8096->8096/tcp sandbox-community-edition_r4_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8070->8070/tcp sandbox-community-edition_r5_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8071->8071/tcp sandbox-community-edition_sandbox-manager-api_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:12000->12000/tcp sandbox-community-edition_sandbox-mysql_1 docker-entrypoint.sh mysqld Up (healthy) 0.0.0.0:3306->3306/tcp, 33060/tcp sandbox-community-edition_sandbox_1 /bin/sh -c sh start.sh Up 0.0.0.0:3000->3000/tcp, 0.0.0.0:3001->3001/tcp, 0.0.0.0:8060->8060/tcp sandbox-community-edition_static-content_1 /docker-entrypoint.sh ngin ... Up 0.0.0.0:8090->80/tcp sandbox-community-edition_stu3_1 sh -c java $JAVA_OPTS -jar ... Up 0.0.0.0:8079->8079/tcp -
Go to http://sandbox:3001 on a browser to go to the sandbox. You will need to register the first time you are there. Save your user and password information.
-
To stop the sandbox
docker compose stop
- After the install, run the following command to start the sandbox
docker compose up - Run this to stop the sandbox
docker compose stop
TODO
If you do not remember your username or password, you will need to go to the Keycloak server and login as an administrator. Go to http://keycloak:8080 on a browser and you will see the following screen.
Click on Administration Console and login with user admin and password admin.
Now click on Users and View all users.
Click on the ID of your user and you will be able to see the username you need to login.
To reset your password, go to the Credentials tab.
Key in your new preferred password into Password and Password Confirmation. Toggle the Temporary setting to OFF. Click on Reset Password and press Reset password on the confirmation screen that pops up asking if you are sure. Now you can logoff as Keycloak administrator by clicking on the Admin drop down on the top right.
Go http://sandbox:3001 and login with your new password.
TODO
Homebrew is a package manager for macOS and Linux. It turns out macOS comes with a minimal and fairly outdated set of command line tools… and no easy way to update and manage new versions. This provides a stable enough base for macOS. However, anyone who lives/eats/breathes command line… or is curious about all things UNIX… will want more. Installing Homebrew gives easy access to thousands of command line tools… and also regular macOS applications… like Docker Desktop.
For information about Homebrew browse to https://brew.sh
To just skip to the chase and get it done, open a terminal and cut and paste the following commands and hit return:
This command will install homebrew:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"This command will install docker:
brew install --cask docker-toolboxThis command will install a VERY handy tool called curl:
brew install curlIf you are running into memory issues with the containers you need to double check you have allocated enough memory in Docker Desktop for the containers.