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RubinLab / epad-dist

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Distribution files and configuration automation tool for ePad

ePad is designed in a modular structure which runs six sub-modules (docker containers) which can be plugged and unplugged for specific usecases. Each sub-module has its own setting files that can be edited. This tool enables users to use one yml file to populate all configuration files with specific setting for their system.

System Requirements

Ram: Min 4gb 
git needs to be installed
docker needs to be installed
docker-compose needs to be installed

Update the epad.yml file according to your needs and run ./configure_epad.sh PATH YML_PATH for generating the configuration files and docker-compose.yml

epad.yml file

host: YOUR_HOSTNAME                     # put your public hostname/ip or local sharing name for macs
mode: lite
config: environment                     # defines if settings will be written in physical files or to environment variables 
cache:                                  # cahce section added in v0.4 version
  size: "10g"
  inactivetime: "60mb"
compression:                            # compression section added in v0.4 version
  minsize: "20"
keycloak:
  mode: build                           # possible modes are build, image, external*
  dockerfiledir: ".\/keycloak"
  user: YOUR_KEYCLOAK_ADMIN_USER        # define your keycloak admin username (admin user can manage realm and add/remove users)
  password: YOUR_KEYCLOAK_ADMIN_PASS    # define your keycloak admin password 
  email: YOUR_KEYCLOAK_ADMIN_EMAIL      # define your keycloak admin email
  port: 8899
  loc: "keycloak"                       # defines the nginx location to be served
couchdb:
  mode: image
  image: "ibmcom\/couchdb3:latest"      # in v0.4 version default value switched from latest to ibmcom/couchdb3 
  user: YOUR_COUCH_ADMIN_USER           # added in v0.4 version define your couchdb admin username
  password: YOUR_COUCH_ADMIN_PASS       # added in v0.4 version efine your couchdb admin password
  port: 8888
  dblocation: "..\/couchdbloc"          # define relative location to where you want to put the couchdb files
dicomweb:
  mode: build
  dockerfiledir: ".\/dicomweb-server"
  port: 8090
  dbname: chronicle
  log: true
  auth: none
  loc: "pacs"
  branch: "master"                      # defines the branch which will be pulled from guthub for dicomweb project.
epadlite:
  mode: build
  dockerfiledir: ".\/epadlite"
  port: 8080
  dbname: epadlite
  log: true
  https: false
  auth: auth
  loc: "api"
  branch: "master"                      # defines the branch which will be pulled from guthub for epadlite project.
epadjs:
  mode: build
  dockerfiledir: ".\/epadjs"
  port: 80
  branch: "master"                      # defines the branch which will be pulled from guthub for epadjs project.
mariadb:
  mode: image
  image: latest
  dbname: epaddb
  user: YOUR_DB_USER                      # define your mariadb username
  pass: YOUR_DB_PASS                      # define your mariadb password
  rootpass: YOUR_DB_ROOT_PASS             # define your mariadb root password
  port: 3306
  log: false
  backuploc: ".\/epaddb_nodata.sql"
  dblocation: "..\/mariadbloc"            # define relative location to where you want to put the mariadb files

*Possible modes for each module are build, image, external

  • build mode requires dockerfiledir to fnd to Dockerfile,
  • image mode requires a image value to specify the image tag,
  • external mode requires a uri value to put in the configuration files and excludes component from docker-compose and nginx configuration/

The command ./configure_epad.sh ../epad_lite_dist ./epad.yml will generate a file structure like following under ../epad_lite_dist

../epad_lite_dist
├── dicomweb-server
│   ├── Dockerfile
├── docker-compose.yml                    # docker-compose file
├── epadjs
│   ├── Dockerfile
├── epadlite
│   ├── Dockerfile
├── keycloak
│   ├── Dockerfile
├── nginx.conf                            # nginx configuration file
├── production_dicomweb.js                # dicomweb-server settings
├── production_keycloak.json              # ePad frontend's keycloak setting
├── production_epadjs.json                # epad frontend settings
├── production_epadlite.js                # ePad backend settings
├── production_epadlite_auth.json         # ePad backend's keycloak setting
├── production_epadlite_dicomweb.json     # ePad backend's dicomweb setting
├── realm-export.json                     # keycloak realm file for dicomweb authentication
├── realm-export_epad.json                # keycloak realm file for ePad authentication
└── terms.ftl                             # terms and conditions for ePad

You can then start ePad with docker-compose up -d in ../epad_lite_dist directory. ePad will be served from the port 80 of the host address specified in epad.yml file

After starting ePad by using docker-compose up -d you will have additional folders for plugins and a tmp folder which will be used to export and import keycoak users. These folder can be found in the same folder where you see epad-dist folder.

Please change the folder rights to public for tmp and pluginData folders. (to change folder rights you can use: chmod 777 tmp )

Installation Script:

Starting from v0.4 version epad-dist folder contains epad_manage.sh script. This script is designed to make ePad installation, update, start, stop, export/import keycloak users easier. IMPORTANT: If your ePad holds crucial patient data don't use epad_manage.sh script to update your ePad since the epad_manage.sh script is still in the experimental phase. You can download the script and the extensive guide from epad.stanford.edu webpage under download section.

Notes: