Open Hospital Patient Portal

The Patient Portal will allow patients to safely and intentionally (informed consent) access their data from outside the hospital that is using Open Hospital software.

⚠️ The current project is a work in progress (WIP) and it is not ready for production.

Summary

• Components
• Prepare the environment (.env)
• Building
  • 1. build images from sources
  • 2. copy the DB scripts
  • 3. build the ui
• Starting
  • 4. start the app mode with output in the terminal
    • Demo data (optional)
  • 5. available services
• Stopping
• Clean everything
  • Clean the DB (only data)
  • Destroy and recreate the DB
  • Remove all containers and volumes
  • Clean all previous data
• Screenshots
• Developing
  • Create DB script from code
  • Generate migration scripts after changes to API codebase
  • API URLs
  • Develop the ui (React)
• Connector (WIP)
  • 1. Setup using a test db
  • 2. Build from sources
  • 3. Start the connector with the output in the terminal
  • 4. Using a production db

Table of contents generated with markdown-toc

Components

Prepare the environment (.env)

First copy dotenv to .env and set up your variables and locations.

Add in the hosts file the following entry 127.0.0.1 develop.ohpp.local api-develop.ohpp.local matomo-develop.ohpp.local

Export the new .env into variables export $(grep -E 'ENVIRONMENT_NAME|BASE_DOMAIN' .env | xargs)

Create the folder structure

mkdir -p data/$ENVIRONMENT_NAME/database data/$ENVIRONMENT_NAME/database-matomo data/$ENVIRONMENT_NAME/logs/mysql data/$ENVIRONMENT_NAME/logs/mysql-matomo data/$ENVIRONMENT_NAME/logs/nginx data/$ENVIRONMENT_NAME/logs/nginx-matomo data/$ENVIRONMENT_NAME/run data/$ENVIRONMENT_NAME/sql/migrations data/$ENVIRONMENT_NAME/letsencrypt

Building

1. build images from sources

docker compose -f docker-compose-ops.yaml -f docker-compose.yaml build --build-arg ENVIRONMENT_NAME --build-arg BASE_DOMAIN build-api

2. copy the DB scripts

When starting API, they will be used by Flyway to create the actual DB:

cp patient-portal/sql/migrations/* data/$ENVIRONMENT_NAME/sql/migrations

3. build the ui

docker compose -f docker-compose-ops.yaml -f docker-compose.yaml build --build-arg ENVIRONMENT_NAME --build-arg BASE_DOMAIN ui

Starting

4. start the app mode with output in the terminal

Start MySQL database/service (in background):

docker compose -f docker-compose-ops.yaml -f docker-compose.yaml up -d mysql

Start Matomo instance (in background, optional)

# matomo instance (optional, in background)
docker compose -f docker-compose-matomo.yaml up -d

Start the loadbalancer (Traefik), API and UI with output in the terminal. At the first boot, API will create the DB using the scripts copied at Step 2.

# the portal (it will create the DB the first time)
docker compose -f docker-compose-ops.yaml -f docker-compose.yaml up loadbalancer api ui

Demo data (optional)

From another window, with everything started, run:

docker compose -f docker-compose-ops.yaml -f docker-compose.yaml run --rm demo-data

Demo users

USER                USERNAME          PASSWORD           ROLE
------------------------------------------------------------------
admin               admin             admin              ADMIN
hospital admin      [email protected]   hospadmin2023      ADMIN
doctor              [email protected]  doctor2023         DOCTOR
Justin Frederick    701010            justin2023         PATIENT
Anthon Geremy       701011            anthon2023         PATIENT
Veronique Fountain  701012            veronique2023      PATIENT
Cypher Marica       701013            cypher2023         PATIENT
Serena Levinson     701014            serena2023         PATIENT
Bardsley Zenaida    701015            bardsley2023       PATIENT
Graney Almedan      701016            graney2023         PATIENT
Ackman Sammy        701017            ackman2023         PATIENT
Pohlman Margot      701018            pohlman2023        PATIENT
Jeana Bennett       701019            jeana2023          PATIENT
Abramo Oliver       701020            abramo2023         PATIENT

To repeat the import, see Clean the DB only (data)

5. available services

• API will be available at https://api-develop.ohpp.local/swagger-ui/ and http://localhost:18080/swagger-ui/ (use the latter to avoid frontend 'Mixed Content' error)

  • use the first one to connect and allow insecure connections for the UI
  • use the second one to actually call the API

• Patient Portal (UI) will be available at https://develop.ohpp.local/

• Loadbalancer dashboard (traefik) will be available at http://localhost:8080

• Matomo will be available at http://matomo-develop.ohpp.local/ and http://localhost:28080/

• Instructions for Matomo (please read it carefully):

  • connect and configure the first time (installation) from http://develop-matomo.ohpp.local/
  • setup DB and users like in .env file
  • setup super user as root and choose a password (main user, don't forget!)
  • Website name: "Open Hospital Patient Portal"
  • Website URL: http://develop.ohpp.local
  • Untick "Enable Do Not Track support" or (after) in Administration > Privacy > Users opt-out, under “Support Do Not Track preference” disable

Patient Portal (ui) graphics:

• Respiratory Rate: Image by storyset on Freepik
• Heart Rate: Image by rawpixel.com on Freepik
• Glicemy: Image by Freepik
• Weight: Image by vectorjuice on Freepik
• Height: Image by macrovector on Freepik
• Diuresis: Image by rawpixel.com on Freepik
• Diuresis Vol: Image by rawpixel.com on Freepik
• Saturation: Image by macrovector on Freepik
• Temperature: Image by macrovector_official on Freepik
• Blood Pressure: Image by Freepik

Stopping

Interrupt with CTRL-C in the terminal from 4. start the app mode with output in the terminal

docker compose -f docker-compose-matomo.yaml stop
docker compose -f docker-compose-ops.yaml -f docker-compose.yaml stop

Clean everything

Use the one you need most.

Clean the DB (only data)

docker compose -f docker-compose-ops.yaml -f docker-compose.yaml run --rm delete-all-data

...and reload demo data (optional)

# (optional) import demo data in the empty DB 
docker compose -f docker-compose-ops.yaml -f docker-compose.yaml run --rm demo-data

Destroy and recreate the DB

# stop api (loadbalancer, matomo and ui can stay)
docker compose -f docker-compose-ops.yaml -f docker-compose.yaml stop api

# remove mysql container, volumes and folders
docker compose rm --stop --volumes --force mysql
docker volume rm oh-patient-portal_mysql_data
docker volume rm oh-patient-portal_mysql_logs
rm -rf data/$ENVIRONMENT_NAME/database/*

# restart mysql
docker compose -f docker-compose-ops.yaml -f docker-compose.yaml up -d mysql

# restart api (will create the db structure using the already existing scripts at data/$ENVIRONMENT_NAME/sql/migrations)
docker compose -f docker-compose-ops.yaml -f docker-compose.yaml up -d api

...and reload demo data (optional)

# (optional) import demo data in the empty DB 
docker compose -f docker-compose-ops.yaml -f docker-compose.yaml run --rm demo-data

Remove all containers and volumes

docker compose rm --stop --volumes --force
docker compose -f docker-compose-matomo.yaml rm --stop --volumes --force
docker volume rm $(docker volume ls --format '{{.Name}}' | grep ${PWD##*/})

Clean all previous data

rm -rf data/$ENVIRONMENT_NAME

Screenshots

Developing

Create DB script from code (init-api)

Start mysql database/service (in background):

docker compose -f docker-compose-ops.yaml -f docker-compose.yaml up -d mysql

Wait several seconds to finish the startup.

Let Hibernate to create the script in data/sql/migrations folder.

docker compose -f docker-compose-ops.yaml -f docker-compose.yaml run --rm init-api

Interrupt with CTRL-C after finish (don't mind the errors)

In folder data/$ENVIRONMENT_NAME/sql/migrations you will find the V1__ddljpacreate.sql script with all needed tables. When started, API will use the scripts to create the DB.

To repeat the process, destroy and recreate the DB and delete the generated script first:

rm data/$ENVIRONMENT_NAME/sql/migrations/*

Generate migration scripts after changes to API codebase (update-api)

Start mysql database/service (in background):

docker compose -f docker-compose-ops.yaml -f docker-compose.yaml up -d mysql

Wait several seconds to finish the startup.

1. build images from sources the let Hibernate to create the script in data/$ENVIRONMENT_NAME/sql/migrations folder:

docker compose -f docker-compose-ops.yaml -f docker-compose.yaml run --rm update-api

Interrupt with CTRL-C after finish (don't mind the errors)

In folder data/$ENVIRONMENT_NAME/sql/migrations you will find the update.sql script with all new tables and changes, rename it to V2__name.sql.

When started normally, API will use the new script to update the actual DB and track the migration changes with Flyway.

API URLs

Api available at https://develop-api.ohpp.local/ and http://localhost:18080/

Swagger UI available at https://develop-api.ohpp.local/swagger-ui/ and https://develop-api.ohpp.local/v3/api-docs

See also ppoh.postman_collection.json

Develop the ui (React)

Just cd into patient-portal-ui and run (ui available at http://localhost:3000/)

npm install
npm start

Codebase in patient-portal-ui/src

Connector (WIP)

A scaffolding for the connector that will retrieve data from an Open Hospital instance (DB) and feed the Patient Portal DB

It uses openhospital-core and it expects the OPENHOSPITAL_CORE_VERSION to point a tagged version

1. Setup using a test db

First create connector settings based on .env

make

Get db scripts from https://github.com/informatici/openhospital-core.git $OPENHOSPITAL_CORE_VERSION

rm -rf deps
export $(grep OPENHOSPITAL_CORE_VERSION .env | xargs)
mkdir deps && pushd deps && git clone --depth=1 -b v$OPENHOSPITAL_CORE_VERSION https://github.com/informatici/openhospital-core.git && popd

Start the database container with:

docker compose -f docker-compose-connector.yml up -d database

Install demo data with:

docker compose -f docker-compose-connector.yml run oh-database-init

2. Build from sources

docker compose -f docker-compose-connector.yml build connector

3. Start the connector with the output in the terminal

docker compose -f docker-compose-connector.yml up connector

4. Using a production db

You can setup the connector to use an existing Open Hospital DB with real data

In docker-compose-connector.yml, comment:

#    networks:
#      - hospital-net

and uncomment:

    network_mode: host

In .env set up variables in [oh connector] section then run make

Rebuild and start with docker compose -f docker-compose-connector.yml up --build connector