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NOSH ChartingSystem 3

Introduction:

NOSH ChartingSystem is an open-source electronic health record that is specifically designed for outpatient clinical practices. NOSH works equally well as a personal health record due to it's patient-centric framework, but with a user interface that is provider-centric for easy entry of clinical data.

NOSH ChartingSystem 3 is completely redesigned from the ground up. Whereas NOSH 1 and 2 were LAMP stack applications based on PHP/Laravel, NOSH 3 is now completely based on Vue.js and CouchDB/PouchDB for the database. NOSH 3 is also now completely FHIR-based in terms of database structures so that using FHIR API endpoints are native and super quick.  

Key Features:

1. Magic link authentication (no passwords!)

2. Encryption at rest in CouchDB with comdb, which uses TweetNaCl for cryptography.

3. Progressive Web App design with Offline mode in case network goes down.

4. Simple user-specific text snippets and templates (dot phrases).

5. PDF document viewer/editor with PDFJS

6. Graphs and growth charts with Highcharts

7. Care Opportunites

 

Preparation for all installation methods:

Make sure you have a Domain Name registered. You can easily get one through Namecheap for a reasonable price. Make sure you have created a CNAME with a wildcard (*) in addition to 1 A Record. If using Namecheap, under your domain settings, click on Advanced DNS. Below is an example of the Host Records section:

Type Host Value TTL
A Record @ xxx.xxx.xx.x 30 min
CNAME Record * example.com Automatic

The easiest way to install NOSH is through Docker. Follow the instructions below based on your operating system for how to download and install Docker Desktop.

Once Docker is installed, follow the next steps.  

Easy Installation:

sudo wget -qO do-install.sh https://raw.githubusercontent.com/shihjay2/nosh3/main/do-install.sh && sudo chmod +x do-install.sh && sudo bash do-install.sh

or if you have curl installed

sudo curl -o do-install.sh https://raw.githubusercontent.com/shihjay2/nosh3/main/do-install.sh && sudo chmod +x do-install.sh && sudo bash do-install.sh

Detailed Installation:

1. Create a new project directory

mkdir nosh
cd nosh

2. Copy docker-compose.yml from the GitHub repository

wget https://raw.githubusercontent.com/shihjay2/nosh3/master/docker-compose.yml

3. Edit the docker-compose.yml

Replace [email protected] with your email address (example line above)

- "traefik.http.routers.couchdb.rule=Host(`db.example.com`)"
- "traefik.http.routers.couchdb-secure.rule=Host(`db.example.com`)"
- "traefik.http.routers.nosh.rule=Host(`example.com`)"
- "traefik.http.routers.nosh-secure.rule=Host(`example.com`)"

Replace example.com with your domain name (example lines above, leave db. as is)

4. Create the environment configuration file (below is an example for a clinical provider instance - mdNOSH)

cat << EOF > .env
COUCHDB_URL=http://couchdb:5984
COUCHDB_USER=admin
COUCHDB_PASSWORD=my_couchdb_password
COUCHDB_ENCRYPT_PIN=my_couchdb_pin
INSTANCE=local
NOSH_ROLE=provider
AUTH=magic
MAGIC_API_KEY=my_magic_api_key
USPSTF_KEY=my_uspstf_key
UMLS_KEY=my_umls_key
NOSH_DISPLAY="My Name"
[email protected]
EOF

Below is an example for a patient health record (pNOSH)

cat << EOF > .env
COUCHDB_URL=http://couchdb:5984
COUCHDB_USER=admin
COUCHDB_PASSWORD=my_couchdb_password
INSTANCE=digitalocean
NOSH_ROLE=patient
AUTH=magic
MAGIC_API_KEY=my_magic_api_key
USPSTF_KEY=my_uspstf_key
UMLS_KEY=my_umls_key
NOSH_DISPLAY="My Name"
[email protected]
NOSH_DID='did:my_decentralized_identifier'
EOF

or copy env from the GitHub repository and edit the file

wget https://raw.githubusercontent.com/shihjay2/nosh3/master/env

5. Start the multi-container application

docker compose up -d

When the process completes, check that all the containers have successfully started, by running docker compose ps. If they are all working correctly, you should see output similar to the one below:

Network nosh3_default  Created
Container couchdb      Started
Container watchtower   Started
Container nosh         Started
Container router       Started

6. Open your browser and enter

http://localhost/start

or

https://yourdomain.xyz/start

if your machine/droplet's public IP address is associated with a domain name. That's it!

 

Notes

What is in docker-compose.yml?

The docker-compose.yml defines the specific containers that when working together, allow NOSH to be able to fully featured (e.g. a bundle). Below are the different containers and what they do:

1. Traefik - this is the router, specifying the ports and routing to the containers in the bundle

2. CouchDB - this is the NoSQL database that stores all documents

3. NOSH - this is the Node.js based server application

4. Watchtower - this service pulls and applies updates to all Docker Images in the bundle automatically

 

A note on the .env file

Setting Name Description Example
COUCHDB_URL URL of CouchDB instance If using docker-compose, default should be http://127.0.0.1:5984 - Required
COUCHDB_USER Admin user of CouchDB instance Default is 'admin' - Required
COUCHDB_PASSWORD Admin user password for CouchDB Required
COUCHDB_ENCRYPT_PIN 4-digt pin for CouchDB encryption/decryption 1234 - Required. except for digitalocean instance
INSTANCE Type of installation [docker, digitalocean, local] - Required
AUTH Default authentication framework [magic, trustee] - Required
MAGIC_API_KEY API Key for magic.link Used if AUTH=magic
NOSH_ROLE Role of initial user [patient, provider]
NOSH_DISPLAY Display name of initial user "My Name" (enclose in double quotes) - Required
NOSH_EMAIL Email address of inital user [email protected] - Required
UMLS_KEY UMLS API Key for SNOMED, LOINC, RXNorm See Additional API Services for how to get this

Selecting an authenticator

NOSH 3 no longer has it's own built-in authenticator as there are too many barriers to use and manage with having a built-in email/authentication service. Furthermore, NOSH would require some administrator user to fix any accounts with forgotten passwords. If you are a solo provider or a patient hosting their how personal health record, this is just way too much work with increased security risks. To simplify the authenticaton process AND make more secure (no more brute-force attacks), NOSH now uses Magic Links and JSON Web Tokens where a user enters their email address (the email address that is previously registered in NOSH) and a verification email will be sent so that the user can then verify their identity. A JSON Web Token (JWT) is then generated for time-limited, token-based authentication for the application. There are 2 authenticator strategies (see below for instructions). For a personal health record framework, use the Trustee authenticator. For a medical provider/institution record framework, use Magic.

Magic instructions:

1. Set up an account for free by visiting Magic. Click on Start now.

2. Once you are in the dashboard, go to Magic Auth and click on New App. Enter the App Name (NOSH ChartingSystem) and hit Create App.

3. Once you are in the home page for the app, scroll down to API Keys and copy the PUBISHABLE API KEY value. This API Key will be usee to interact with Magic's APIs as specified in the env file

 

Trustee instructions:

To be determined...

 

Additional API Services

National Library of Medicine UMLS Terminology Services - this is to allow search queries for SNOMED CT LOINC, and RXNorm definitions.

1. Set up an account here

2. Edit your profile and click on Generate new API Key. Copy and enter this in the .env file

 

US Preventive Services Task Force - this provides Care Opportunties guidance based on USPSTF guidelines

 

Endpoints

For all instances besides patient NOSH on DigitalOcean App Platform:

Browser:

https://yourdomain.xyz/start

API:

https://yourdomain.xyz/fhir/api/v1/Patient
https://yourdomain.xyz/fhir/api/v1/Condition
https://yourdomain.xyz/fhir/api/v1/MedicationStatement
https://yourdomain.xyz/fhir/api/v1/AllergyIntolerance
https://yourdomain.xyz/fhir/api/v1/Immunization

 

For patient NOSH on DigitalOcean App Platform:

Browser:

https://nosh-app-xxx.ondigitalocean.app/app/chart/nosh_xxx

API:

https://nosh-app-xxx.ondigitalocean.app/fhir/api/nosh_xxx/Patient
https://nosh-app-xxx.ondigitalocean.app/fhir/api/nosh_xxx/Condition
https://nosh-app-xxx.ondigitalocean.app/fhir/api/nosh_xxx/MedicationStatement
https://nosh-app-xxx.ondigitalocean.app/fhir/api/nosh_xxx/AllergyIntolerance
https://nosh-app-xxx.ondigitalocean.app/fhir/api/nosh_xxx/Immunization

where nosh_xxx refers to the patient ID.

 

For MD NOSH, there is a dashboard endpoint

https://yourdomain.xyz/app/dashboard

 

API

To access API endpoints as listed above, client will need to present a valid Bearer Token (JWT) in the Authentication header that has been passed during successful authentication for the user.

If the JWT presented is expired, the response will be:

{"code":"ERR_JWT_EXPIRED","name":"JWTExpired","claim":"exp","reason":"check_failed"}

or if the JWT doesn't match access permissions or the GNAP authorization server is down:

{"error": "locations and actions do not match"},
{"error": "access token invalid"},
{"error": "unable to introspect"},
{"error": "unable to reach GNAP AS"}

and the client should redirect to the authentication workflow to present a new JWT.

Below examples are where

  • nosh_yyy is the patient ID
  • xxx is ID given by DigitalOcean app platform
  • zzz is the ID of the resource

Read

GET https://nosh-app-xxx.ondigitalocean.app/fhir/api/nosh_yyy/Condition/zzz

Read all

GET https://nosh-app-xxx.ondigitalocean.app/fhir/api/nosh_yyy/Condition

Create

POST https://nosh-app-xxx.ondigitalocean.app/fhir/api/nosh_yyy/Condition

Update

PUT https://nosh-app-xxx.ondigitalocean.app/fhir/api/nosh_yyy/Condition/zzz

Delete

DELETE https://nosh-app-xxx.ondigitalocean.app/fhir/api/nosh_yyy/Condition/zzz

Example GNAP access declarations

Below examples are where

  • nosh_yyy is the patient ID
  • xxx is ID given by DigitalOcean app platform
{
  "type": "Timeline",
  "actions": ["read"],
  "locations": ["https://nosh-app-xxx.ondigitalocean.app/api/nosh_yyy/Timeline"],
  "purpose": "Clinical - Routine"
},
{
  "type": "Markdown",
  "actions": ["write"],
  "locations": ["https://nosh-app-xxx.ondigitalocean.app/api/nosh_yyy/md"],
  "purpose": "Clinical - Routine"
},
{
  "type": "App",
  "actions": ["read, write"],
  "locations": ["https://nosh-app-xxx.ondigitalocean.app/app/chart/nosh_yyy"],
  "purpose": "Clinical - Routine"
},
{
  "type": "Condition",
  "actions": ["read, write, delete"],
  "locations": ["https://nosh-app-xxx.ondigitalocean.app/fhir/api/nosh_yyy/Condition"],
  "purpose": "Clinical - Routine"
}

Contributing To NOSH ChartingSystem

All issues and pull requests should be filed on the shihjay2/nosh3 repository.  
 

License

NOSH ChartingSystem is open-sourced software licensed under the GNU Affero General Public License

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