pocket-fhir

All of this is based on the fabulous PocketBase, but designed for FHIR®

Local Run

• Generate: $ ./generate_local.sh - this will also start the server the first time
• After that, you can just do: $ ./pocketfhir serve

Local-Docker Branch

• Regenerate: $ ./build/generate.sh - can still be run as the executable
• Generating will create two directories pb_data/ and pb_migrations/, which normally stay in the primary directory, but for this case, we copy them into the data/ directory
• You should then be able to run: $ docker-compose up --build
• This will create a client, and while the command line says that it is serving at:

Server started at http://0.0.0.0:8090
pocketfhir-caddy | ├─ REST API: http://0.0.0.0:8090/api/
pocketfhir-caddy | └─ Admin UI: http://0.0.0.0:8090/_/

• It's actually located at https://localhost
• Admin UI: [https://localhost/_/]
• If you want to upload some ValueSets and things to it using dart, in the dart directory, you can use the upload_all.dart file. You'll want to put in your username and password to make it work. Notice in this case, we also used the https://localhost for the PocketBase instance
• when you're done, use $ docker-compose down

GCP

• Based on Rody Davis's version
• Go to GCP, make sure you have Cloud Storage
• Create a new bucket
• Give it a name, click continue
• Region - whatever your preference, continue
• Standard class, continue
• Control Access - whatever the default is, continue
• Data Protection - default
• Create
• run the generate script $ ./build/generate.sh
• Copy the 2 folders (pb_data/ and pb_migrations/) to the storage bucket (you can just drag and drop)
• Complete the gcloud.sh file with appropriate values
• Run $ ./gcloud.sh - this should build and upload your docker container with Caddy to cloud run
• Go back into cloud run and select the new service
• Click Edit & Deploy New Revision
• Click Volume Tab
• Add Volume
• Volume Type -> Cloud Storage Bucket
• Volume name -> remote-storage (or whatever you want)
• Bucket -> the bucket you created that contains your folders
• Ensure you DO NOT check Read-only
• Click Container(s) Tab
• Partway down select Volume Mounts
• Name1 -> remote-storage (matches above)
• Mount path 1 -> /cloud/storage
• +Add Health Check
• Select health check type -> Liveness check
• Select probe type -> HTTP
• Path -> /api/health
• Initial delay -> 10
• Period -> 240
• Failure threshold -> 2
• Timeout -> 240
• Submit
• TODO

Fly.io

• Generate locally: $ ./build/generate.sh
• You need a Fly.io account (obviously) if you don't already have one
• Install on your local system
  • macOS: brew install superfly/tap/flyctl
  • Linux: curl -L https://fly.io/install.sh | sh
• CLI login: $ flyctl auth login
• Make sure you have dotenv-cli installed: $ npm install -g dotenv-cli
• Create app: $ flyctl apps create pocketfhir --org mayjuun
• Create and mount the volume: $ flyctl volumes create pb_data --size=1 --app pocketfhir --region=atl
• Set secrets: $ flyctl secrets set PB_ENCRYPTION_KEY=y5E69SptuHgUzspVNipzjl9ZmsKVPkIH --app pocketfhir
• Deploy: $ flyctl deploy --app pocketfhir
• May need to deploy a second time: $ flyctl deploy --app pocketfhir --wait-timeout 300

FHIR Definitions

• put all .json files in this directory from the FHIR downloads except for the main FHIR json schema itself
• in the fhir_definitions directory is a dart file
• cd into fhir_definitions and run the dart file, this will organize all of the downloads into .ndjson files, by resourceType, which are included in PocketFHIR the first time it is run