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fhir-operator's Introduction

fhir-operator

Kubernetes operator to handle FHIR databases and resources.

The Operator works off of FhirStore and FhirResource CRD. These resources give the power to create GCP FhirStores and FhirResources.

Getting up and running

Configure the values.yaml , make sure you have access to the kubernetes cluster, and run...

make deploy

Apply the example basic fhir store

kubectl apply -f examples/stores/fhirstore_basic.yaml

Describe resource and make sure it states CREATED in status
Apply the example fhir resources

kubectl apply -f examples/resources

Describe the resources and make sure they state CREATED in status

Resources

*FhirStore

Resource used to create a GCP FhirStore within a dataset. Currently requires the dataset to exist. FhirStore's are namespace scoped and provide the ability to specify the name of the store and any IAM permission policies to apply to the API. Reference examples/stores for examples. If the fhir store already exists, it will simply bind the resource definition of the existing store.

  • FhirStore.Spec.auth: each key represents a role to bind to a list of members
  • FhirStore.Spec.options:
    • preventDelete: prevent the delete of the resource and fhirStore in case of resrouce deletion

*FhirResource

Resource is used to create a Fhir resource in the FhirStore specified in the selector. NOTE: The selector points to the actual FhirStore resource and not the GCP Fhir store. A FhirResource can accomodate any FHIR representation. Reference examples/resources for examples

*FhirGCSConnector

Resource is used to create a subscription to a pubsub topic that listenes for GCS bucket events that holds json data that represents a fhir resource. The name of the file stored in the bucket must be DNS compliant for kubernetes as each file will create a fhir resource that is bound to the same namespace as the FhirGCSConnector resource. Reference examples/fhirgcsconnector for examples. You must have a kubernetes fhirstore resource to use this

  • FhirGCSConnector.Spec.topic: name of the topic to bind the subscription to
  • FhirGCSConnector.Spec.subscriptionName: name of the subscription to create
  • FhirGCSConnector.Spec.filter(optional): subscription filter that can be applied to the resource NOTE: this filter can not be changed once the resource is create. Must delete and re-create to update filter
  • FhirGCSConnector.Spec.fhirStoreSelector:
    • name: name of the fhirstore to bind the fhir resoures too

Testing

Make sure you have a GCP service account confgiured and pointing to GOOGLE_APPLICATION_CREDENTIALS envar

make test

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fhir-operator's Issues

Dependency Dashboard

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.

Repository problems

These problems occurred while renovating this repository. View logs.

  • WARN: Package lookup failures

Pending Approval

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  • chore(deps): update golang to v1.20

Rate-Limited

These updates are currently rate-limited. Click on a checkbox below to force their creation now.

  • chore(deps): update cloud.google.com/go/storage to v1.42.0
  • chore(deps): update github.com/getsentry/sentry-go to v0.28.1
  • chore(deps): update actions/checkout to v4
  • chore(deps): update actions/setup-go to v5
  • chore(deps): update cycjimmy/semantic-release-action to v4
  • chore(deps): update docker/login-action to v3
  • chore(deps): update github/codeql-action to v3
  • chore(deps): update google-github-actions/auth to v2
  • chore(deps): update google-github-actions/setup-gcloud to v2
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Warning

Renovate failed to look up the following dependencies: Failed to look up docker package gcr.io/imaware-test/fhir-operator.

Files affected: charts/values.yaml


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Detected dependencies

dockerfile
Dockerfile
  • golang 1.17
github-actions
.github/workflows/codeql-analysis.yml
  • actions/checkout v2
  • github/codeql-action v1
  • github/codeql-action v1
  • github/codeql-action v1
.github/workflows/deploy.yaml
  • actions/checkout v2
  • docker/login-action v1
  • google-github-actions/auth v0
  • google-github-actions/setup-gcloud v0
.github/workflows/release.yaml
  • actions/checkout v2
  • cycjimmy/semantic-release-action v2.7.0
.github/workflows/renovate.yaml
  • actions/checkout v2
  • actions/setup-go v2
.github/workflows/test.yaml
  • actions/checkout v2
  • google-github-actions/auth v0
  • google-github-actions/setup-gcloud v0
  • actions/setup-go v2
gomod
go.mod
  • go 1.16
  • cloud.google.com/go/pubsub v1.18.0
  • cloud.google.com/go/storage v1.21.0
  • github.com/getsentry/sentry-go v0.13.0
  • github.com/googleapis/gax-go/v2 v2.1.1
  • google.golang.org/api v0.69.0
  • k8s.io/apimachinery v0.23.4
  • k8s.io/client-go v0.23.4
  • sigs.k8s.io/controller-runtime v0.11.1
helm-values
charts/values.yaml
  • gcr.io/imaware-test/fhir-operator 1.0.0

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