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Create a Google Cloud FHIR Store and BigQuery Dataset

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williamito edited this page Jan 30, 2023 · 1 revision

One of the supported FHIR sinks is Google Cloud FHIR store and BigQuery. These instructions will guide you in creating a FHIR store and BigQuery dataset.

To set up GCP project that you can use as a sink FHIR store:

  • Create a new project in GCP. For an overview of projects, datasets and data stores check this document.

  • Enable Google Cloud Healthcare API in the project and create a Google Cloud Healthcare dataset

  • Create a FHIR data store in the dataset with the R4 FHIR version

  • Enable the BigQuery API in the project and dataset with the same name in the project

  • Download, install, and initialize the gcloud cli: https://cloud.google.com/sdk/docs/quickstart

  • Make sure you can authenticate with the project using the CLI: https://developers.google.com/identity/sign-in/web/sign-in

    • $ gcloud init
    • $ gcloud auth application-default login
    • Create a service account for the project, generate a key, and save it securely locally
    • Add the bigquery.dataEditor and bigquery.jobUser roles to the project in the IAM & Admin/Roles settings or using the cli:
      • $ gcloud projects add-iam-policy-binding openmrs-260803 --role roles/bigquery.admin --member serviceAccount:[email protected]
      • $ gcloud projects add-iam-policy-binding openmrs-260803 --role roles/healthcare.datasetAdmin --member serviceAccount:[email protected]
    • Activate the service account for your project using gcloud auth activate-service-account <your-service-account> --key-file=<your-key-file> --project=<your project>
    • Set the GOOGLE_APPLICATION_CREDENTIALS environment variable: https://cloud.google.com/docs/authentication/getting-started#setting_the_environment_variable

  • Use the script utils/create_fhir_store.sh to create a FHIR store in this dataset which stream the changes to the BigQuery dataset as well: ./utils/create_fhir_store.sh PROJECT LOCATION DATASET FHIR-STORE-NAME

    • PROJECT is your GCP project.
    • LOCATION is GCP location where your dataset resides, e.g., us-central1.
    • DATASET is the name of the dataset you created.
    • FHIR-STORE-NAME is what it says.

    Note: If you get PERMISSION_DENIED errors, make sure to IAM & ADMIN/IAM/Members and add the bigquery.dataEditor and bigquery.jobUser roles to the Cloud Healthcare Service Agent service account that shows up.

You can run the script with no arguments to see a sample usage. After you create the FHIR store, its full URL would be:

https://healthcare.googleapis.com/v1/projects/PROJECT/locations/LOCATION/datasets/DATASET/fhirStores/FHIR-STORE-NAME

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