GCP Patient everything - kind-lab/mimic-fhir GitHub Wiki
The process to get patient bundles from the Google Healthcare API.
Patient-everything background
Patient-everything requests get all resources associated with a patient resource. The REST request will typically look like:
GET [base url]/Patient/[id]/$everything
The main argument that can be added is _type, which allows users to request certain types of resources associated with a patient (ie only Conditions and Procedures). A request with _type looks like:
GET [base url]/Patient/[id]/$everything?_type=Patient,Condition,Procedure
Configuring Patient-everything requests in GCP
Initialize project
To start from the command line, initialize gcloud:
gcloud init
Set some environment variables:
export GOOGLE_LOCATION=us-central1
export GOOGLE_TOPIC='patient-everything'
export GCP_BUCKET=mimic-fhir
Setting up PubSub
Create a topic to submit patient-everything requests
gcloud pubsub topics create $GOOGLE_TOPIC
Cloud Function
The cloud function will be triggered by the Topic, and take the patient_id to do the following:
- The cloud function will accomplish:
- Start a patient-everything request on the datastore
- Include resource_types argument if present to narrow the resources to be output
- Store patient bundle in Cloud Storage
- Iterate over pages (if there are more resources than can fit in one page response)
- store each page as in Cloud Storage with patient_id and page #
- Start a patient-everything request on the datastore
- Create cloud function
- First move into the directory gcp/functions/patient_everything
- Then run the command:
gcloud functions deploy patient_everything \
--runtime=python39 \
--region=$GOOGLE_LOCATION \
--source=. \
--entry-point=patient_everything \
--trigger-topic=$GOOGLE_TOPIC
Setting up logging
bq mk -f=true mimic_fhir_log
bq query < pat_everything_pass.sql --use_legacy_sql=false
bq query < pat_everything_error.sql --use_legacy_sql=false
Running patient-everything from py_mimic_fhir
Send the command:
py_mimic_fhir export --patient_bundle --num_patients=10 --resources='Patient,Encounter,Condition' --count=100
Where:
| Argument | Default | Description |
|---|---|---|
| patient_bundle | false | a flag to set export to patient-everything |
| num_patients | 1 | Sets the number of patients to export |
| resources | Patient,Encounter,Condition,Procedure | A comma separated list of all the resource types to export |
| count | 100 | The size of the page returned from the fhir server (for pagination) |
Storage Notes
The final bundles will be sent to Cloud Storage at $GCP_BUCKET/patient-everything/[patient_id]-[current_time]