switch to using the small test dataset

Author: bashir2

docker/README.md

@@ -17,20 +17,25 @@ image is based on the HAPI FHIR
 [Synthea](https://synthea.mitre.org/downloads) stored in the container itself.
 To load this dataset into the HAPI FHIR image, do the following:
 
-1. Run a local version of the HAPI FHIR server:
+1. Run a local version of the HAPI FHIR server. Note by default this uses an
+   in-memory database but we want to persist the uploaded data, hence we change
+   the configuration by the following environment variables:
 
    ```
-   docker run --rm -d  -p 8080:8080 --name hapi_fhir hapiproject/hapi:latest
+   docker run --rm -d  -p 8080:8080 --name hapi-fhir-add-synthea \
+     -e spring.datasource.url='jdbc:h2:file:/app/data/hapi_db;DB_CLOSE_ON_EXIT=FALSE;AUTO_RECONNECT=TRUE' \
+     -e spring.jpa.hibernate.ddl-auto=update \
+     hapiproject/hapi:latest
    ```
 
-2. Download the `1K Sample Synthetic Patient Records, FHIR R4` dataset:
+2. Download the `1K+ Sample Synthetic Patient Records, FHIR R4` dataset:
 
    ```
    wget https://synthetichealth.github.io/synthea-sample-data/downloads/synthea_sample_data_fhir_r4_sep2019.zip \
      -O fhir.zip
    ```
 
-3. Unzip the file, a directory named `fhir` should be created containig JSON
+3. Unzip the file, a directory named `fhir` should be created containing JSON
    files:
 
    ```
@@ -39,8 +44,15 @@ To load this dataset into the HAPI FHIR image, do the following:
 
 4. Use the Synthetic Data Uploader from the
    [FHIR Analytics](https://github.com/GoogleCloudPlatform/openmrs-fhir-analytics/tree/master/synthea-hiv)
-   repo to upload the files into the HAPI FHIR container
-   `docker run -it --network=host \ -e SINK_TYPE="HAPI" \ -e FHIR_ENDPOINT=http://localhost:8080/fhir \ -e INPUT_DIR="/workspace/output/fhir" \ -e CORES="--cores 1" \ -v $(pwd)/fhir:/workspace/output/fhir \ us-docker.pkg.dev/cloud-build-fhir/fhir-analytics/synthea-uploader:latest`
+   repo to upload the files into the HAPI FHIR container. Note instead of
+   uploading all patients, you can pick a small subset instead. In that case
+   adjust the `INPUT_DIR` accordingly. Using the whole dataset increases the
+   container init time by a few minutes (and slows down e2e tests which depend
+   on this):
+
+   ```
+   docker run -it --network=host \ -e SINK_TYPE="HAPI" \ -e FHIR_ENDPOINT=http://localhost:8080/fhir \ -e INPUT_DIR="/workspace/output/fhir" \ -e CORES="--cores 1" \ -v $(pwd)/fhir:/workspace/output/fhir \ us-docker.pkg.dev/cloud-build-fhir/fhir-analytics/synthea-uploader:latest
+   ```
 
 5. As the uploader uses `POST` to upload the JSON files, the server will create
    the ID used to refer to resources. We would like to upload a patient list
@@ -82,7 +94,7 @@ To load this dataset into the HAPI FHIR image, do the following:
 7. Commit the Docker container. This saves its state into a new image
 
    ```
-    docker commit hapi_fhir us-docker.pkg.dev/fhir-proxy-build/stable/hapi-synthea:latest
+    docker commit hapi-fhir-add-synthea us-docker.pkg.dev/fhir-proxy-build/stable/hapi-synthea:latest
    ```
 
 8. Push the image

docker/hapi-proxy-compose.yaml

@@ -55,6 +55,6 @@ services:
       timeout: 10s
 
   hapi-server:
-    image: us-docker.pkg.dev/fhir-proxy-build/stable/hapi-synthea:latest
+    image: us-docker.pkg.dev/fhir-proxy-build/stable/hapi-synthea:small
     ports:
     - "8099:8080"

e2e-test/e2e.py

@@ -292,7 +292,7 @@ def _assert_audit_events(expected_audit_event: Dict[str, Any],
 if __name__ == "__main__":
     logging.basicConfig(level=logging.INFO)
 
-    patients = ["Patient/75270", "Patient/3810"]
+    patients = ["Patient/3177", "Patient/2835"]
     resources = [("Encounter", "patient"), ("Observation", "subject")]
     auth_client = clients.AuthClient()
     fhir_proxy_client = clients.FhirProxyClient()
@@ -306,7 +306,7 @@ def _assert_audit_events(expected_audit_event: Dict[str, Any],
     test_post_resource_increase_count(
         ("Observation", "subject"),
         "e2e-test/obs.json",
-        "Patient/75270",
+        "Patient/3177",
         hapi_client,
         fhir_proxy_client,
         auth_client,

e2e-test/obs.json

@@ -23,10 +23,10 @@
       "text": "Body Weight"
     },
     "subject": {
-      "reference": "Patient/75270"
+      "reference": "Patient/3177"
     },
     "encounter": {
-      "reference": "Encounter/76366"
+      "reference": "Encounter/3186"
     },
     "effectiveDateTime": "2015-07-05T10:11:41-04:00",
     "issued": "2015-07-05T10:11:41.981-04:00",

e2e-test/observation_audit_events.json

@@ -135,7 +135,7 @@
       },
       {
         "what": {
-          "reference": "Patient/75270"
+          "reference": "Patient/3177"
         },
         "type": {
           "system": "http://terminology.hl7.org/CodeSystem/audit-entity-type",

e2e-test/transaction_bundle.json

@@ -5,7 +5,7 @@
         {
             "request": {
                 "method": "GET",
-                "url": "Observation?_count=1&subject=Patient/75270"
+                "url": "Observation?_count=1&subject=Patient/3177"
             }
         },
         {

e2e-test/transaction_bundle_audit_events.json

@@ -301,7 +301,7 @@
       },
       {
         "what": {
-          "reference": "Patient/75270"
+          "reference": "Patient/3177"
         },
         "type": {
           "system": "http://terminology.hl7.org/CodeSystem/audit-entity-type",
@@ -340,7 +340,7 @@
           "code": "24",
           "display": "Query"
         },
-        "description": "GET http://localhost:8080/fhir/Observation?_count=1&subject=Patient/75270",
+        "description": "GET http://localhost:8080/fhir/Observation?_count=1&subject=Patient/3177",
         "query": "aHR0cDovL2xvY2FsaG9zdDo4MDgwL2ZoaXIvT2JzZXJ2YXRpb24/X2NvdW50PTEmc3ViamVjdD1QYXRpZW50JTJGNzUyNzA="
       }
     ]