Update docs for Jan 2024 Connectathon

README.md

@@ -1,8 +1,10 @@
 # EHR FHIR Server
-This subproject hosts a HAPI FHIR server that is based on the [hapi-fhir-jpaserver-example](https://github.com/jamesagnew/hapi-fhir/tree/master/hapi-fhir-jpaserver-example).
+
+This subproject hosts a HAPI FHIR server that is based on the now-deprecated [hapi-fhir-jpaserver-example](https://github.com/jamesagnew/hapi-fhir/tree/master/hapi-fhir-jpaserver-example). The new repo is found [here](https://github.com/hapifhir/hapi-fhir-jpaserver-starter).
 
 ## Running the server
-1. Make sure `gradle` is installed on your machine. Gradle v8 or higher.
+
+1. Make sure `gradle` is installed on your machine. Gradle v6.9 or higher.
 2. Run `gradle bootRun`
 3. In a separate terminal tab, run `gradle loadData` to load resources
 
@@ -11,33 +13,50 @@ This will start the server running on http://localhost:8080/test-ehr.
 **If you've loaded resources before, and want a clean slate, delete the `target` and `build` folders from test-ehr if they exist.**
 
 ## Adding resources to the database
+
 The FHIR server will persist FHIR resources between restarts. You can delete the folder `target` to clear all resources.
 
 To load the data from the json files in fhirResourcesToLoad, run the following script:  
-`gradle loadData` 
+`gradle loadData`
 
->Note: 'gradle loadData' can only be run while the FHIR server is running and `use_oauth` is false in         `src/main/resources/fhirServer.properties`
+> Note: 'gradle loadData' can only be run while the FHIR server is running and `use_oauth` is false in `src/main/resources/fhirServer.properties`
 
 ## Using OAuth security features
-The FHIR server is open by default, but this can be changed in the `fhirServer.properties` file.  
 
-First, change the `use_oauth` flag to `true` to turn on security.  Then set the `client_id`, `client_secret`, and `oauth_token` fields.
+The FHIR server is open by default, but this can be changed in the `fhirServer.properties` file.
 
-If using Keycloak and following the [CRD](https://github.com/mcode/CRD) guide, the `client_id` and `oauth_token` fields can be left as default.  The `client_secret` can be found with the following steps:
+First, change the `use_oauth` flag to `true` to turn on security. Then set the `client_id`, `client_secret`, and `oauth_token` fields.
 
-1) Open the keycloak admin console (http://localhost:8180/auth) and log in
-2) Open the ClientFhirServer, then the `clients` tab, and click `app-token`.  
-3) Click on the `Credentials` tab, use the `regenerate secret` option if needed.
-4) Copy the client secret into the properties file under `client_secret`
+If using Keycloak and following the [REMS Admin](https://github.com/mcode/rems-admin) guide, the `client_id` and `oauth_token` fields can be left as default. The `client_secret` can be found with the following steps:
 
-Finally, ensure that the [request generator](https://github.com/mcode/crd-request-generator) has the correct username and password in the `properties.json` file.  If following the CRD guide, this will be one of the users created when setting up Keycloak.
+1. Open the Keycloak admin console (http://localhost:8180/auth) and log in
+2. Open the ClientFhirServer, then the `clients` tab, and click `app-token`.
+3. Click on the `Credentials` tab, use the `regenerate secret` option if needed.
+4. Copy the client secret into the properties file under `client_secret`
+
+Finally, ensure that the [request generator](https://github.com/mcode/request-generator) has the correct username and password in the `properties.json` file. If following the REMS Admin guide, this will be one of the users created when setting up Keycloak.
 
 ## Server endpoints
-|Relative URL|Endpoint Description|
-|----|----|
-|`/test-ehr/`|Base server endpoint|
-|`/test-ehr/r4`|EHR FHIR Server endpoint (will not resolve in browser)|
+
+| Relative URL   | Endpoint Description                                   |
+| -------------- | ------------------------------------------------------ |
+| `/test-ehr/`   | Base server endpoint                                   |
+| `/test-ehr/r4` | EHR FHIR Server endpoint (will not resolve in browser) |
 
 ## Version
+
 Java v11 or higher is required to run this application.
-
+
+## Run configurations
+
+Run configurations to run, clean, and load data for the FHIR server can be used for the IntelliJ IDEA CE IDE. You can set breakpoints on the `Boot Run` configuration.
+
+These were last used with IntelliJ IDEA 2021.2.2 (Community Edition) and Microsoft Edge DevTools.
+
+### Steps:
+
+1. Select "Boot Run" as a Run Configuration from the dropdown menu.
+2. Put a breakpoint (red dot) on the desired line, e.g. line 43 of `test-ehr/src/main/java/org/hl7/davinci/ehrserver/interceptor/QuestionnaireResponseSearchParameterInterceptor.java`.
+3. Click the debug icon (green bug) up top.
+4. Go to http://localhost:3000 (where a locally run request-generator is served at) and try to select a patient. You may have to wait for bootRun to finish starting up if you see a "Network Request Failed Error". request-generator will ask test-ehr for QuestionnaireResponse resources (to get the list of in-progress forms).
+5. request-generator will pause as the breakpoint at line 43 gets hit. Hit F12 to open up DevTools on http://localhost:3000. You will see the QuestionnaireResponse (and other FHIR resources) have yet to be received.

build.gradle

@@ -193,7 +193,7 @@ task loadRequestBuilder() {
 void setup() {
     exec {
         workingDir 'src/main/webapp/'
-        commandLine 'git','clone','--single-branch', '--branch','settings-change-hotfix','https://github.com/HL7-DaVinci/crd-request-generator.git','tempFolder'
+        commandLine 'git','clone','--single-branch', '--branch','settings-change-hotfix','https://github.com/mcode/request-generator.git','tempFolder'
     }
     exec {
         workingDir 'src/main/webapp/tempFolder'