Update NVI on upload

README.md

@@ -12,8 +12,7 @@ source software licensed under the business-friendly [Apache Software License 2.
 ### JPA server
 The HAPI FHIR JPA server offers a complete RESTful FHIR server implementation using JPA 2.0 for database persistence. This project is build up from a [starter repository](https://github.com/hapifhir/hapi-fhir-jpaserver-starter) to deploy an FHIR server, the full source can be found [here](https://github.com/hapifhir/hapi-fhir).
 In the extensive [DOCS](https://hapifhir.io/hapi-fhir/docs/getting_started/introduction.html) much is explained about the JPA server, how it works and how it can be extended for particular use-cases. The project does not provide any security or enterprise audit logging.
-
-**[HAPI JPA Server](https://hapifhir.io/hapi-fhir/docs/server_jpa/architecture.html) has the following components:** ![](https://lh7-rt.googleusercontent.com/docsz/AD_4nXdL7rKrfOpq7myofkaXeSW-Pv1i7pHQe53rX1v61pa_ls7IC6UL2JIKZ5Xtd8OEB31l3NRfjLBQvSW0qinkDcz-Jw500DjTRkHicwuIv3GzNl6Y3Ldz3mtII8FA-Arq2v1VLKxPWk_HKutRQL6C6j7AU41G?key=flRIJ62mIRWJ10ofPwigtw)
+**[HAPI JPA Server](https://hapifhir.io/hapi-fhir/docs/server_jpa/architecture.html) has the following components:** !
 - **[Resource Providers](https://hapifhir.io/hapi-fhir/docs/server_plain/resource_providers.html):** A RESTful server Resource Provider is provided for each resource type in a given release of FHIR. Each resource provider implements all the FHIR methods, such as Search, Read, Create, Delete, etc.
 - **[HAPI DAOs](https://hapifhir.io/hapi-fhir/apidocs/hapi-fhir-storage/ca/uhn/fhir/jpa/api/dao/IFhirResourceDao.html):** The Data Access Objects (_DAO_) implement all the database business logic relating to the storage, indexing, and retrieval of FHIR resources, using the underlying JPA API.
 - **[Database](https://hapifhir.io/hapi-fhir/docs/server_jpa/database_support.html):** The RESTful server uses an embedded database but can be configured to communicate with any database supported by [Hibernate](https://hibernate.org/orm/). The JPA Server maintains active support for several databases such as: [MS SQL Server](https://www.microsoft.com/en-us/sql-server/sql-server-downloads), [PostgreSQL](https://www.postgresql.org/), [ORACLE](https://www.oracle.com/database/).
@@ -56,26 +55,25 @@ To get started:
 
 
 _To test the HAPI with the [Timeline](https://github.com/minvws/nl-irealisatie-zmodules-pgo-demo) service,
-add at least an ImagingStudy to the HAPI fhir database._
+at least one ImagingStudy has to be added to the HAPI database._
 
 **To easily set up sample FHIR entries use the following steps:**
-1. Run JPA server
-2. Open new terminal in project directory
-3. Run the following command to get a bundle with sample data loaded in:
-
-```curl
-   curl -X POST http://localhost:8080/fhir \
-   -H "Content-Type: application/json" \
-   --data @fhir_examples/bundle.json
+1. Start the JPA server as shown above
+2. Start all the needed modules as shown in [GFModules project](https://github.com/minvws/gfmodules-coordination)
+3. Open new terminal in project directory
+4. Run the following command to get a bundle with sample data loaded in:
+
+```bash
+   sh create_patient.sh
 ```
 
-4. Test whether the HAPI has successfully gotten the data:
+5. Test whether the HAPI has successfully gotten the data:
 
 ```curl 
 curl -X GET http://localhost:8080/fhir/Patient/3
 ```
 
-5. It should return something like:
+6. It should return something like:
 ```json
 {
    "resourceType": "Patient",
@@ -99,39 +97,13 @@ curl -X GET http://localhost:8080/fhir/Patient/3
 }
 ```
 
-Before you request the timeline service ensure your endpoint is registered in the [address](https://github.com/minvws/nl-irealisatie-zmodules-addressing-register) and
-the [pseudonym-exchange-service](https://github.com/minvws/nl-irealisatie-zmodules-pseudonym-service) knows your provider-id.
-To find your provider-id, look in the [settings file](src/main/resources/application.yaml).
-
-In the address DB you should have a entry that sets the address endpoint to: http://host.docker.internal:8080/fhir
-and to set up the provider in the pseudonym service with the following steps:
-1. do the following curl request in the terminal
-```curl
-curl -X 'POST' \
-  'http://localhost:8504/register' \
-  -H 'accept: application/json' \
-  -H 'Content-Type: application/json' \
-  -d '{
-  "provider_id": "MY_HAPI",
-  "bsn_hash": "2b826afa1c71f571a007dad61ce9fb9b63a24a328aa4ac009484a198ff565c51"
-}'
-```
-2. Copy generated pseudonym, it would look like the following:
-```{"pseudonym":"79693551-2195-464f-9e8f-b5a7b90ec854"}```
-3. Open database editor to the `hapi` database
-4. Go to table `hfj_res_ver`
-5. Edit the extension in the `patient` resource entry
-![assets/img.png](assets/img.png)
-6. Replace the patient's extensions UUID with the copied pseudonym
-
-Finally test whether the pseudonym service and the right pseudonym are all setup correctly:
-1. Do curl request, this same pseudonym is used by the timeline service as a sample pseudonym and it is coupled to the same bsn_hash that was used with setting the provider ID:
-```curl
-curl 'http://localhost:8080/fhir/ImagingStudy/_search?pseudonym=677b33c7-30e0-4fe1-a740-87fd73c4dfaf'
-```
-If you do not get any imaging studies back in the response then the HAPI is not set up correctly. 
+7. If you do get a correct result back then try if [timeline service](http://localhost:8500/) works as well
+8. Use for the BSN the input: `123456789` This will load the created patient
 
-2. If you do get imaging studies back then try if [timeline service](http://localhost:8500/) works as well
+### Review
+* Addresses database received a new endpoint, pointing to this HAPI.
+* The pseudonyms  database contains three extra pseudonyms from three providers, Timeline service, HAPI, referral service.
+* In the referrals database, a row is added with a pseudonym, URA that corresponds with the addresses DB and with data domain set to beeldbank.
 
 ### Setting properties
 In the [application.yaml](src/main/resources/application.yaml) file, you can configure most server and HAPI settings, enable or disable components, and set custom resource providers and interceptors.  

add_imagingStudy.sh

@@ -0,0 +1,73 @@
+#!/bin/bash
+
+curl -X 'POST' \
+  'http://host.docker.internal:8080/fhir/ImagingStudy' \
+  -H 'accept: application/json' \
+  -H 'Content-Type: application/json' \
+  -d '{
+          "resourceType": "ImagingStudy",
+          "status": "available",
+          "subject": {
+              "reference": "Patient/3"
+          },
+          "started": "2011-01-01T11:01:20+03:00",
+          "series": [
+              {
+                  "uid": "series1",
+                  "started": "2011-01-01T11:01:20+03:00",
+                  "modality": {
+                      "coding": [
+                          {
+                              "system": "https://dicom.nema.org/resources/ontology/DCM",
+                              "code": "CT"
+                          }
+                      ]
+                  },
+                  "performer": [
+                      {
+                          "actor": {
+                              "reference": "Organization/1",
+                              "type": "Organization"
+                          }
+                      },
+                      {
+                          "actor": {
+                              "reference": "Practitioner/2",
+                              "type": "Practitioner"
+                          }
+                      }
+                  ],
+                  "bodySite": {
+                      "concept": {
+                          "coding": [
+                              {
+                                  "system": "https://snomed.info/sct",
+                                  "code": "51185008",
+                                  "display": "CT of Head"
+                              }
+                          ]
+                      }
+                  },
+                  "instance": [
+                      {
+                          "uid": "instance201",
+                          "sopClass": {
+                              "system": "https://dicom.nema.org/resources/ontology/DCM",
+                              "code": "CT01",
+                              "display": "CT Head"
+                          },
+                          "title": "CT Head Image 1"
+                      },
+                      {
+                          "uid": "instance202",
+                          "sopClass": {
+                              "system": "https://dicom.nema.org/resources/ontology/DCM",
+                              "code": "CT02",
+                              "display": "CT Head"
+                          },
+                          "title": "CT Head Image 2"
+                      }
+                  ]
+              }
+          ]
+      }' > /dev/null

create_patient.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+curl -X 'POST' \
+  'http://localhost:8502/metadata_endpoint/add-one' \
+  -H 'accept: application/json' \
+  -H 'Content-Type: application/json' \
+  -d '{
+  "ura_number": 12345678,
+  "data_domain": "beeldbank",
+  "endpoint": "http://host.docker.internal:8080/fhir",
+  "request_type": "GET",
+  "parameters": []
+}' > /dev/null
+
+
+curl -X POST http://host.docker.internal:8080/fhir \
+   -H "Content-Type: application/json" \
+   --data @fhir_examples/bundle.json > /dev/null

src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java

@@ -80,6 +80,7 @@ public class AppProperties {
   private Subscription subscription = new Subscription();
   private Cors cors = null;
   private PseudonymExchangeService pseudonymExchangeService = null;
+  private AddReferralService addReferralService	= null;
   private Partitioning partitioning = null;
   private Boolean install_transitive_ig_dependencies = true;
   private Map<String, PackageInstallationSpec> implementationGuides = null;
@@ -212,6 +213,13 @@ public void setPseudonymExchangeService(PseudonymExchangeService pseudonymExchan
 		this.pseudonymExchangeService = pseudonymExchangeService;
   }
 
+  public AddReferralService addReferralService() {
+		return addReferralService;
+  }
+  public void setAddReferralService(AddReferralService addReferralService) {
+		this.addReferralService = addReferralService;
+  }
+
   public List<Bundle.BundleType> getAllowed_bundle_types() {
     return allowed_bundle_types;
   }
@@ -670,7 +678,18 @@ public String getTargetProviderId() {
 		public void setTargetProviderId(String targetProviderId) {
 			this.targetProviderId = targetProviderId;
 		}
+	}
 
+	public static class AddReferralService {
+		private String endpoint = "";
+
+		public String getEndpoint() {
+			return endpoint;
+		}
+
+		public void setEndpoint(String endpoint) {
+			this.endpoint = endpoint;
+		}
 	}
 
 	public static class Cors {

src/main/java/ca/uhn/fhir/jpa/starter/EnablePlainProvider.java

@@ -2,6 +2,7 @@
 
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.starter.ResourceProvider.BundlePlainProvider;
+import ca.uhn.fhir.jpa.starter.services.CommonServices;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import org.hl7.fhir.r5.model.*;
@@ -13,9 +14,10 @@ public class EnablePlainProvider extends RestfulServer {
 	public EnablePlainProvider(IFhirResourceDao<Patient> patientDao,
 								 IFhirResourceDao<Organization> orgDao,
 								 IFhirResourceDao<Practitioner> pracDao,
-								 IFhirResourceDao<ImagingStudy> imageDao
+								 IFhirResourceDao<ImagingStudy> imageDao,
+										CommonServices commonServices
 	) {
-		registerProvider(new BundlePlainProvider(patientDao, orgDao, pracDao, imageDao));
+		registerProvider(new BundlePlainProvider(patientDao, orgDao, pracDao, imageDao, commonServices));
 
 		List<IResourceProvider> resourceProviders = new ArrayList<>();
 		registerProviders(resourceProviders);

src/main/java/ca/uhn/fhir/jpa/starter/Interceptors/RemovePatientExtensionsInterceptor.java

@@ -5,9 +5,12 @@
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.model.Bundle;
+import org.hl7.fhir.r5.model.Extension;
 import org.hl7.fhir.r5.model.Patient;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
-import java.util.Collections;
+import java.util.List;
 
 /**
  * This class intercepts outgoing responses and removes patient extensions since they contain pseudonyms and
@@ -17,23 +20,42 @@
 @Interceptor
 public class RemovePatientExtensionsInterceptor {
 
+	private static final Logger log = LoggerFactory.getLogger(RemovePatientExtensionsInterceptor.class);
+
+	/**
+	 * This function hooks into the server outgoing responses and removes
+	 * any pseudonym extensions that patients might have.
+	 *
+	 * @param resource
+	 * 	The resource of the outgoing response
+	 */
 	@Hook(Pointcut.SERVER_OUTGOING_RESPONSE)
-	public void removeExtensions(IBaseResource resource) {
+	public void checkForPatient(IBaseResource resource) {
+		log.info("Removing patient pseudonym extensions");
 		if (resource instanceof Patient patient) {
-			if (patient.hasExtension()) {
-				patient.setExtension(Collections.emptyList());
-			}
+			removeExtension(patient);
 		}
 		if (resource instanceof Bundle bundle) {
 			if (bundle.hasEntry()) {
 				for (Bundle.BundleEntryComponent entry: bundle.getEntry()){
 					if (entry.getResource() instanceof Patient patient) {
-						if (patient.hasExtension()) {
-							patient.setExtension(Collections.emptyList());
-						}
+						removeExtension(patient);
 					}
 				}
 			}
 		}
 	}
+
+	/**
+	 * @param patient
+	 * 	The patient that could have a pseudonym extension
+	 */
+	private void removeExtension(Patient patient) {
+		// Retrieve the list of current extensions, excluding the one with the specific URL
+		List<Extension> updatedExtensions = patient.getExtension().stream()
+			.filter(ext -> !ext.getUrl().equals("https://example.com/extensions#pseudonym"))
+			.toList();
+		patient.setExtension(updatedExtensions);
+		log.info("Patient pseudonym extensions removed");
+	}
 }