#2 Add support for Remove Metadata (ITI-62)

* Some documentation improvement
* Some validation fixes

README.md

@@ -18,6 +18,8 @@ Target goal is a blueprint project to see how [IPF](https://github.com/oehf/ipf)
 (default endpoint: http://localhost:8081/services/registry/iti42)
 * [ITI-18](https://profiles.ihe.net/ITI/TF/Volume2/ITI-18.html) to query documents from the registry  
 (default endpoint: http://localhost:8081/services/registry/iti18)
+* [ITI-62](https://profiles.ihe.net/ITI/TF/Volume2/ITI-62.html) to remove document metadata from the registry  
+(default endpoint: http://localhost:8081/services/registry/iti62)
 * [ITI-8](https://profiles.ihe.net/ITI/TF/Volume2/ITI-8.html) to receive a patient-identity-feed and make sure the patient exists  
 (default endpoint: MLLP Port 2575)
 
@@ -41,7 +43,7 @@ mvn failsafe:integration-test -Pit-tests
 ```
 
 ## Run
-The CI build push the container to [dockerhub](https://hub.docker.com/r/thopap/xds-registry-to-fhir). To pull the latest image an e.g. configure the public firely FHIR server, run:
+The CI build push the container to [dockerhub](https://hub.docker.com/r/thopap/xds-registry-to-fhir). To pull the latest image an e.g. configure the public [firely](https://fire.ly/) FHIR server, run:
 
 ```
 docker run -it -p8080:8080 registry.hub.docker.com/thopap/xds-registry-to-fhir -e FHIR_SERVER_BASE=https://server.fire.ly
@@ -58,5 +60,4 @@ The application is not yet intended as a production ready application.
 
 * Security concerns are not yet covered (e.g. https, mllps, SAML, audit, ...)
 * More testing
-* IHE compliance test (using the [XDS Toolkit](https://github.com/usnistgov/iheos-toolkit2))
-* Tests against fhir server beyond hapi
+* IHE compliance test (using the [XDS Toolkit](https://github.com/usnistgov/iheos-toolkit2))

src/main/java/org/openehealth/app/xdstofhir/registry/remove/Iti62Service.java

@@ -5,5 +5,15 @@
 
 @FunctionalInterface
 public interface Iti62Service {
+
+    /**
+     * Perform the ITI-62 processing as described by IHE for https://profiles.ihe.net/ITI/TF/Volume2/ITI-62.html
+     *
+     * System will collect the corresponding FHIR resources and then invoke a batch update to the fhir resource,
+     * either deleting or partially updating (e.g. in case just a reference is removed) resource.
+     *
+     * @param metadataToRemove - the metadata remove request message.
+     * @return Response with Success or Failure, depending on the operation outcome.
+     */
     Response remove(RemoveMetadata metadataToRemove);
 }

src/main/java/org/openehealth/app/xdstofhir/registry/remove/RemoveDocumentsProcessor.java

@@ -18,7 +18,10 @@
 import org.hl7.fhir.instance.model.api.IBaseElement;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.DocumentReference;
+import org.hl7.fhir.r4.model.DocumentReference.DocumentReferenceRelatesToComponent;
+import org.hl7.fhir.r4.model.DocumentReference.DocumentRelationshipType;
 import org.hl7.fhir.r4.model.ListResource;
+import org.hl7.fhir.r4.model.Reference;
 import org.openehealth.app.xdstofhir.registry.common.MappingSupport;
 import org.openehealth.app.xdstofhir.registry.common.PagingFhirResultIterator;
 import org.openehealth.app.xdstofhir.registry.query.StoredQueryMapper;
@@ -40,22 +43,26 @@ public class RemoveDocumentsProcessor implements Iti62Service {
     public Response remove(RemoveMetadata metadataToRemove) {
         var errorInfo = new ArrayList<ErrorInfo>();
         var uuidsToDelete = new ArrayList<String>(metadataToRemove.getReferences().stream().map(ObjectReference::getId).toList());
+        var unmodifiedUuidsToDelete = new ArrayList<String>(uuidsToDelete);
         var builder = new BundleBuilder(client.getFhirContext());
 
-        var documentFhirQuery = client.search().forResource(DocumentReference.class)
+        var docBundleResult = client.search().forResource(DocumentReference.class)
                 .withProfile(MappingSupport.MHD_COMPREHENSIVE_PROFILE)
-                .revInclude(ListResource.INCLUDE_ITEM)
+                .revInclude(DocumentReference.INCLUDE_RELATESTO)
                 .where(DocumentReference.IDENTIFIER.exactly().systemAndValues(URI_URN,uuidsToDelete))
-                .returnBundle(Bundle.class);
+                .returnBundle(Bundle.class)
+                .execute();
 
+        // collect all List Resources (SubmissionSet, Folder) without duplicates (hapi domain objects do not implement equal / hashcode)
         var uniqueResults = new TreeSet<ListResource>((a, b) -> Comparator.comparing(IAnyResource::getId).compare(a,  b));
 
-        var docBundleResult = documentFhirQuery.execute();
         var docResult = new PagingFhirResultIterator<DocumentReference>(docBundleResult, DocumentReference.class, client);
         uniqueResults.addAll(BundleUtil.toListOfResourcesOfType(client.getFhirContext(), docBundleResult, ListResource.class));
         docResult.forEachRemaining(doc -> {
             processAssociations(doc, doc.getRelatesTo(), uuidsToDelete, builder);
-            addToDeleteTransaction(doc, uuidsToDelete, builder);
+            if (addToDeleteTransaction(doc, uuidsToDelete, builder)) {
+                validateNoReferencesExists(doc, docResult, unmodifiedUuidsToDelete, errorInfo);
+            }
         });
 
         var reverseSearchCriteria = Collections.singletonMap("item:identifier", Collections.singletonList(
@@ -70,11 +77,11 @@ public Response remove(RemoveMetadata metadataToRemove) {
                 .revInclude(ListResource.INCLUDE_ITEM)
                 .returnBundle(Bundle.class);
 
-        new PagingFhirResultIterator<ListResource>(referenceQuery.execute(),
-                ListResource.class, client).forEachRemaining(uniqueResults::add);
+        new PagingFhirResultIterator<ListResource>(referenceQuery.execute(), ListResource.class, client)
+                .forEachRemaining(uniqueResults::add);
 
-        new PagingFhirResultIterator<ListResource>(listQuery.execute(),
-                ListResource.class, client).forEachRemaining(uniqueResults::add);
+        new PagingFhirResultIterator<ListResource>(listQuery.execute(), ListResource.class, client)
+                .forEachRemaining(uniqueResults::add);
 
         uniqueResults.forEach(ref -> {
             processAssociations(ref, ref.getEntry(), uuidsToDelete, builder);
@@ -108,6 +115,29 @@ public Response remove(RemoveMetadata metadataToRemove) {
         return response;
     }
 
+    private void validateNoReferencesExists(DocumentReference doc,
+            PagingFhirResultIterator<DocumentReference> docResult, ArrayList<String> uuidsToDelete, List<ErrorInfo> errorInfo) {
+        var listOfRelations = new ArrayList<DocumentReferenceRelatesToComponent>();
+        docResult.forEachRemaining(aDoc -> {
+            var entryUuid = StoredQueryMapper.entryUuidFrom(aDoc);
+            if (!uuidsToDelete.contains(entryUuid) && aDoc != doc)
+                listOfRelations.addAll(aDoc.getRelatesTo());
+        });
+        doc.getRelatesTo().stream().filter(docRel -> docRel.getCode().equals(DocumentRelationshipType.REPLACES)).forEach(relDoc -> {
+            var entryUuid = StoredQueryMapper.entryUuidFrom(relDoc.getTarget().getResource());
+            if (!uuidsToDelete.contains(entryUuid)){
+                errorInfo.add(new ErrorInfo(ErrorCode.REFERENCE_EXISTS_EXCEPTION, "Some references still exists to " + entryUuid,
+                        Severity.ERROR, null, null));
+            }
+        });
+        listOfRelations.stream().map(DocumentReferenceRelatesToComponent::getTarget).filter(Objects::nonNull)
+                .map(Reference::getResource).filter(DocumentReference.class::isInstance)
+                .map(DocumentReference.class::cast)
+                .filter(docRef -> docRef.equalsDeep(doc))
+                .findAny().ifPresent(res -> errorInfo.add(new ErrorInfo(ErrorCode.REFERENCE_EXISTS_EXCEPTION, "Some references still exists to " + res.getId(),
+                        Severity.ERROR, null, null)));
+    }
+
     /**
      * Remove metadata will also remove associations between registry entries. This method will ensure that these
      * entries are correctly removed.