#1 XDS registry conformance Tests

* Add XDS response mapping for Submissionsets
oehf · Nov 18, 2023 · 96d4bc9 · 96d4bc9
1 parent 43f2233
commit 96d4bc9
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Showing 9 changed files with 145 additions and 21 deletions.
diff --git a/src/main/java/org/openehealth/app/xdstofhir/registry/XdsSpringContext.java b/src/main/java/org/openehealth/app/xdstofhir/registry/XdsSpringContext.java
@@ -15,6 +15,7 @@
 import org.openehealth.ipf.commons.spring.map.config.CustomMappings;
 import org.springframework.beans.factory.SmartInitializingSingleton;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.core.io.Resource;
@@ -66,6 +67,7 @@ public CustomMappings customMapping() {
      * @param fhirClient
      * @return
      */
+    @ConditionalOnProperty(value = "fhir.server.profile.bootstrap", havingValue = "true", matchIfMissing = true)
     @Bean
     public SmartInitializingSingleton createProfilesIfNeeded(IGenericClient fhirClient) {
         return () -> {

diff --git a/src/main/java/org/openehealth/app/xdstofhir/registry/common/MappingSupport.java b/src/main/java/org/openehealth/app/xdstofhir/registry/common/MappingSupport.java
@@ -23,6 +23,7 @@ public class MappingSupport {
     public static String XDS_URN = "urn:ihe:xds:";
     public static String URI_URN = "urn:ietf:rfc:3986";
     public static final String MHD_COMPREHENSIVE_PROFILE = "https://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Comprehensive.DocumentReference";
+    public static final String MHD_COMPREHENSIVE_SUBMISSIONSET_PROFILE = "https://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Comprehensive.SubmissionSet";
 
     public static final Map<Precision, TemporalPrecisionEnum> PRECISION_MAP_FROM_XDS = new EnumMap<>(
             Map.of(Precision.DAY, TemporalPrecisionEnum.DAY,

diff --git a/src/main/java/org/openehealth/app/xdstofhir/registry/common/fhir/MhdSubmissionSet.java b/src/main/java/org/openehealth/app/xdstofhir/registry/common/fhir/MhdSubmissionSet.java
@@ -10,12 +10,13 @@
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.ListResource;
+import org.openehealth.app.xdstofhir.registry.common.MappingSupport;
 
-@ResourceDef(name = "List", profile = "https://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Comprehensive.SubmissionSet")
+@ResourceDef(name = "List", profile = MappingSupport.MHD_COMPREHENSIVE_SUBMISSIONSET_PROFILE)
 public class MhdSubmissionSet extends ListResource {
     private static final long serialVersionUID = 6730967324453182475L;
 
-    private static final CodeableConcept SUBMISSIONSET_CODEING = new CodeableConcept(
+    public static final CodeableConcept SUBMISSIONSET_CODEING = new CodeableConcept(
             new Coding("https://profiles.ihe.net/ITI/MHD/CodeSystem/MHDlistTypes", "submissionset",
                     "SubmissionSet as a FHIR List"));
 

diff --git a/...va/org/openehealth/app/xdstofhir/registry/common/mapper/FhirToXdsSubmissionsetMapper.java b/...va/org/openehealth/app/xdstofhir/registry/common/mapper/FhirToXdsSubmissionsetMapper.java
@@ -11,7 +11,9 @@
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.AvailabilityStatus;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.LocalizedString;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.SubmissionSet;
+import org.springframework.stereotype.Component;
 
+@Component
 @RequiredArgsConstructor
 public class FhirToXdsSubmissionsetMapper extends AbstractFhirToXdsMapper
         implements Function<MhdSubmissionSet, SubmissionSet> {

diff --git a/src/main/java/org/openehealth/app/xdstofhir/registry/query/StoredQueryProcessor.java b/src/main/java/org/openehealth/app/xdstofhir/registry/query/StoredQueryProcessor.java
@@ -6,15 +6,18 @@
 import java.util.function.Consumer;
 import java.util.function.Function;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.util.BundleUtil;
 import lombok.RequiredArgsConstructor;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.DocumentReference;
+import org.openehealth.app.xdstofhir.registry.common.fhir.MhdSubmissionSet;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.DocumentEntry;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.ObjectReference;
+import org.openehealth.ipf.commons.ihe.xds.core.metadata.SubmissionSet;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.Version;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.QueryRegistry;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.query.QueryReturnType;
@@ -33,6 +36,7 @@ public class StoredQueryProcessor implements Iti18Service {
     private int maxResultCount;
     private final IGenericClient client;
     private final Function<DocumentReference, DocumentEntry> documentMapper;
+    private final Function<MhdSubmissionSet, SubmissionSet> submissionMapper;
     private static final Version DEFAULT_VERSION = new Version("1");
 
     @Override
@@ -45,10 +49,12 @@ public QueryResponse processQuery(QueryRegistry query) {
         var response = new QueryResponse(Status.SUCCESS);
 
         var xdsDocuments = getDocumentsFrom(resultBundle);
+        var submissionSets = getSubmissionSetsFrom(resultBundle);
 
         while (resultBundle.getLink(IBaseBundle.LINK_NEXT) != null) {
             resultBundle = client.loadPage().next(resultBundle).execute();
             xdsDocuments.addAll(getDocumentsFrom(resultBundle));
+            submissionSets.addAll(getSubmissionSetsFrom(resultBundle));
             if (xdsDocuments.size() > maxResultCount) {
                 response.setStatus(Status.PARTIAL_SUCCESS);
                 response.setErrors(Collections.singletonList(new ErrorInfo(ErrorCode.TOO_MANY_RESULTS,
@@ -59,14 +65,17 @@ public QueryResponse processQuery(QueryRegistry query) {
 
         if (query.getReturnType().equals(QueryReturnType.LEAF_CLASS)) {
             response.setDocumentEntries(xdsDocuments);
+            response.setSubmissionSets(submissionSets);
         } else {
-            response.setReferences(xdsDocuments.stream().map(doc -> new ObjectReference(doc.getEntryUuid()))
+            response.setReferences(Stream.concat(xdsDocuments.stream(), submissionSets.stream())
+                    .map(xdsObject -> new ObjectReference(xdsObject.getEntryUuid()))
                     .collect(Collectors.toList()));
         }
 
         return response;
     }
 
+
     private List<DocumentEntry> getDocumentsFrom(Bundle resultBundle) {
         var listOfResources = BundleUtil.toListOfResourcesOfType(client.getFhirContext(),
                 resultBundle, DocumentReference.class);
@@ -78,6 +87,16 @@ private List<DocumentEntry> getDocumentsFrom(Bundle resultBundle) {
         return xdsDocuments;
     }
 
+    private List<SubmissionSet> getSubmissionSetsFrom(Bundle resultBundle) {
+        var listOfResources = BundleUtil.toListOfResourcesOfType(client.getFhirContext(),
+                resultBundle, MhdSubmissionSet.class);
+        var xdsSubmissions = listOfResources.stream()
+                .map(submissionMapper)
+                .filter(Objects::nonNull)
+                .collect(Collectors.toList());
+        return xdsSubmissions;
+    }
+
     /**
      * ebRIM chapter 2.5.1 requires versionInfo and lid to be set.
      *

diff --git a/src/main/java/org/openehealth/app/xdstofhir/registry/query/StoredQueryVistorImpl.java b/src/main/java/org/openehealth/app/xdstofhir/registry/query/StoredQueryVistorImpl.java
@@ -10,17 +10,20 @@
 import java.util.Objects;
 import java.util.stream.Collectors;
 
+import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.gclient.DateClientParam;
 import ca.uhn.fhir.rest.gclient.IQuery;
 import ca.uhn.fhir.rest.gclient.TokenClientParam;
+import com.google.common.collect.Lists;
 import lombok.Getter;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.DocumentReference;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.codesystems.DocumentReferenceStatus;
 import org.openehealth.app.xdstofhir.registry.common.MappingSupport;
+import org.openehealth.app.xdstofhir.registry.common.fhir.MhdSubmissionSet;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.AvailabilityStatus;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.Code;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.ReferenceId;
@@ -50,28 +53,26 @@
 import org.openehealth.ipf.commons.ihe.xds.core.requests.query.GetRelatedDocumentsQuery;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.query.GetSubmissionSetAndContentsQuery;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.query.GetSubmissionSetsQuery;
+import org.openehealth.ipf.commons.ihe.xds.core.requests.query.PatientIdBasedStoredQuery;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.query.Query.Visitor;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.query.QueryList;
 
 public class StoredQueryVistorImpl implements Visitor {
     @Getter
-    private final IQuery<Bundle> fhirQuery;
+    private IQuery<Bundle> fhirQuery;
+    private final IGenericClient client;
 
     public StoredQueryVistorImpl(IGenericClient client) {
-        this.fhirQuery = client.search().forResource(DocumentReference.class)
-                .withProfile(MappingSupport.MHD_COMPREHENSIVE_PROFILE)
-                .include(DocumentReference.INCLUDE_SUBJECT)
-                .returnBundle(Bundle.class);
+        this.client = client;
     }
 
     @Override
     public void visit(FindDocumentsQuery query) {
-        var patientId = query.getPatientId();
-
-        var identifier = DocumentReference.PATIENT
-                .hasChainedProperty(Patient.IDENTIFIER.exactly().systemAndIdentifier(
-                        OID_URN + patientId.getAssigningAuthority().getUniversalId(), patientId.getId()));
-        fhirQuery.where(identifier);
+        this.fhirQuery = client.search().forResource(DocumentReference.class)
+                .withProfile(MappingSupport.MHD_COMPREHENSIVE_PROFILE)
+                .include(DocumentReference.INCLUDE_SUBJECT)
+                .returnBundle(Bundle.class);
+        mapPatientIdToQuery(query);
 
         map(query.getClassCodes(), DocumentReference.CATEGORY);
         map(query.getTypeCodes(),DocumentReference.TYPE);
@@ -87,6 +88,15 @@ public void visit(FindDocumentsQuery query) {
         //TODO: author
     }
 
+    private void mapPatientIdToQuery(PatientIdBasedStoredQuery query) {
+        var patientId = query.getPatientId();
+
+        var identifier = DocumentReference.PATIENT
+                .hasChainedProperty(Patient.IDENTIFIER.exactly().systemAndIdentifier(
+                        OID_URN + patientId.getAssigningAuthority().getUniversalId(), patientId.getId()));
+        fhirQuery.where(identifier);
+    }
+
     @Override
     public void visit(GetDocumentsQuery query) {
         var searchIdentifiers = new ArrayList<String>();
@@ -194,12 +204,27 @@ public void visit(GetAssociationsQuery query) {
 
     @Override
     public void visit(GetAllQuery query) {
-        throw new UnsupportedOperationException("Not yet implemented");
+        // TODO: Need to find another solution, since Hapi do not yet support Fhir's multi resource query
+        // https://github.com/hapifhir/hapi-fhir/issues/685
+        this.fhirQuery = client.search().forAllResources()
+                .withAnyProfile(Lists.newArrayList(MappingSupport.MHD_COMPREHENSIVE_SUBMISSIONSET_PROFILE,
+                        MappingSupport.MHD_COMPREHENSIVE_PROFILE))
+                .where(new TokenClientParam(Constants.PARAM_TYPE).exactly().codes("Patient","List"))
+                .include(DocumentReference.INCLUDE_SUBJECT)
+                .include(MhdSubmissionSet.INCLUDE_SUBJECT)
+                .returnBundle(Bundle.class);
+        mapPatientIdToQuery(query);
     }
 
     @Override
     public void visit(FindSubmissionSetsQuery query) {
-        throw new UnsupportedOperationException("Not yet implemented");
+        this.fhirQuery = client.search().forResource(MhdSubmissionSet.class)
+                .withProfile(MappingSupport.MHD_COMPREHENSIVE_SUBMISSIONSET_PROFILE)
+                .where(MhdSubmissionSet.CODE.exactly()
+                        .codings(MhdSubmissionSet.SUBMISSIONSET_CODEING.getCodingFirstRep()))
+                .include(MhdSubmissionSet.INCLUDE_SUBJECT)
+                .returnBundle(Bundle.class);
+        mapPatientIdToQuery(query);
     }
 
     @Override

diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
@@ -17,4 +17,6 @@ xds.endpoint.iti18=xds-iti18:registry/iti18
 xds.endpoint.iti42=xds-iti42:registry/iti42
 xds.endpoint.iti8=xds-iti8:0.0.0.0:2575
 
+fhir.server.profile.bootstrap=false
+
 server.port=8081
diff --git a/src/test/java/org/openehealth/app/xdstofhir/registry/XdsToFhirApplicationIT.java b/src/test/java/org/openehealth/app/xdstofhir/registry/XdsToFhirApplicationIT.java
@@ -24,6 +24,8 @@
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.Identifiable;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.QueryRegistry;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.query.FindDocumentsQuery;
+import org.openehealth.ipf.commons.ihe.xds.core.requests.query.FindSubmissionSetsQuery;
+import org.openehealth.ipf.commons.ihe.xds.core.requests.query.GetAllQuery;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.query.QueryReturnType;
 import org.openehealth.ipf.commons.ihe.xds.core.responses.ErrorCode;
 import org.openehealth.ipf.commons.ihe.xds.core.responses.QueryResponse;
@@ -62,8 +64,20 @@ void xdsRoundTrip() throws InterruptedException {
 
         var response = findDocumentFor(patientId);
         assertEquals(SUCCESS, response.getStatus());
+        assertEquals(1, response.getDocumentEntries().size());
+        assertEquals(0, response.getSubmissionSets().size());
+
+
+        response = findSubmissionSetsFor(patientId);
+        assertEquals(SUCCESS, response.getStatus());
+        assertEquals(1, response.getSubmissionSets().size());
+        assertEquals(0, response.getDocumentEntries().size());
+
+//        response = getAllFor(patientId);
+//        assertEquals(SUCCESS, response.getStatus());
+//        assertEquals(1, response.getSubmissionSets().size());
+//        assertEquals(1, response.getDocumentEntries().size());
 
-        assertTrue(response.getDocumentEntries().size() == 1);
     }
 
     @Test
@@ -95,6 +109,27 @@ private QueryResponse findDocumentFor(Identifiable patientId) {
         return response;
     }
 
+    private QueryResponse getAllFor(Identifiable patientId) {
+        var ga = new GetAllQuery();
+        ga.setStatusSubmissionSets(List.of(AvailabilityStatus.APPROVED));
+        ga.setStatusDocuments(List.of(AvailabilityStatus.APPROVED));
+        ga.setStatusFolders(List.of(AvailabilityStatus.APPROVED));
+        ga.setPatientId(patientId);
+        var query = new QueryRegistry(ga, QueryReturnType.LEAF_CLASS);
+        var response = storedQuery.processQuery(query);
+        return response;
+    }
+
+    private QueryResponse findSubmissionSetsFor(Identifiable patientId) {
+        var fd = new FindSubmissionSetsQuery();
+        fd.setStatus(List.of(AvailabilityStatus.APPROVED));
+        // https://hapi.fhir.org/baseR4/DocumentReference?_pretty=true&_profile=https://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Comprehensive.DocumentReference&patient.identifier=urn:oid:1.2.40.0.10.1.4.3.1|1419180172&_include=DocumentReference:subject
+        fd.setPatientId(patientId);
+        var query = new QueryRegistry(fd, QueryReturnType.LEAF_CLASS);
+        var response = storedQuery.processQuery(query);
+        return response;
+    }
+
     private void registerSampleDocForPatient(Identifiable patientId) {
         var register = SampleData.createRegisterDocumentSet();
         register.getDocumentEntries().forEach(doc -> doc.setPatientId(patientId));

diff --git a/src/test/java/org/openehealth/app/xdstofhir/registry/query/StoredQueryVistorImplTest.java b/src/test/java/org/openehealth/app/xdstofhir/registry/query/StoredQueryVistorImplTest.java
@@ -16,6 +16,8 @@
 import org.mockserver.model.MediaType;
 import org.openehealth.ipf.commons.ihe.xds.core.SampleData;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.query.FindDocumentsQuery;
+import org.openehealth.ipf.commons.ihe.xds.core.requests.query.FindSubmissionSetsQuery;
+import org.openehealth.ipf.commons.ihe.xds.core.requests.query.GetAllQuery;
 
 @ExtendWith(MockServerExtension.class)
 public class StoredQueryVistorImplTest {
@@ -32,17 +34,17 @@ void beforeEachLifecyleMethod(MockServerClient mockServer) {
     @BeforeEach
     void initClassUnderTest() throws IOException {
         var ctx = FhirContext.forR4Cached();
-        mockServer.when(
-                request().withPath("/DocumentReference"))
-                .respond(response().withStatusCode(200).withContentType(MediaType.APPLICATION_JSON)
-                .withBody("{\"resourceType\":\"Bundle\",\"type\":\"searchset\"}"));
         ctx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
         newRestfulGenericClient = (GenericClient) ctx.newRestfulGenericClient("http://localhost:"+mockServer.getPort()+"/");
         classUnderTest = new StoredQueryVistorImpl(newRestfulGenericClient);
     }
 
     @Test
     void testFindDocumentsQuery (){
+        mockServer.when(
+                request().withPath("/DocumentReference"))
+                .respond(response().withStatusCode(200).withContentType(MediaType.APPLICATION_JSON)
+                .withBody("{\"resourceType\":\"Bundle\",\"type\":\"searchset\"}"));
         var query = (FindDocumentsQuery) SampleData.createFindDocumentsQuery().getQuery();
         classUnderTest.visit(query);
         classUnderTest.getFhirQuery().execute();
@@ -61,7 +63,42 @@ void testFindDocumentsQuery (){
                 .withQueryStringParameter("facility", "urn:ihe:xds:scheme5|code5,urn:ihe:xds:scheme6|code6")
                 .withQueryStringParameter("status", "current")
                 );
+    }
+
+    @Test
+    void testFindSubmissionSetQuery (){
+        mockServer.when(
+                request().withPath("/List"))
+                .respond(response().withStatusCode(200).withContentType(MediaType.APPLICATION_JSON)
+                .withBody("{\"resourceType\":\"Bundle\",\"type\":\"searchset\"}"));
+        var query = (FindSubmissionSetsQuery) SampleData.createFindSubmissionSetsQuery().getQuery();
+        classUnderTest.visit(query);
+        classUnderTest.getFhirQuery().execute();
+
+        mockServer.verify(request()
+                .withQueryStringParameter("patient.identifier", "urn:oid:1.2|id1")
+                .withQueryStringParameter("_include", "List:subject")
+                .withQueryStringParameter("_profile", "https://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Comprehensive.SubmissionSet")
+                .withQueryStringParameter("code", "https://profiles.ihe.net/ITI/MHD/CodeSystem/MHDlistTypes|submissionset")
+                );
+    }
+
+    @Test
+    void testGetAllQuery (){
+        mockServer.when(
+                request().withPath("/"))
+                .respond(response().withStatusCode(200).withContentType(MediaType.APPLICATION_JSON)
+                .withBody("{\"resourceType\":\"Bundle\",\"type\":\"searchset\"}"));
+        var query = (GetAllQuery) SampleData.createGetAllQuery().getQuery();
+        classUnderTest.visit(query);
+        classUnderTest.getFhirQuery().execute();
 
+        mockServer.verify(request().withQueryStringParameter("patient.identifier", "urn:oid:1.2|id1")
+                .withQueryStringParameter("_include", "DocumentReference:subject", "List:subject")
+                .withQueryStringParameter("_profile",
+                        "https://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Comprehensive.SubmissionSet,"
+                        + "https://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Comprehensive.DocumentReference")
+                .withQueryStringParameter("_type", "Patient,List"));
     }
 
 }