Merge pull request #15 from oehf/14-small-fixes-to-xds-fhir-metadata-…

…mappers Small fixes to XDS <> FHIR metadata mappers
oehf · Oct 27, 2024 · b7c925a · b7c925a
2 parents 8c1c490 + 551808d
commit b7c925a
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Showing 5 changed files with 99 additions and 65 deletions.
diff --git a/...in/java/org/openehealth/app/xdstofhir/registry/common/mapper/AbstractFhirToXdsMapper.java b/...in/java/org/openehealth/app/xdstofhir/registry/common/mapper/AbstractFhirToXdsMapper.java
@@ -1,34 +1,19 @@
 package org.openehealth.app.xdstofhir.registry.common.mapper;
 
-import static org.openehealth.app.xdstofhir.registry.common.MappingSupport.urnDecodedScheme;
+import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.ContactPoint.ContactPointSystem;
+import org.openehealth.app.xdstofhir.registry.common.MappingSupport;
+import org.openehealth.ipf.commons.ihe.xds.core.metadata.Organization;
+import org.openehealth.ipf.commons.ihe.xds.core.metadata.Person;
+import org.openehealth.ipf.commons.ihe.xds.core.metadata.*;
+import org.openehealth.ipf.commons.ihe.xds.core.validate.OIDValidator;
 
 import java.time.ZoneId;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 
-import org.hl7.fhir.r4.model.BaseDateTimeType;
-import org.hl7.fhir.r4.model.CodeableConcept;
-import org.hl7.fhir.r4.model.Coding;
-import org.hl7.fhir.r4.model.ContactPoint;
-import org.hl7.fhir.r4.model.ContactPoint.ContactPointSystem;
-import org.hl7.fhir.r4.model.HumanName;
-import org.hl7.fhir.r4.model.Identifier;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Practitioner;
-import org.hl7.fhir.r4.model.PractitionerRole;
-import org.hl7.fhir.r4.model.Reference;
-import org.openehealth.app.xdstofhir.registry.common.MappingSupport;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.AssigningAuthority;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Author;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Code;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Identifiable;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.LocalizedString;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Organization;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Person;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Telecom;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Timestamp;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.XcnName;
+import static org.openehealth.app.xdstofhir.registry.common.MappingSupport.urnDecodedScheme;
 
 public abstract class AbstractFhirToXdsMapper {
 
@@ -71,7 +56,7 @@ protected Author fromAuthor(Reference author) {
             doc = (Practitioner) fhirPractRole.getPractitioner().getResource();
             xdsAuthor.getAuthorRole().addAll(fhirPractRole.getCode().stream().map(this::fromCodeableConcept).toList());
             xdsAuthor.getAuthorSpecialty().addAll(fhirPractRole.getSpecialty().stream().map(this::fromCodeableConcept).toList());
-            fromOrganization((org.hl7.fhir.r4.model.Organization)fhirPractRole.getOrganization().getResource()).ifPresent(org -> xdsAuthor.getAuthorInstitution().add(org));
+            fromOrganization((org.hl7.fhir.r4.model.Organization) fhirPractRole.getOrganization().getResource()).ifPresent(org -> xdsAuthor.getAuthorInstitution().add(org));
         } else if (resource instanceof Practitioner docResource) {
             doc = docResource;
         }
@@ -105,13 +90,19 @@ protected XcnName mapName(HumanName name) {
         return xdsName;
     }
 
-    private Optional<Organization> fromOrganization(org.hl7.fhir.r4.model.Organization fhirAuthOrg){
+    private Optional<Organization> fromOrganization(org.hl7.fhir.r4.model.Organization fhirAuthOrg) {
         if (fhirAuthOrg != null) {
             var xdsOrg = new Organization();
             var identifierFirstRep = fhirAuthOrg.getIdentifierFirstRep();
             if (identifierFirstRep != null && !identifierFirstRep.isEmpty()) {
                 xdsOrg.setIdNumber(identifierFirstRep.getValue());
-                xdsOrg.setAssigningAuthority(new AssigningAuthority(urnDecodedScheme(identifierFirstRep.getSystem())));
+
+                if (identifierFirstRep.getSystem() != null) {
+                    xdsOrg.setAssigningAuthority(new AssigningAuthority(urnDecodedScheme(identifierFirstRep.getSystem())));
+                } else {
+                    // without assigning authority, the ID needs to be a valid OID.
+                    new OIDValidator().validate(identifierFirstRep.getValue());
+                }
             }
             xdsOrg.setOrganizationName(fhirAuthOrg.getName());
             return Optional.of(xdsOrg);
@@ -120,7 +111,7 @@ private Optional<Organization> fromOrganization(org.hl7.fhir.r4.model.Organizati
         }
     }
 
-    private Identifiable fromCodeableConcept(CodeableConcept codeConcept ) {
+    private Identifiable fromCodeableConcept(CodeableConcept codeConcept) {
         var id = new Identifiable();
         var code = codeConcept.getCodingFirstRep();
         if (code.getSystem() != null) {

diff --git a/...in/java/org/openehealth/app/xdstofhir/registry/common/mapper/AbstractXdsToFhirMapper.java b/...in/java/org/openehealth/app/xdstofhir/registry/common/mapper/AbstractXdsToFhirMapper.java
@@ -22,13 +22,7 @@
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.StringType;
 import org.openehealth.app.xdstofhir.registry.common.MappingSupport;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Author;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Code;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Identifiable;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Name;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Telecom;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.Timestamp;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.XDSMetaClass;
+import org.openehealth.ipf.commons.ihe.xds.core.metadata.*;
 
 public abstract class AbstractXdsToFhirMapper {
 
@@ -51,7 +45,7 @@ protected Identifier fromIdentifier(final String urnIdValue, final Identifier.Id
 
     protected Identifier fromIdentifier(final Identifiable id) {
         var identifier = new Identifier();
-        identifier.setSystem(OID_URN + id.getAssigningAuthority().getUniversalId());
+        identifier.setSystem(nullSafeConvertToUrn(id.getAssigningAuthority()));
         identifier.setValue(id.getId());
         return identifier;
     }
@@ -77,7 +71,7 @@ protected Coding map(final Code code) {
     protected Reference fromAuthor(final Author author) {
         var role = new PractitionerRole();
         var doc = new Practitioner();
-        if((author.getAuthorPerson() != null) && !author.getAuthorPerson().isEmpty()) {
+        if (author.getAuthorPerson() != null && !author.getAuthorPerson().isEmpty()) {
             if (!author.getAuthorPerson().getName().isEmpty())
                 doc.setName(singletonList(fromName(author.getAuthorPerson().getName())));
             if (!author.getAuthorPerson().getId().isEmpty())
@@ -95,7 +89,7 @@ protected Reference fromAuthor(final Author author) {
             org.setName(xdsAuthorOrg.getOrganizationName());
             if (xdsAuthorOrg.getIdNumber() != null) {
                 var identifier = new Identifier();
-                identifier.setSystem(OID_URN + xdsAuthorOrg.getAssigningAuthority().getUniversalId());
+                identifier.setSystem(nullSafeConvertToUrn(xdsAuthorOrg.getAssigningAuthority()));
                 identifier.setValue(xdsAuthorOrg.getIdNumber());
                 org.addIdentifier(identifier);
             }
@@ -105,6 +99,10 @@ protected Reference fromAuthor(final Author author) {
         return reference;
     }
 
+    private static String nullSafeConvertToUrn(AssigningAuthority xdsAuthorOrg) {
+        return xdsAuthorOrg == null ? null : OID_URN + xdsAuthorOrg.getUniversalId();
+    }
+
     protected CodeableConcept convertToCode(final Identifiable id) {
         var fhirConcept = new CodeableConcept();
         Coding codeing;
@@ -117,7 +115,7 @@ protected CodeableConcept convertToCode(final Identifiable id) {
         return fhirConcept;
     }
 
-    protected ContactPoint fromTelecom (final Telecom xdsTelecom) {
+    protected ContactPoint fromTelecom(final Telecom xdsTelecom) {
         var cp = new ContactPoint();
         if (xdsTelecom.getEmail() != null) {
             cp.setSystem(ContactPointSystem.EMAIL);

diff --git a/...in/java/org/openehealth/app/xdstofhir/registry/common/mapper/XdsToFhirDocumentMapper.java b/...in/java/org/openehealth/app/xdstofhir/registry/common/mapper/XdsToFhirDocumentMapper.java
@@ -1,37 +1,27 @@
 package org.openehealth.app.xdstofhir.registry.common.mapper;
 
-import static java.util.Collections.singletonList;
-import static org.openehealth.app.xdstofhir.registry.common.MappingSupport.MHD_COMPREHENSIVE_PROFILE;
-import static org.openehealth.app.xdstofhir.registry.common.MappingSupport.toUrnCoded;
-import static org.openehealth.ipf.commons.ihe.xds.core.metadata.AvailabilityStatus.APPROVED;
-
-import java.util.List;
-import java.util.function.BiFunction;
-
+import ca.uhn.hl7v2.model.v25.datatype.XCN;
 import lombok.RequiredArgsConstructor;
 import org.hl7.fhir.r4.model.Address;
-import org.hl7.fhir.r4.model.Base64BinaryType;
-import org.hl7.fhir.r4.model.CanonicalType;
-import org.hl7.fhir.r4.model.DateTimeType;
-import org.hl7.fhir.r4.model.DateType;
-import org.hl7.fhir.r4.model.DocumentReference;
+import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.DocumentReference.DocumentReferenceRelatesToComponent;
 import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.r4.model.Enumerations.DocumentReferenceStatus;
-import org.hl7.fhir.r4.model.Identifier;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Period;
-import org.hl7.fhir.r4.model.Practitioner;
-import org.hl7.fhir.r4.model.Reference;
 import org.openehealth.app.xdstofhir.registry.common.MappingSupport;
 import org.openehealth.app.xdstofhir.registry.common.RegistryConfiguration;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.DocumentEntry;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.PatientInfo;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.Person;
-import org.openehealth.ipf.commons.ihe.xds.core.metadata.ReferenceId;
+import org.openehealth.ipf.commons.ihe.xds.core.metadata.*;
 import org.openehealth.ipf.commons.map.BidiMappingService;
 import org.springframework.stereotype.Component;
 
+import java.util.List;
+import java.util.function.BiFunction;
+
+import static java.util.Collections.singletonList;
+import static org.openehealth.app.xdstofhir.registry.common.MappingSupport.MHD_COMPREHENSIVE_PROFILE;
+import static org.openehealth.app.xdstofhir.registry.common.MappingSupport.toUrnCoded;
+import static org.openehealth.ipf.commons.ihe.xds.core.metadata.AvailabilityStatus.APPROVED;
+
 @Component
 @RequiredArgsConstructor
 public class XdsToFhirDocumentMapper extends AbstractXdsToFhirMapper
@@ -98,10 +88,19 @@ public DocumentReference apply(final DocumentEntry xdsDoc, List<DocumentReferenc
     private Reference fromAuthenticator(Person xdsAuthenticator) {
         var authenticator = new Reference();
         authenticator.setType(Practitioner.class.getSimpleName());
-        var practitoner = new Practitioner();
-        practitoner.setName(singletonList(fromName(xdsAuthenticator.getName())));
-        practitoner.addIdentifier(fromIdentifier(xdsAuthenticator.getId()));
-        authenticator.setResource(practitoner);
+        var practitioner = new Practitioner();
+
+        // XCN parser already verifies presence of either name or ID
+        Name<XCN> name = xdsAuthenticator.getName();
+        if (!name.isEmpty()) {
+            practitioner.setName(singletonList(fromName(name)));
+        }
+        Identifiable id = xdsAuthenticator.getId();
+        if (!id.isEmpty()) {
+            practitioner.addIdentifier(fromIdentifier(id));
+        }
+
+        authenticator.setResource(practitioner);
         return authenticator;
     }
 

diff --git a/...main/java/org/openehealth/app/xdstofhir/registry/register/RegisterDocumentsProcessor.java b/...main/java/org/openehealth/app/xdstofhir/registry/register/RegisterDocumentsProcessor.java
@@ -394,9 +394,9 @@ private void assignRegistryValues(XDSMetaClass xdsObject, List<Association> asso
      */
     private void assignRegistryValues(List<Association> associations) {
         for (var assoc : associations) {
-            if (!assoc.getEntryUuid().startsWith(MappingSupport.UUID_URN)) {
-                var previousIdentifier = assoc.getEntryUuid();
+            if (assoc.getEntryUuid() == null || !assoc.getEntryUuid().startsWith(MappingSupport.UUID_URN)) {
                 assoc.assignEntryUuid();
+                var previousIdentifier = assoc.getEntryUuid();
                 associations.stream().forEach(as -> {
                     as.setSourceUuid(as.getSourceUuid().replace(previousIdentifier, assoc.getEntryUuid()));
                     as.setTargetUuid(as.getTargetUuid().replace(previousIdentifier, assoc.getEntryUuid()));

diff --git a/...st/java/org/openehealth/app/xdstofhir/registry/common/mapper/DocumentMappingImplTest.java b/...st/java/org/openehealth/app/xdstofhir/registry/common/mapper/DocumentMappingImplTest.java
@@ -1,6 +1,7 @@
 package org.openehealth.app.xdstofhir.registry.common.mapper;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrowsExactly;
 
 import jakarta.xml.bind.JAXBContext;
 import jakarta.xml.bind.JAXBException;
@@ -21,6 +22,8 @@
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.AssigningAuthority;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.DocumentEntry;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.Identifiable;
+import org.openehealth.ipf.commons.ihe.xds.core.metadata.Organization;
+import org.openehealth.ipf.commons.ihe.xds.core.validate.XDSMetaDataException;
 import org.openehealth.ipf.commons.spring.map.SpringBidiMappingService;
 import org.openehealth.ipf.commons.xml.XmlUtils;
 import org.springframework.core.io.ClassPathResource;
@@ -49,6 +52,49 @@ void verifyBirectionalMapping() throws JAXBException {
         verifyFhirXdsMapping(testDocument);
     }
 
+    @Test
+    void verifyXcnWithNoIdentifierShallBeMapped() throws JAXBException {
+        DocumentEntry testDocument = SampleData
+                .createDocumentEntry(new Identifiable("123", new AssigningAuthority("2.999.3.4")));
+        testDocument.setUri(null);
+        testDocument.getLegalAuthenticator().setId(null);
+
+        verifyFhirXdsMapping(testDocument);
+    }
+
+    @Test
+    void verifyXcnWithNoNameShallBeMapped() throws JAXBException {
+        DocumentEntry testDocument = SampleData
+                .createDocumentEntry(new Identifiable("123", new AssigningAuthority("2.999.3.4")));
+        testDocument.setUri(null);
+        testDocument.getLegalAuthenticator().setName(null);
+
+        verifyFhirXdsMapping(testDocument);
+    }
+
+    @Test
+    void verifyXonWithNoAssigningAuthorityShallBeMapped() throws JAXBException {
+        DocumentEntry testDocument = SampleData
+                .createDocumentEntry(new Identifiable("123", new AssigningAuthority("2.999.3.4")));
+        testDocument.setUri(null);
+        Organization organization = testDocument.getAuthors().getFirst().getAuthorInstitution().getFirst();
+        organization.setIdNumber("1.2.3");
+        organization.setAssigningAuthority(null);
+
+        verifyFhirXdsMapping(testDocument);
+    }
+
+    @Test
+    void verifyXonWithNonOidIdentifierAndNoAssigningAuthorityShallNotBeAccepted() {
+        DocumentEntry testDocument = SampleData
+                .createDocumentEntry(new Identifiable("123", new AssigningAuthority("2.999.3.4")));
+        testDocument.setUri(null);
+        Organization organization = testDocument.getAuthors().getFirst().getAuthorInstitution().getFirst();
+        organization.setIdNumber("112");
+        organization.setAssigningAuthority(null);
+
+        assertThrowsExactly(XDSMetaDataException.class, () -> verifyFhirXdsMapping(testDocument));
+    }
 
     @Test
     void minimalDocumentMapping() throws JAXBException, IOException {