#1 XDS registry conformance Tests

* Fix first observations in context of xdstools execution * adapt default port to 8081 to avoid conflict with xdstools
oehf · Oct 31, 2023 · 0100df2 · 0100df2
1 parent 8786713
commit 0100df2
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diff --git a/README.md b/README.md
@@ -13,9 +13,12 @@ Target goal is a blueprint project to see how [IPF](https://github.com/oehf/ipf)
 * Implementation try to stay as simple as possible to allow a blueprint (Design Principles DRY and KISS)
 
 ## Features
-* [ITI-42](https://profiles.ihe.net/ITI/TF/Volume2/ITI-42.html) to register documents to the registry
-* [ITI-18](https://profiles.ihe.net/ITI/TF/Volume2/ITI-18.html) to query documents from the registry
-* [ITI-8](https://profiles.ihe.net/ITI/TF/Volume2/ITI-8.html) to receive a patient-identity-feed and make sure the patient exists
+* [ITI-42](https://profiles.ihe.net/ITI/TF/Volume2/ITI-42.html) to register documents to the registry  
+(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-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)
 
 ## Build and run
 

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
@@ -9,9 +9,11 @@
 
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
 import lombok.experimental.UtilityClass;
+import org.hl7.fhir.r4.model.codesystems.DocumentReferenceStatus;
 import org.ietf.jgss.GSSException;
 import org.ietf.jgss.Oid;
 import org.openehealth.ipf.commons.core.URN;
+import org.openehealth.ipf.commons.ihe.xds.core.metadata.AvailabilityStatus;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.Timestamp.Precision;
 
 @UtilityClass
@@ -24,15 +26,22 @@ public class MappingSupport {
 
     public static final Map<Precision, TemporalPrecisionEnum> PRECISION_MAP_FROM_XDS = new EnumMap<>(
             Map.of(Precision.DAY, TemporalPrecisionEnum.DAY,
-                    Precision.HOUR, TemporalPrecisionEnum.MINUTE,
-                    Precision.MINUTE, TemporalPrecisionEnum.MINUTE,
+                    Precision.HOUR, TemporalPrecisionEnum.SECOND,
+                    Precision.MINUTE, TemporalPrecisionEnum.SECOND,
                     Precision.MONTH, TemporalPrecisionEnum.MONTH,
                     Precision.SECOND, TemporalPrecisionEnum.SECOND,
                     Precision.YEAR, TemporalPrecisionEnum.YEAR));
     public static final Map<TemporalPrecisionEnum, Precision> PRECISION_MAP_FROM_FHIR = PRECISION_MAP_FROM_XDS
             .entrySet().stream()
             .collect(Collectors.toMap(Map.Entry::getValue, Map.Entry::getKey, (x, y) -> y, LinkedHashMap::new));
 
+    public static final Map<AvailabilityStatus, DocumentReferenceStatus> STATUS_MAPPING_FROM_XDS = new EnumMap<>(
+            Map.of(AvailabilityStatus.APPROVED, DocumentReferenceStatus.CURRENT,
+                    AvailabilityStatus.DEPRECATED, DocumentReferenceStatus.SUPERSEDED));
+    public static final Map<DocumentReferenceStatus, AvailabilityStatus> STATUS_MAPPING_FROM_FHIR = STATUS_MAPPING_FROM_XDS
+            .entrySet().stream()
+            .collect(Collectors.toMap(Map.Entry::getValue, Map.Entry::getKey, (x, y) -> y, LinkedHashMap::new));
+
 
     public static String toUrnCoded(String value) {
         String adaptedValue = value;

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
@@ -160,8 +160,10 @@ private Reference fromAuthor(final Author author) {
         var role = new PractitionerRole();
         var doc = new Practitioner();
         if(!author.getAuthorPerson().isEmpty()) {
-            doc.setName(singletonList(fromName(author.getAuthorPerson().getName())));
-            doc.addIdentifier(fromIdentifier(author.getAuthorPerson().getId()));
+            if (!author.getAuthorPerson().getName().isEmpty())
+                doc.setName(singletonList(fromName(author.getAuthorPerson().getName())));
+            if (!author.getAuthorPerson().getId().isEmpty())
+                doc.addIdentifier(fromIdentifier(author.getAuthorPerson().getId()));
         }
         doc.setTelecom(author.getAuthorTelecom().stream().map(this::fromTelecom).collect(Collectors.toList()));
         var reference = new Reference();

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
@@ -3,6 +3,7 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.Objects;
+import java.util.function.Consumer;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
@@ -14,6 +15,7 @@
 import org.hl7.fhir.r4.model.DocumentReference;
 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.Version;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.QueryRegistry;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.query.QueryReturnType;
 import org.openehealth.ipf.commons.ihe.xds.core.responses.ErrorCode;
@@ -31,6 +33,7 @@ public class StoredQueryProcessor implements Iti18Service {
     private int maxResultCount;
     private final IGenericClient client;
     private final Function<DocumentReference, DocumentEntry> documentMapper;
+    private static final Version DEFAULT_VERSION = new Version("1");
 
     @Override
     public QueryResponse processQuery(QueryRegistry query) {
@@ -71,7 +74,20 @@ private List<DocumentEntry> getDocumentsFrom(Bundle resultBundle) {
                 .map(documentMapper)
                 .filter(Objects::nonNull)
                 .collect(Collectors.toList());
+        xdsDocuments.forEach(assignDefaultVersioning());
         return xdsDocuments;
     }
 
+    /**
+     * ebRIM chapter 2.5.1 requires versionInfo and lid to be set.
+     *
+     * @return consumer setting proper defaults for lid and versionInfo
+     */
+    private Consumer<? super DocumentEntry> assignDefaultVersioning() {
+        return doc -> {
+          doc.setLogicalUuid(doc.getEntryUuid());
+          doc.setVersion(DEFAULT_VERSION);
+        };
+    }
+
 }
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
@@ -13,8 +13,10 @@
 import ca.uhn.fhir.rest.gclient.TokenClientParam;
 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.ipf.commons.ihe.xds.core.metadata.Code;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.query.FetchQuery;
@@ -69,6 +71,12 @@ public void visit(FindDocumentsQuery query) {
         map(query.getPracticeSettingCodes(),DocumentReference.SETTING);
         map(query.getHealthcareFacilityTypeCodes(),DocumentReference.FACILITY);
         map(query.getFormatCodes(),DocumentReference.FORMAT);
+        List<String> fhirStatus = query.getStatus().stream()
+                .map(status -> MappingSupport.STATUS_MAPPING_FROM_XDS.get(status))
+                .map(DocumentReferenceStatus::toCode)
+                .collect(Collectors.toList());
+        if (!fhirStatus.isEmpty())
+            fhirQuery.where(DocumentReference.STATUS.exactly().codes(fhirStatus));
     }
 
     @Override
@@ -86,11 +94,11 @@ public void visit(GetDocumentsQuery query) {
     }
 
     private void map(List<Code> codes, TokenClientParam param) {
-        if (codes != null) {
-            codes.forEach(code -> {
-                var codeCriteria = param.exactly().systemAndCode(toUrnCoded(code.getSchemeName()), code.getCode());
-                fhirQuery.where(codeCriteria);
-            });
+        if (codes != null && !codes.isEmpty()) {
+            fhirQuery.where(param.exactly()
+                    .codings(codes.stream()
+                            .map(xdsCode -> new Coding(toUrnCoded(xdsCode.getSchemeName()), xdsCode.getCode(), null))
+                            .collect(Collectors.toList()).toArray(new Coding[0])));
         }
     }
 

diff --git a/...main/java/org/openehealth/app/xdstofhir/registry/register/RegisterDocumentsProcessor.java b/...main/java/org/openehealth/app/xdstofhir/registry/register/RegisterDocumentsProcessor.java
@@ -1,6 +1,7 @@
 package org.openehealth.app.xdstofhir.registry.register;
 
 import static org.openehealth.app.xdstofhir.registry.common.MappingSupport.OID_URN;
+import static org.openehealth.app.xdstofhir.registry.common.MappingSupport.URI_URN;
 
 import java.util.function.Consumer;
 import java.util.function.Function;
@@ -9,11 +10,15 @@
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.util.BundleBuilder;
 import lombok.RequiredArgsConstructor;
+import lombok.extern.slf4j.Slf4j;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.DocumentReference;
+import org.hl7.fhir.r4.model.Enumerations.DocumentReferenceStatus;
 import org.hl7.fhir.r4.model.Patient;
 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.AssociationType;
+import org.openehealth.ipf.commons.ihe.xds.core.metadata.AvailabilityStatus;
 import org.openehealth.ipf.commons.ihe.xds.core.metadata.DocumentEntry;
 import org.openehealth.ipf.commons.ihe.xds.core.requests.RegisterDocumentSet;
 import org.openehealth.ipf.commons.ihe.xds.core.responses.Response;
@@ -24,6 +29,7 @@
 
 @Component
 @RequiredArgsConstructor
+@Slf4j
 public class RegisterDocumentsProcessor implements Iti42Service {
     private final IGenericClient client;
     private final Function<DocumentEntry, DocumentReference> documentMapper;
@@ -34,8 +40,14 @@ public Response processRegister(RegisterDocumentSet register) {
         BundleBuilder builder = new BundleBuilder(client.getFhirContext());
 
         validateKnownRepository(register);
-        register.getDocumentEntries().forEach(this::assignEntryUuid);
+        register.getDocumentEntries().forEach(this::assignRegistryValues);
         register.getDocumentEntries().forEach(assignPatientId());
+        register.getAssociations().stream().filter(assoc -> assoc.getAssociationType() == AssociationType.REPLACE)
+                .forEach(assoc -> builder.addTransactionUpdateEntry(replacePreviousDocument(assoc.getTargetUuid(),
+                        register.getDocumentEntries().stream()
+                                .filter(doc -> doc.getEntryUuid().equals(assoc.getSourceUuid())).findFirst().map(documentMapper)
+                                .orElseThrow(() -> new XDSMetaDataException(ValidationMessage.UNRESOLVED_REFERENCE,
+                                        assoc.getSourceUuid())))));
         register.getDocumentEntries().forEach(doc -> builder.addTransactionCreateEntry(documentMapper.apply(doc)));
 
         // Execute the transaction
@@ -44,6 +56,33 @@ public Response processRegister(RegisterDocumentSet register) {
         return new Response(Status.SUCCESS);
     }
 
+    /**
+     * Perform replace according to https://profiles.ihe.net/ITI/TF/Volume2/ITI-42.html#3.42.4.1.3.5
+     *
+     * @param entryUuid
+     * @param replacingDocument
+     * @return Replaced document with status set to superseded
+     */
+    private DocumentReference replacePreviousDocument(String entryUuid, DocumentReference replacingDocument) {
+        var result = client.search().forResource(DocumentReference.class).count(1)
+                .where(DocumentReference.IDENTIFIER.exactly().systemAndValues(URI_URN, entryUuid))
+                .returnBundle(Bundle.class).execute();
+        if (result.getEntry().isEmpty()) {
+            throw new XDSMetaDataException(ValidationMessage.UNRESOLVED_REFERENCE, entryUuid);
+        }
+        var replacedDocument = (DocumentReference)result.getEntryFirstRep().getResource();
+        if (replacedDocument.getStatus() != DocumentReferenceStatus.CURRENT) {
+            throw new XDSMetaDataException(ValidationMessage.DEPRECATED_OBJ_CANNOT_BE_TRANSFORMED);
+        }
+        if (!replacedDocument.getSubject().getReference().equals(replacingDocument.getSubject().getReference())) {
+            log.debug("Replacing and replaced document do not have the same patientid {} and {}",
+                    replacedDocument.getSubject().getReference(), replacingDocument.getSubject().getReference());
+            throw new XDSMetaDataException(ValidationMessage.DOC_ENTRY_PATIENT_ID_WRONG);
+        }
+        replacedDocument.setStatus(DocumentReferenceStatus.SUPERSEDED);
+        return replacedDocument;
+    }
+
     private void validateKnownRepository(RegisterDocumentSet register) {
         register.getDocumentEntries().forEach(doc -> {
             if (!registryConfig.getRepositoryEndpoint().containsKey(doc.getRepositoryUniqueId())) {
@@ -52,10 +91,11 @@ private void validateKnownRepository(RegisterDocumentSet register) {
         });
     }
 
-    private void assignEntryUuid(DocumentEntry doc) {
+    private void assignRegistryValues(DocumentEntry doc) {
         if (!doc.getEntryUuid().startsWith(MappingSupport.UUID_URN)) {
             doc.assignEntryUuid();
         }
+        doc.setAvailabilityStatus(AvailabilityStatus.APPROVED);
     }
 
     private Consumer<DocumentEntry> assignPatientId() {

diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
@@ -6,6 +6,7 @@ fhir.server.base=http://hapi.fhir.org/baseR4
 # List of repositories in syntax xds.repositoryEndpoint.REPOSITORY-uniqueid=Download_endpoint
 # Is used for mapping from xds to fhir and reverse.
 xds.repositoryEndpoint.1.2.3.4=http://my.doc.retrieve/binary/$documentUniqueId
+xds.repositoryEndpoint.1.19.6.24.109.42.1=http://gazelle/binary/$documentUniqueId
 
 # Any document in fhir that can not be mapped will get a placeholder repository uniquieid
 xds.unknownRepositoryId=2.999.1.2.3
@@ -14,4 +15,6 @@ xds.defaultHash=0000000000000000000000000000000000000000
 
 xds.endpoint.iti18=xds-iti18:registry/iti18
 xds.endpoint.iti42=xds-iti42:registry/iti42
-xds.endpoint.iti8=xds-iti8:0.0.0.0:2575
+xds.endpoint.iti8=xds-iti8:0.0.0.0:2575
+
+server.port=8081
diff --git a/src/test/resources/logback.xml b/src/test/resources/logback.xml
@@ -4,5 +4,6 @@
 	<logger name="org.springframework.web" level="WARN"/>
 	<logger name="org.apache.cxf" level="INFO"/>
 	<logger name="ca.uhn.fhir.rest.client.interceptor" level="DEBUG" />
+	<logger name="org.openehealth.app.xdstofhir.registry" level="DEBUG" />
 	<root level="warn" />
 </configuration>