From d82cf687f78865bc9a0f309d7e40f53c948c20ba Mon Sep 17 00:00:00 2001
From: Thomas Papke <web@thopap.de>
Date: Mon, 18 Oct 2021 20:56:53 +0200
Subject: [PATCH] #365 XDS ExtraMetadata slots might get duplicated if
SubmitObjectsRequest's are unmarshalled and marshalled on the same instance
* Fix extra metadata slot duplication
---
.../ihe/xds/core/XdsJaxbDataBinding.java | 2 +
.../transform/ebxml/Ebrs30MarshalingTest.java | 60 +++--
...mitObjectsRequest_ebrs3_extra_metadata.xml | 244 ++++++++++++++++++
3 files changed, 286 insertions(+), 20 deletions(-)
create mode 100644 commons/ihe/xds/src/test/resources/SubmitObjectsRequest_ebrs3_extra_metadata.xml
diff --git a/commons/ihe/xds/src/main/java/org/openehealth/ipf/commons/ihe/xds/core/XdsJaxbDataBinding.java b/commons/ihe/xds/src/main/java/org/openehealth/ipf/commons/ihe/xds/core/XdsJaxbDataBinding.java
index 14df8e3513..d168ffbadf 100644
--- a/commons/ihe/xds/src/main/java/org/openehealth/ipf/commons/ihe/xds/core/XdsJaxbDataBinding.java
+++ b/commons/ihe/xds/src/main/java/org/openehealth/ipf/commons/ihe/xds/core/XdsJaxbDataBinding.java
@@ -122,6 +122,8 @@ public void beforeMarshal(Object source) {
private static void injectExtraMetadata(List<SlotType1> slots, ExtraMetadataHolder holder) {
if (holder.getExtraMetadata() != null) {
+ slots.removeIf(slot -> isExtraMetadataSlotName(slot.getName())
+ && holder.getExtraMetadata().containsKey(slot.getName()));
holder.getExtraMetadata().entrySet().stream()
.filter(entry -> isExtraMetadataSlotName(entry.getKey()))
.forEach(entry -> {
diff --git a/commons/ihe/xds/src/test/java/org/openehealth/ipf/commons/ihe/xds/core/transform/ebxml/Ebrs30MarshalingTest.java b/commons/ihe/xds/src/test/java/org/openehealth/ipf/commons/ihe/xds/core/transform/ebxml/Ebrs30MarshalingTest.java
index 8a1fcda49d..c114475dde 100644
--- a/commons/ihe/xds/src/test/java/org/openehealth/ipf/commons/ihe/xds/core/transform/ebxml/Ebrs30MarshalingTest.java
+++ b/commons/ihe/xds/src/test/java/org/openehealth/ipf/commons/ihe/xds/core/transform/ebxml/Ebrs30MarshalingTest.java
@@ -17,6 +17,7 @@
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
+import org.openehealth.ipf.commons.ihe.xds.core.XdsJaxbDataBinding;
import org.openehealth.ipf.commons.ihe.xds.core.ebxml.EbXMLExtrinsicObject;
import org.openehealth.ipf.commons.ihe.xds.core.ebxml.EbXMLObjectLibrary;
import org.openehealth.ipf.commons.ihe.xds.core.ebxml.ebxml30.EbXMLAdhocQueryRequest30;
@@ -29,21 +30,26 @@
import org.openehealth.ipf.commons.ihe.xds.core.stub.ebrs30.lcm.SubmitObjectsRequest;
import org.openehealth.ipf.commons.ihe.xds.core.stub.ebrs30.query.AdhocQueryRequest;
import org.openehealth.ipf.commons.ihe.xds.core.stub.ebrs30.rim.ExtrinsicObjectType;
-import org.openehealth.ipf.commons.ihe.xds.core.stub.ebrs30.rim.IdentifiableType;
+import org.openehealth.ipf.commons.ihe.xds.core.stub.ebrs30.rim.ObjectFactory;
import org.openehealth.ipf.commons.ihe.xds.core.stub.ebrs30.rim.RegistryObjectListType;
import org.openehealth.ipf.commons.ihe.xds.core.transform.requests.QueryParameter;
import org.openehealth.ipf.commons.ihe.xds.core.transform.requests.RegisterDocumentSetTransformer;
import org.openehealth.ipf.commons.ihe.xds.core.transform.requests.query.QuerySlotHelper;
import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
import javax.xml.bind.JAXBException;
-import javax.xml.namespace.QName;
+
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
+import java.io.StringReader;
+import java.io.StringWriter;
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.fail;
/**
* Tests for marshaling objects created with our ebxml 2.1 classes.
@@ -54,14 +60,13 @@ public class Ebrs30MarshalingTest {
private EbXMLExtrinsicObject docEntry;
private EbXMLFactory30 factory;
private EbXMLObjectLibrary objectLibrary;
-
- private static final QName EXTRINSIC_OBJECT_QNAME =
- new QName("urn:oasis:names:tc:ebxml-regrep:xsd:rim:3.0", "ExtrinsicObject", "rim");
+ private JAXBContext context;
@BeforeEach
- public void setUp() {
+ public void setUp() throws JAXBException {
factory = new EbXMLFactory30();
objectLibrary = factory.createObjectLibrary();
+ context = JAXBContext.newInstance("org.openehealth.ipf.commons.ihe.xds.core.stub.ebrs30.rs");
request = new SubmitObjectsRequest();
var objListElement = new RegistryObjectListType();
@@ -70,12 +75,7 @@ public void setUp() {
docEntry = factory.createExtrinsic("Document01", objectLibrary);
docEntry.setObjectType(DocumentEntryType.STABLE.getUuid());
- objList.add(getJaxbElement(EXTRINSIC_OBJECT_QNAME, ((EbXMLExtrinsicObject30)docEntry).getInternal()));
- }
-
- @SuppressWarnings("unchecked")
- private static JAXBElement<IdentifiableType> getJaxbElement(QName qname, IdentifiableType object) {
- return new JAXBElement<>(qname, (Class)object.getClass(), object);
+ objList.add(new ObjectFactory().createExtrinsicObject(((EbXMLExtrinsicObject30)docEntry).getInternal()));
}
@Test
@@ -131,8 +131,7 @@ public void testAddSlot() throws Exception {
@Test
public void testFromRealEbXML() throws Exception {
var file = new File(getClass().getClassLoader().getResource("SubmitObjectsRequest_ebrs30.xml").toURI());
-
- var context = JAXBContext.newInstance("org.openehealth.ipf.commons.ihe.xds.core.stub.ebrs30.rs");
+
var unmarshaller = context.createUnmarshaller();
var unmarshalled = unmarshaller.unmarshal(file);
@@ -158,8 +157,6 @@ public void testFromRealEbXML() throws Exception {
@Test
public void testPatientIdSlotRegexp() throws Exception {
var file = new File(getClass().getClassLoader().getResource("iti18request.xml").toURI());
-
- var context = JAXBContext.newInstance("org.openehealth.ipf.commons.ihe.xds.core.stub.ebrs30.rs");
var unmarshaller = context.createUnmarshaller();
var unmarshalled = unmarshaller.unmarshal(file);
@@ -174,7 +171,6 @@ public void testPatientIdSlotRegexp() throws Exception {
public void testPatientIdMPQSlotRegexp() throws Exception {
var file = new File(getClass().getClassLoader().getResource("iti51request.xml").toURI());
- var context = JAXBContext.newInstance("org.openehealth.ipf.commons.ihe.xds.core.stub.ebrs30.rs");
var unmarshaller = context.createUnmarshaller();
var unmarshalled = unmarshaller.unmarshal(file);
@@ -184,9 +180,33 @@ public void testPatientIdMPQSlotRegexp() throws Exception {
var patientIdList = slotHelper.toStringList(QueryParameter.DOC_ENTRY_PATIENT_ID);
assertEquals(2, patientIdList.size());
}
+
+ @Test
+ public void verifyExtraMetadataWithJaxbBinding() throws Exception {
+ var file = new File(
+ getClass().getClassLoader().getResource("SubmitObjectsRequest_ebrs3_extra_metadata.xml").toURI());
+ var unmarshaller = context.createUnmarshaller();
+ unmarshaller.setListener(new XdsJaxbDataBinding().getUnmarshallerListener());
+
+ var unmarshalled = unmarshaller.unmarshal(file);
+ var original = (SubmitObjectsRequest) unmarshalled;
+ int numberOfSlotsInFirstDoc = new EbXMLSubmitObjectsRequest30(original).getExtrinsicObjects().get(0).getSlots()
+ .size();
+
+ var marshaller = context.createMarshaller();
+ marshaller.setListener(new XdsJaxbDataBinding().getMarshallerListener());
+ StringWriter writer = new StringWriter();
+ marshaller.marshal(original, writer);
+
+ var unmarshalledSecond = (SubmitObjectsRequest) unmarshaller.unmarshal(new StringReader(writer.toString()));
+ int numberOfSlotsInSecondDoc = new EbXMLSubmitObjectsRequest30(unmarshalledSecond).getExtrinsicObjects().get(0)
+ .getSlots().size();
+
+ assertEquals(numberOfSlotsInFirstDoc, numberOfSlotsInSecondDoc,
+ "Number of slots after Marshalling and Unmarsshalling does not match");
+ }
private SubmitObjectsRequest send() throws JAXBException {
- var context = JAXBContext.newInstance("org.openehealth.ipf.commons.ihe.xds.core.stub.ebrs30.rs");
var marshaller = context.createMarshaller();
var unmarshaller = context.createUnmarshaller();
var outputStream = new ByteArrayOutputStream();
diff --git a/commons/ihe/xds/src/test/resources/SubmitObjectsRequest_ebrs3_extra_metadata.xml b/commons/ihe/xds/src/test/resources/SubmitObjectsRequest_ebrs3_extra_metadata.xml
new file mode 100644
index 0000000000..8e8dbd46a1
--- /dev/null
+++ b/commons/ihe/xds/src/test/resources/SubmitObjectsRequest_ebrs3_extra_metadata.xml
@@ -0,0 +1,244 @@
+<lcm:SubmitObjectsRequest xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="urn:oasis:names:tc:ebxml-regrep:xsd:lcm:3.0 ../schema/ebRS/lcm.xsd"
+ xmlns:lcm="urn:oasis:names:tc:ebxml-regrep:xsd:lcm:3.0" xmlns:rim="urn:oasis:names:tc:ebxml-regrep:xsd:rim:3.0"
+ xmlns:rs="urn:oasis:names:tc:ebxml-regrep:xsd:rs:3.0">
+ <rim:RegistryObjectList>
+ <rim:ExtrinsicObject id="Document01" mimeType="text/xml"
+ objectType="urn:uuid:7edca82f-054d-47f2-a032-9b2a5b5186c1">
+ <rim:Slot name="creationTime">
+ <rim:ValueList>
+ <rim:Value>20051224</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="languageCode">
+ <rim:ValueList>
+ <rim:Value>en-us</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="serviceStartTime">
+ <rim:ValueList>
+ <rim:Value>200412230800</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="serviceStopTime">
+ <rim:ValueList>
+ <rim:Value>200412230801</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="sourcePatientId">
+ <rim:ValueList>
+ <rim:Value>ST-1000^^^&1.3.6.1.4.1.21367.2003.3.9&ISO</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="sourcePatientInfo">
+ <rim:ValueList>
+ <rim:Value>PID-3|ST-1000^^^&1.3.6.1.4.1.21367.2003.3.9&ISO</rim:Value>
+ <rim:Value>PID-5|Doe^John^^^</rim:Value>
+ <rim:Value>PID-7|19560527</rim:Value>
+ <rim:Value>PID-8|M</rim:Value>
+ <rim:Value>PID-11|100 Main St^^Metropolis^Il^44130^USA</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="urn:my:company:slot">
+ <rim:ValueList>
+ <rim:Value>somevalue</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Name>
+ <rim:LocalizedString value="Physical"/>
+ </rim:Name>
+ <rim:Description/>
+ <rim:Classification id="cl01"
+ classificationScheme="urn:uuid:93606bcf-9494-43ec-9b4e-a7748d1a838d"
+ classifiedObject="Document01">
+ <rim:Slot name="authorPerson">
+ <rim:ValueList>
+ <rim:Value>Gerald Smitty</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="authorInstitution">
+ <rim:ValueList>
+ <rim:Value>Cleveland Clinic</rim:Value>
+ <rim:Value>Parma Community</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="authorRole">
+ <rim:ValueList>
+ <rim:Value>Attending</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="authorSpeciality">
+ <rim:ValueList>
+ <rim:Value>Orthopedic</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ </rim:Classification>
+ <rim:Classification id="cl02"
+ classificationScheme="urn:uuid:41a5887f-8865-4c09-adf7-e362475b143a"
+ classifiedObject="Document01" nodeRepresentation="History and Physical">
+ <rim:Slot name="codingScheme">
+ <rim:ValueList>
+ <rim:Value>Connect-a-thon classCodes</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Name>
+ <rim:LocalizedString value="History and Physical"/>
+ </rim:Name>
+ </rim:Classification>
+ <rim:Classification id="cl03"
+ classificationScheme="urn:uuid:f4f85eac-e6cb-4883-b524-f2705394840f"
+ classifiedObject="Document01" nodeRepresentation="1.3.6.1.4.1.21367.2006.7.101">
+ <rim:Slot name="codingScheme">
+ <rim:ValueList>
+ <rim:Value>Connect-a-thon confidentialityCodes</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Name>
+ <rim:LocalizedString value="Clinical-Staff"/>
+ </rim:Name>
+ </rim:Classification>
+ <rim:Classification id="cl04"
+ classificationScheme="urn:uuid:a09d5840-386c-46f2-b5ad-9c3699a4309d"
+ classifiedObject="Document01" nodeRepresentation="CDAR2/IHE 1.0">
+ <rim:Slot name="codingScheme">
+ <rim:ValueList>
+ <rim:Value>Connect-a-thon formatCodes</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Name>
+ <rim:LocalizedString value="CDAR2/IHE 1.0"/>
+ </rim:Name>
+ </rim:Classification>
+ <rim:Classification id="cl05"
+ classificationScheme="urn:uuid:f33fb8ac-18af-42cc-ae0e-ed0b0bdb91e1"
+ classifiedObject="Document01" nodeRepresentation="Outpatient">
+ <rim:Slot name="codingScheme">
+ <rim:ValueList>
+ <rim:Value>Connect-a-thon healthcareFacilityTypeCodes</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Name>
+ <rim:LocalizedString value="Outpatient"/>
+ </rim:Name>
+ </rim:Classification>
+ <rim:Classification id="cl06"
+ classificationScheme="urn:uuid:cccf5598-8b07-4b77-a05e-ae952c785ead"
+ classifiedObject="Document01" nodeRepresentation="General Medicine">
+ <rim:Slot name="codingScheme">
+ <rim:ValueList>
+ <rim:Value>Connect-a-thon practiceSettingCodes</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Name>
+ <rim:LocalizedString value="General Medicine"/>
+ </rim:Name>
+ </rim:Classification>
+ <rim:Classification id="cl07"
+ classificationScheme="urn:uuid:f0306f51-975f-434e-a61c-c59651d33983"
+ classifiedObject="Document01" nodeRepresentation="34108-1">
+ <rim:Slot name="codingScheme">
+ <rim:ValueList>
+ <rim:Value>LOINC</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Name>
+ <rim:LocalizedString value="Outpatient Evaluation And Management"/>
+ </rim:Name>
+ </rim:Classification>
+ <rim:ExternalIdentifier id="ei01" registryObject="Document01"
+ identificationScheme="urn:uuid:58a6f841-87b3-4a3e-92fd- a8ffeff98427"
+ value="SELF-5^^^&1.3.6.1.4.1.21367.2005.3.7&ISO">
+ <rim:Name>
+ <rim:LocalizedString value="XDSDocumentEntry.patientId"/>
+ </rim:Name>
+ </rim:ExternalIdentifier>
+ <rim:ExternalIdentifier id="ei02" registryObject="Document01"
+ identificationScheme="urn:uuid:2e82c1f6-a085-4c72-9da3-8640a32e42ab"
+ value="1.3.6.1.4.1.21367.2005.3.9999.32">
+ <rim:Name>
+ <rim:LocalizedString value="XDSDocumentEntry.uniqueId"/>
+ </rim:Name>
+ </rim:ExternalIdentifier>
+ </rim:ExtrinsicObject>
+ <rim:RegistryPackage id="SubmissionSet01">
+ <rim:Slot name="submissionTime">
+ <rim:ValueList>
+ <rim:Value>20041225235050</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Name>
+ <rim:LocalizedString value="Physical"/>
+ </rim:Name>
+ <rim:Description>
+ <rim:LocalizedString value="Annual physical"/>
+ </rim:Description>
+ <rim:Classification id="cl08"
+ classificationScheme="urn:uuid:a7058bb9-b4e4-4307-ba5b-e3f0ab85e12d"
+ classifiedObject="SubmissionSet01">
+ <rim:Slot name="authorPerson">
+ <rim:ValueList>
+ <rim:Value>Sherry Dopplemeyer</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="authorInstitution">
+ <rim:ValueList>
+ <rim:Value>Cleveland Clinic</rim:Value>
+ <rim:Value>Berea Community</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="authorRole">
+ <rim:ValueList>
+ <rim:Value>Primary Surgon</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Slot name="authorSpeciality">
+ <rim:ValueList>
+ <rim:Value>Orthopedic</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ </rim:Classification>
+ <rim:Classification id="cl09"
+ classificationScheme="urn:uuid:aa543740-bdda-424e-8c96- df4873be8500"
+ classifiedObject="SubmissionSet01" nodeRepresentation="History and Physical">
+ <rim:Slot name="codingScheme">
+ <rim:ValueList>
+ <rim:Value>Connect-a-thon contentTypeCodes</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ <rim:Name>
+ <rim:LocalizedString value="History and Physical"/>
+ </rim:Name>
+ </rim:Classification>
+ <rim:ExternalIdentifier id="ei03" registryObject="SubmissionSet01"
+ identificationScheme="urn:uuid:96fdda7c-d067-4183-912e- bf5ee74998a8"
+ value="1.3.6.1.4.1.21367.2005.3.9999.33">
+ <rim:Name>
+ <rim:LocalizedString value="XDSSubmissionSet.uniqueId"/>
+ </rim:Name>
+ </rim:ExternalIdentifier>
+ <rim:ExternalIdentifier id="ei04" registryObject="SubmissionSet01"
+ identificationScheme="urn:uuid:554ac39e-e3fe-47fe-b233-965d2a147832" value="3670984664">
+ <rim:Name>
+ <rim:LocalizedString value="XDSSubmissionSet.sourceId"/>
+ </rim:Name>
+ </rim:ExternalIdentifier>
+ <rim:ExternalIdentifier id="ei05" registryObject="SubmissionSet01"
+ identificationScheme="urn:uuid:6b5aea1a-874d-4603-a4bc- 96a0a7b38446"
+ value="SELF-5^^^&1.3.6.1.4.1.21367.2005.3.7&ISO">
+ <rim:Name>
+ <rim:LocalizedString value="XDSSubmissionSet.patientId"/>
+ </rim:Name>
+ </rim:ExternalIdentifier>
+ </rim:RegistryPackage>
+ <rim:Classification id="cl10" classifiedObject="SubmissionSet01"
+ classificationNode="urn:uuid:a54d6aa5-d40d-43f9-88c5-b4633d873bdd"/>
+ <rim:Association id="as01" associationType="urn:oasis:names:tc:ebxml-regrep:AssociationType:HasMember" sourceObject="SubmissionSet01" targetObject="Document01">
+ <rim:Slot name="SubmissionSetStatus">
+ <rim:ValueList>
+ <rim:Value>Original</rim:Value>
+ </rim:ValueList>
+ </rim:Slot>
+ </rim:Association>
+ <rim:Association id="as02" associationType="urn:ihe:iti:2010:AssociationType:IsSnapshotOf" sourceObject="Document01" targetObject="urn:uuid:e0985823-dc50-45a5-a6c8-a11a829893bd" />
+ </rim:RegistryObjectList>
+</lcm:SubmitObjectsRequest>