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#365 XDS ExtraMetadata slots might get duplicated if
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SubmitObjectsRequest's are unmarshalled and marshalled on the same
instance

* Fix extra metadata slot duplication
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@Thopap
Thopap committed Oct 18, 2021
1 parent 0a28758 commit d82cf68
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Showing 3 changed files with 286 additions and 20 deletions.
2 changes: 2 additions & 0 deletions ...ns/ihe/xds/src/main/java/org/openehealth/ipf/commons/ihe/xds/core/XdsJaxbDataBinding.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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 -> {
Expand Down
60 changes: 40 additions & 20 deletions ...t/java/org/openehealth/ipf/commons/ihe/xds/core/transform/ebxml/Ebrs30MarshalingTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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.
Expand All @@ -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();
Expand All @@ -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
Expand Down Expand Up @@ -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);
Expand All @@ -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);
Expand All @@ -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);
Expand All @@ -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();
Expand Down
244 changes: 244 additions & 0 deletions commons/ihe/xds/src/test/resources/SubmitObjectsRequest_ebrs3_extra_metadata.xml
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Original file line number Diff line number Diff line change
@@ -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^^^&amp;1.3.6.1.4.1.21367.2003.3.9&amp;ISO</rim:Value>
</rim:ValueList>
</rim:Slot>
<rim:Slot name="sourcePatientInfo">
<rim:ValueList>
<rim:Value>PID-3|ST-1000^^^&amp;1.3.6.1.4.1.21367.2003.3.9&amp;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^^^&amp;1.3.6.1.4.1.21367.2005.3.7&amp;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^^^&amp;1.3.6.1.4.1.21367.2005.3.7&amp;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>

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