Properly deserialize bound codes
This commit is contained in:
James Agnew
parent
232afee955
commit
ce253bed70
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@ -1,5 +1,9 @@
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package ca.uhn.fhir.model.primitive;
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import java.io.IOException;
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import java.io.ObjectInput;
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import java.io.ObjectOutput;
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/*
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* #%L
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* HAPI FHIR - Core Library
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@ -42,7 +46,7 @@ public class BoundCodeDt<T extends Enum<?>> extends CodeDt {
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Validate.notNull(theBinder, "theBinder must not be null");
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myBinder = theBinder;
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}
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public BoundCodeDt(IValueSetEnumBinder<T> theBinder, T theValue) {
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Validate.notNull(theBinder, "theBinder must not be null");
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myBinder = theBinder;
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@ -52,7 +56,7 @@ public class BoundCodeDt<T extends Enum<?>> extends CodeDt {
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public IValueSetEnumBinder<T> getBinder() {
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return myBinder;
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}
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public T getValueAsEnum() {
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Validate.notNull(myBinder, "This object does not have a binder. Constructor BoundCodeDt() should not be called!");
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T retVal = myBinder.fromCodeString(getValue());
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@ -62,6 +66,13 @@ public class BoundCodeDt<T extends Enum<?>> extends CodeDt {
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return retVal;
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}
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@SuppressWarnings("unchecked")
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@Override
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public void readExternal(ObjectInput theIn) throws IOException, ClassNotFoundException {
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super.readExternal(theIn);
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myBinder = (IValueSetEnumBinder<T>) theIn.readObject();
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}
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public void setValueAsEnum(T theValue) {
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Validate.notNull(myBinder, "This object does not have a binder. Constructor BoundCodeDt() should not be called!");
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if (theValue==null) {
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@ -70,4 +81,10 @@ public class BoundCodeDt<T extends Enum<?>> extends CodeDt {
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setValue(myBinder.toCodeString(theValue));
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}
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}
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@Override
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public void writeExternal(ObjectOutput theOut) throws IOException {
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super.writeExternal(theOut);
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theOut.writeObject(myBinder);
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}
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}
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@ -1,5 +1,7 @@
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package org.hl7.fhir.instance.model.api;
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import java.io.Serializable;
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/*
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* #%L
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* HAPI FHIR - Core Library
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@ -20,7 +22,7 @@ package org.hl7.fhir.instance.model.api;
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* #L%
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*/
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public interface IBaseEnumFactory<T extends Enum<?>> {
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public interface IBaseEnumFactory<T extends Enum<?>> extends Serializable {
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/**
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* Read an enumeration value from the string that represents it on the XML or JSON
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@ -1,56 +0,0 @@
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package ca.uhn.fhir.jpa.config;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.model.dstu2.resource.Bundle;
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import ca.uhn.fhir.model.dstu2.resource.Organization;
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import ca.uhn.fhir.model.dstu2.resource.Patient;
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import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
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import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.rest.client.IGenericClient;
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import ca.uhn.fhir.rest.client.ServerValidationModeEnum;
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public class Tmp {
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public static void main(String[] args) {
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FhirContext ctx = FhirContext.forDstu2();
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ctx.getRestfulClientFactory().setSocketTimeout(200000);
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ctx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
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IGenericClient client = ctx.newRestfulGenericClient("http://localhost:8080/hapi-fhir-jpaserver-example/baseDstu2");
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Bundle b = new Bundle();
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b.setType(BundleTypeEnum.TRANSACTION);
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int resCount = 20;
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for (int i = 0; i < (resCount / 2); i++) {
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Organization org = new Organization();
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org.setId(IdDt.newRandomUuid());
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org.setName("Random Org " + i);
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org.addAddress().addLine("Random Org Line 1");
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org.addIdentifier().setSystem("urn:foo").setValue("some_system" + i);
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b.addEntry().setResource(org).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Organization");
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Patient patient = new Patient();
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patient.setId(IdDt.newRandomUuid());
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patient.addName().addFamily("Family" + i).addGiven("Gigven " + i);
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patient.addAddress().addLine("Random Patient Line 1");
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patient.addIdentifier().setSystem("urn:bar").setValue("some_system" + i);
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b.addEntry().setResource(patient).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
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}
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int total = 0;
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long start = System.currentTimeMillis();
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for (int i = 0; i < 300; i++) {
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client.transaction().withBundle(b).execute();
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ourLog.info("" + i);
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total += resCount;
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}
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long delay = System.currentTimeMillis() - start;
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ourLog.info("Wrote {} resources at {}ms / res", total, delay / total);
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//sync 13:57:14.683 [main] INFO ca.uhn.fhir.jpa.config.Tmp - Wrote 6000 resources at 7ms / res
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}
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Tmp.class);
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}
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@ -31,8 +31,6 @@ import org.apache.commons.lang3.Validate;
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import ca.uhn.fhir.model.api.IBoundCodeableConcept;
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import ca.uhn.fhir.model.api.IValueSetEnumBinder;
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import ca.uhn.fhir.model.api.annotation.DatatypeDef;
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import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
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import ca.uhn.fhir.model.dstu2.composite.CodingDt;
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@DatatypeDef(name = "CodeableConcept", isSpecialization = true)
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public class BoundCodeableConceptDt<T extends Enum<?>> extends CodeableConceptDt implements IBoundCodeableConcept {
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@ -3,7 +3,6 @@ package ca.uhn.fhir.model.dstu2;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertTrue;
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import java.io.Serializable;
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import java.util.Date;
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import org.apache.commons.io.IOUtils;
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@ -15,18 +14,71 @@ import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
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import ca.uhn.fhir.model.dstu2.composite.AddressDt;
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import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
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import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
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import ca.uhn.fhir.model.dstu2.resource.Bundle;
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import ca.uhn.fhir.model.dstu2.resource.Patient;
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import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
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import ca.uhn.fhir.model.dstu2.valueset.IdentifierTypeCodesEnum;
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import ca.uhn.fhir.model.dstu2.valueset.MaritalStatusCodesEnum;
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import ca.uhn.fhir.parser.IParser;
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public class ModelSerializationTest {
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public class ModelSerializationDstu2Test {
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private static final FhirContext ourCtx = FhirContext.forDstu2();
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/**
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* Verify that MaritalStatusCodeEnum (and, by extension, BoundCodeableConcepts in general) are serializable. Author: Nick Peterson (nrpeterson@gmail.com)
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*/
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@Test
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public void testBoundCodeableConceptSerialization() {
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MaritalStatusCodesEnum maritalStatus = MaritalStatusCodesEnum.M;
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byte[] bytes = SerializationUtils.serialize(maritalStatus);
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assertTrue(bytes.length > 0);
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MaritalStatusCodesEnum deserialized = SerializationUtils.deserialize(bytes);
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assertEquals(maritalStatus.getCode(), deserialized.getCode());
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assertEquals(maritalStatus.getSystem(), deserialized.getSystem());
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}
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@Test
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public void testBoundCodeSerialization() {
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Patient p = new Patient();
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p.setGender(AdministrativeGenderEnum.MALE);
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IdentifierDt identifier = p.addIdentifier();
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identifier.setType(IdentifierTypeCodesEnum.DL);
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Patient out = testIsSerializable(p);
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/*
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* Make sure the binder still works for Code
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*/
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assertEquals(AdministrativeGenderEnum.MALE, out.getGenderElement().getValueAsEnum());
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out.getGenderElement().setValue("female");
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assertEquals(AdministrativeGenderEnum.FEMALE, out.getGenderElement().getValueAsEnum());
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assertEquals(IdentifierTypeCodesEnum.DL, out.getIdentifier().get(0).getType().getValueAsEnum().iterator().next());
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out.getIdentifier().get(0).getType().setValueAsEnum(IdentifierTypeCodesEnum.MR);
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assertEquals("MR", out.getIdentifier().get(0).getType().getCoding().get(0).getCode());
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assertEquals("http://hl7.org/fhir/v2/0203", out.getIdentifier().get(0).getType().getCoding().get(0).getSystem());
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}
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@SuppressWarnings("unchecked")
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private <T extends IBaseResource> T testIsSerializable(T theObject) {
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byte[] bytes = SerializationUtils.serialize(theObject);
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assertTrue(bytes.length > 0);
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IBaseResource obj = SerializationUtils.deserialize(bytes);
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assertTrue(obj != null);
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IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
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assertEquals(p.encodeResourceToString(theObject), p.encodeResourceToString(obj));
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return (T) obj;
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}
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@Test
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public void testSerialization() throws Exception {
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String input = IOUtils.toString(ModelSerializationTest.class.getResourceAsStream("/diagnosticreport-examples-lab-text(72ac8493-52ac-41bd-8d5d-7258c289b5ea).xml"));
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String input = IOUtils.toString(ModelSerializationDstu2Test.class.getResourceAsStream("/diagnosticreport-examples-lab-text(72ac8493-52ac-41bd-8d5d-7258c289b5ea).xml"));
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Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
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testIsSerializable(parsed);
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@ -44,31 +96,4 @@ public class ModelSerializationTest {
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testIsSerializable(patient);
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}
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private void testIsSerializable(IBaseResource theObject) {
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byte[] bytes = SerializationUtils.serialize(theObject);
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assertTrue(bytes.length > 0);
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IBaseResource obj = SerializationUtils.deserialize(bytes);
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assertTrue(obj != null);
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IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
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assertEquals(p.encodeResourceToString(theObject), p.encodeResourceToString(obj));
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}
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/**
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* Verify that MaritalStatusCodeEnum (and, by extension, BoundCodeableConcepts in general) are serializable.
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* Author: Nick Peterson (nrpeterson@gmail.com)
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*/
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@Test
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public void testBoundCodeableConceptSerialization() {
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MaritalStatusCodesEnum maritalStatus = MaritalStatusCodesEnum.M;
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byte[] bytes = SerializationUtils.serialize(maritalStatus);
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assertTrue(bytes.length > 0);
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MaritalStatusCodesEnum deserialized = SerializationUtils.deserialize(bytes);
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assertEquals(maritalStatus.getCode(), deserialized.getCode());
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assertEquals(maritalStatus.getSystem(), deserialized.getSystem());
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}
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}
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@ -1,5 +1,10 @@
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package org.hl7.fhir.dstu3.model;
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import java.io.Externalizable;
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import java.io.IOException;
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import java.io.ObjectInput;
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import java.io.ObjectOutput;
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import org.hl7.fhir.instance.model.api.IBaseEnumeration;
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import ca.uhn.fhir.model.api.annotation.DatatypeDef;
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@ -38,11 +43,20 @@ POSSIBILITY OF SUCH DAMAGE.
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*
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*/
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@DatatypeDef(name = "code", isSpecialization = true)
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public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements IBaseEnumeration<T> {
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public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements IBaseEnumeration<T>, Externalizable {
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private static final long serialVersionUID = 1L;
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private final EnumFactory<T> myEnumFactory;
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private EnumFactory<T> myEnumFactory;
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/**
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* Constructor
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* @deprecated This no-arg constructor is provided for serialization only - Do not use
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*/
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@Deprecated
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public Enumeration() {
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// nothing
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}
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/**
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* Constructor
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*/
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@ -100,4 +114,18 @@ public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements
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}
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return null;
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}
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@SuppressWarnings("unchecked")
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@Override
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public void readExternal(ObjectInput theIn) throws IOException, ClassNotFoundException {
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myEnumFactory = (EnumFactory<T>) theIn.readObject();
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super.readExternal(theIn);
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}
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@Override
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public void writeExternal(ObjectOutput theOut) throws IOException {
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theOut.writeObject(myEnumFactory);
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super.writeExternal(theOut);
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}
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}
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@ -1,5 +1,10 @@
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package org.hl7.fhir.dstu3.model;
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import java.io.Externalizable;
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import java.io.IOException;
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import java.io.ObjectInput;
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import java.io.ObjectOutput;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.builder.EqualsBuilder;
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import org.apache.commons.lang3.builder.HashCodeBuilder;
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@ -8,64 +13,18 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import ca.uhn.fhir.model.api.IElement;
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public abstract class PrimitiveType<T> extends Type implements IPrimitiveType<T>, IBaseHasExtensions, IElement {
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public abstract class PrimitiveType<T> extends Type implements IPrimitiveType<T>, IBaseHasExtensions, IElement, Externalizable {
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private static final long serialVersionUID = 3L;
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private T myCoercedValue;
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private String myStringValue;
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public T getValue() {
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return myCoercedValue;
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}
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public String asStringValue() {
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return myStringValue;
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}
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@Override
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public int hashCode() {
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return new HashCodeBuilder().append(getValue()).toHashCode();
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}
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public PrimitiveType<T> setValue(T theValue) {
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myCoercedValue = theValue;
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updateStringValue();
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return this;
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}
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protected void updateStringValue() {
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if (myCoercedValue == null) {
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myStringValue = null;
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} else {
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// NB this might be null
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myStringValue = encode(myCoercedValue);
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}
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}
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@Override
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public boolean isEmpty() {
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return super.isEmpty() && StringUtils.isBlank(getValueAsString());
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}
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public void fromStringValue(String theValue) {
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if (theValue == null) {
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myCoercedValue = null;
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} else {
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// NB this might be null
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myCoercedValue = parse(theValue);
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}
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myStringValue = theValue;
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}
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/**
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* Subclasses must override to convert an encoded representation of this datatype into a "coerced" one
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*
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* @param theValue
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* Will not be null
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* @return May return null if the value does not correspond to anything
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*/
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protected abstract T parse(String theValue);
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public abstract Type copy();
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/**
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* Subclasses must override to convert a "coerced" value into an encoded one.
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@ -76,37 +35,6 @@ public abstract class PrimitiveType<T> extends Type implements IPrimitiveType<T>
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*/
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protected abstract String encode(T theValue);
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public boolean isPrimitive() {
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return true;
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}
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public String primitiveValue() {
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return asStringValue();
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}
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@Override
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public String toString() {
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return getClass().getSimpleName() + "[" + asStringValue() + "]";
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}
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public boolean hasValue() {
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return !StringUtils.isBlank(getValueAsString());
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}
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public String getValueAsString() {
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return asStringValue();
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}
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public void setValueAsString(String theValue) {
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fromStringValue(theValue);
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}
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protected Type typedCopy() {
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return copy();
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}
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public abstract Type copy();
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@Override
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public boolean equalsDeep(Base obj) {
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if (!super.equalsDeep(obj))
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@ -141,4 +69,92 @@ public abstract class PrimitiveType<T> extends Type implements IPrimitiveType<T>
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return b.isEquals();
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}
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public void fromStringValue(String theValue) {
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if (theValue == null) {
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myCoercedValue = null;
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} else {
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// NB this might be null
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myCoercedValue = parse(theValue);
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}
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myStringValue = theValue;
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}
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public T getValue() {
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return myCoercedValue;
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}
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public String getValueAsString() {
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return asStringValue();
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}
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@Override
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public int hashCode() {
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return new HashCodeBuilder().append(getValue()).toHashCode();
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}
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public boolean hasValue() {
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return !StringUtils.isBlank(getValueAsString());
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}
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@Override
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public boolean isEmpty() {
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return super.isEmpty() && StringUtils.isBlank(getValueAsString());
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}
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|
||||
public boolean isPrimitive() {
|
||||
return true;
|
||||
}
|
||||
|
||||
/**
|
||||
* Subclasses must override to convert an encoded representation of this datatype into a "coerced" one
|
||||
*
|
||||
* @param theValue
|
||||
* Will not be null
|
||||
* @return May return null if the value does not correspond to anything
|
||||
*/
|
||||
protected abstract T parse(String theValue);
|
||||
|
||||
public String primitiveValue() {
|
||||
return asStringValue();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void readExternal(ObjectInput theIn) throws IOException, ClassNotFoundException {
|
||||
String object = (String) theIn.readObject();
|
||||
setValueAsString(object);
|
||||
}
|
||||
|
||||
public PrimitiveType<T> setValue(T theValue) {
|
||||
myCoercedValue = theValue;
|
||||
updateStringValue();
|
||||
return this;
|
||||
}
|
||||
|
||||
public void setValueAsString(String theValue) {
|
||||
fromStringValue(theValue);
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return getClass().getSimpleName() + "[" + asStringValue() + "]";
|
||||
}
|
||||
|
||||
protected Type typedCopy() {
|
||||
return copy();
|
||||
}
|
||||
|
||||
protected void updateStringValue() {
|
||||
if (myCoercedValue == null) {
|
||||
myStringValue = null;
|
||||
} else {
|
||||
// NB this might be null
|
||||
myStringValue = encode(myCoercedValue);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void writeExternal(ObjectOutput theOut) throws IOException {
|
||||
theOut.writeObject(getValueAsString());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,82 @@
|
|||
package ca.uhn.fhir.model;
|
||||
|
||||
import static org.junit.Assert.assertEquals;
|
||||
import static org.junit.Assert.assertTrue;
|
||||
|
||||
import java.util.Date;
|
||||
|
||||
import org.apache.commons.lang3.SerializationUtils;
|
||||
import org.hl7.fhir.dstu3.model.Address;
|
||||
import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
|
||||
import org.hl7.fhir.dstu3.model.HumanName;
|
||||
import org.hl7.fhir.dstu3.model.Patient;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.junit.Test;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
|
||||
import ca.uhn.fhir.parser.IParser;
|
||||
|
||||
public class ModelSerializationDstu3Test {
|
||||
|
||||
private static final FhirContext ourCtx = FhirContext.forDstu3();
|
||||
|
||||
/**
|
||||
* Verify that MaritalStatusCodeEnum (and, by extension, BoundCodeableConcepts in general) are serializable. Author: Nick Peterson (nrpeterson@gmail.com)
|
||||
*/
|
||||
@Test
|
||||
public void testBoundCodeableConceptSerialization() {
|
||||
AdministrativeGender maritalStatus = AdministrativeGender.MALE;
|
||||
byte[] bytes = SerializationUtils.serialize(maritalStatus);
|
||||
assertTrue(bytes.length > 0);
|
||||
|
||||
AdministrativeGender deserialized = SerializationUtils.deserialize(bytes);
|
||||
assertEquals(AdministrativeGender.MALE, deserialized);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testBoundCodeSerialization() {
|
||||
Patient p = new Patient();
|
||||
p.setGender(AdministrativeGender.MALE);
|
||||
|
||||
Patient out = testIsSerializable(p);
|
||||
|
||||
/*
|
||||
* Make sure the binder still works for Code
|
||||
*/
|
||||
assertEquals(AdministrativeGender.MALE, out.getGender());
|
||||
out.getGenderElement().setValueAsString("female");
|
||||
assertEquals(AdministrativeGender.FEMALE, out.getGender());
|
||||
|
||||
}
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
private <T extends IBaseResource> T testIsSerializable(T theObject) {
|
||||
byte[] bytes = SerializationUtils.serialize(theObject);
|
||||
assertTrue(bytes.length > 0);
|
||||
|
||||
IBaseResource obj = SerializationUtils.deserialize(bytes);
|
||||
assertTrue(obj != null);
|
||||
|
||||
IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
|
||||
assertEquals(p.encodeResourceToString(theObject), p.encodeResourceToString(obj));
|
||||
|
||||
return (T) obj;
|
||||
}
|
||||
|
||||
/**
|
||||
* Contributed by Travis from iSalus
|
||||
*/
|
||||
@Test
|
||||
public void testSerialization2() {
|
||||
Patient patient = new Patient();
|
||||
patient.addName(new HumanName().addGiven("George").addFamily("Washington"));
|
||||
patient.addName(new HumanName().addGiven("George2").addFamily("Washington2"));
|
||||
patient.addAddress(new Address().addLine("line 1").addLine("line 2").setCity("city").setState("UT"));
|
||||
patient.addAddress(new Address().addLine("line 1b").addLine("line 2b").setCity("cityb").setState("UT"));
|
||||
patient.setBirthDate(new Date());
|
||||
|
||||
testIsSerializable(patient);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -216,6 +216,14 @@
|
|||
requests where the URL does not contain an ID but needs to (e.g. for
|
||||
an update) or contains an ID but shouldn't (e.g. for a create)
|
||||
</action>
|
||||
<action type="fix">
|
||||
When fields of type BoundCodeDt (e.g. Patient.gender)
|
||||
are serialized and deserialized using Java's native
|
||||
object serialization, the enum binder was not
|
||||
serialized too. This meant that values for the
|
||||
field in the deserialized object could not be
|
||||
modified. Thanks to Thomas Andersen for reporting!
|
||||
</action>
|
||||
</release>
|
||||
<release version="1.4" date="2016-02-04">
|
||||
<action type="add">
|
||||
|
|
|
|||
Loading…
Reference in New Issue