Properly deserialize bound codes

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/BoundCodeDt.java

@@ -1,5 +1,9 @@
 package ca.uhn.fhir.model.primitive;
 
+import java.io.IOException;
+import java.io.ObjectInput;
+import java.io.ObjectOutput;
+
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -42,7 +46,7 @@ public class BoundCodeDt<T extends Enum<?>> extends CodeDt {
 		Validate.notNull(theBinder, "theBinder must not be null");
 		myBinder = theBinder;
 	}
-	
+
 	public BoundCodeDt(IValueSetEnumBinder<T> theBinder, T theValue) {
 		Validate.notNull(theBinder, "theBinder must not be null");
 		myBinder = theBinder;
@@ -52,7 +56,7 @@ public class BoundCodeDt<T extends Enum<?>> extends CodeDt {
 	public IValueSetEnumBinder<T> getBinder() {
 		return myBinder;
 	}
-
+	
 	public T getValueAsEnum() {
 		Validate.notNull(myBinder, "This object does not have a binder. Constructor BoundCodeDt() should not be called!");
 		T retVal = myBinder.fromCodeString(getValue());
@@ -62,6 +66,13 @@ public class BoundCodeDt<T extends Enum<?>> extends CodeDt {
 		return retVal;
 	}
 
+	@SuppressWarnings("unchecked")
+	@Override
+	public void readExternal(ObjectInput theIn) throws IOException, ClassNotFoundException {
+		super.readExternal(theIn);
+		myBinder = (IValueSetEnumBinder<T>) theIn.readObject();
+	}
+
 	public void setValueAsEnum(T theValue) {
 		Validate.notNull(myBinder, "This object does not have a binder. Constructor BoundCodeDt() should not be called!");
 		if (theValue==null) {
@@ -70,4 +81,10 @@ public class BoundCodeDt<T extends Enum<?>> extends CodeDt {
 			setValue(myBinder.toCodeString(theValue));
 		}
 	}
+
+	@Override
+	public void writeExternal(ObjectOutput theOut) throws IOException {
+		super.writeExternal(theOut);
+		theOut.writeObject(myBinder);
+	}
 }

hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBaseEnumFactory.java

@@ -1,5 +1,7 @@
 package org.hl7.fhir.instance.model.api;
 
+import java.io.Serializable;
+
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -20,7 +22,7 @@ package org.hl7.fhir.instance.model.api;
  * #L%
  */
 
-public interface IBaseEnumFactory<T extends Enum<?>> {
+public interface IBaseEnumFactory<T extends Enum<?>> extends Serializable {
 
     /**
      * Read an enumeration value from the string that represents it on the XML or JSON

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/Tmp.java

@@ -1,56 +0,0 @@
-package ca.uhn.fhir.jpa.config;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.dstu2.resource.Bundle;
-import ca.uhn.fhir.model.dstu2.resource.Organization;
-import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
-import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
-import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.rest.client.IGenericClient;
-import ca.uhn.fhir.rest.client.ServerValidationModeEnum;
-
-public class Tmp {
-
-	public static void main(String[] args) {
-		
-		FhirContext ctx = FhirContext.forDstu2();
-		ctx.getRestfulClientFactory().setSocketTimeout(200000);
-		ctx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
-		IGenericClient client = ctx.newRestfulGenericClient("http://localhost:8080/hapi-fhir-jpaserver-example/baseDstu2");
-		
-		Bundle b = new Bundle();
-		b.setType(BundleTypeEnum.TRANSACTION);
-		int resCount = 20;
-		for (int i = 0; i < (resCount / 2); i++) {
-			Organization org = new Organization();
-			org.setId(IdDt.newRandomUuid());
-			org.setName("Random Org " + i);
-			org.addAddress().addLine("Random Org Line 1");
-			org.addIdentifier().setSystem("urn:foo").setValue("some_system" + i);
-			b.addEntry().setResource(org).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Organization");
-			
-			Patient patient = new Patient();
-			patient.setId(IdDt.newRandomUuid());
-			patient.addName().addFamily("Family" + i).addGiven("Gigven " + i);
-			patient.addAddress().addLine("Random Patient Line 1");
-			patient.addIdentifier().setSystem("urn:bar").setValue("some_system" + i);
-			b.addEntry().setResource(patient).getRequest().setMethod(HTTPVerbEnum.POST).setUrl("Patient");
-		}
-		
-		int total = 0;
-		long start = System.currentTimeMillis();
-		for (int i = 0; i < 300; i++) {
-		client.transaction().withBundle(b).execute();
-		ourLog.info("" + i);
-		total += resCount;
-		}
-		
-		long delay = System.currentTimeMillis() - start;
-		ourLog.info("Wrote {} resources at {}ms / res", total, delay / total);
-		
-		//sync  13:57:14.683 [main] INFO  ca.uhn.fhir.jpa.config.Tmp - Wrote 6000 resources at 7ms / res
-	}
-private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Tmp.class);
-
-}

hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/model/dstu2/composite/BoundCodeableConceptDt.java

@@ -31,8 +31,6 @@ import org.apache.commons.lang3.Validate;
 import ca.uhn.fhir.model.api.IBoundCodeableConcept;
 import ca.uhn.fhir.model.api.IValueSetEnumBinder;
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
-import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
-import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 
 @DatatypeDef(name = "CodeableConcept", isSpecialization = true)
 public class BoundCodeableConceptDt<T extends Enum<?>> extends CodeableConceptDt implements IBoundCodeableConcept {

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/model/dstu2/ModelSerializationDstu2Test.java

@@ -3,7 +3,6 @@ package ca.uhn.fhir.model.dstu2;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
 
-import java.io.Serializable;
 import java.util.Date;
 
 import org.apache.commons.io.IOUtils;
@@ -15,18 +14,71 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
 import ca.uhn.fhir.model.dstu2.composite.AddressDt;
 import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
+import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
+import ca.uhn.fhir.model.dstu2.valueset.IdentifierTypeCodesEnum;
 import ca.uhn.fhir.model.dstu2.valueset.MaritalStatusCodesEnum;
 import ca.uhn.fhir.parser.IParser;
 
-public class ModelSerializationTest {
+public class ModelSerializationDstu2Test {
 
 	private static final FhirContext ourCtx = FhirContext.forDstu2();
 
+	/**
+	 * Verify that MaritalStatusCodeEnum (and, by extension, BoundCodeableConcepts in general) are serializable. Author: Nick Peterson (nrpeterson@gmail.com)
+	 */
+	@Test
+	public void testBoundCodeableConceptSerialization() {
+		MaritalStatusCodesEnum maritalStatus = MaritalStatusCodesEnum.M;
+		byte[] bytes = SerializationUtils.serialize(maritalStatus);
+		assertTrue(bytes.length > 0);
+
+		MaritalStatusCodesEnum deserialized = SerializationUtils.deserialize(bytes);
+		assertEquals(maritalStatus.getCode(), deserialized.getCode());
+		assertEquals(maritalStatus.getSystem(), deserialized.getSystem());
+	}
+
+	@Test
+	public void testBoundCodeSerialization() {
+		Patient p = new Patient();
+		p.setGender(AdministrativeGenderEnum.MALE);
+		IdentifierDt identifier = p.addIdentifier();
+		identifier.setType(IdentifierTypeCodesEnum.DL);
+
+		Patient out = testIsSerializable(p);
+
+		/*
+		 * Make sure the binder still works for Code
+		 */
+		assertEquals(AdministrativeGenderEnum.MALE, out.getGenderElement().getValueAsEnum());
+		out.getGenderElement().setValue("female");
+		assertEquals(AdministrativeGenderEnum.FEMALE, out.getGenderElement().getValueAsEnum());
+
+		assertEquals(IdentifierTypeCodesEnum.DL, out.getIdentifier().get(0).getType().getValueAsEnum().iterator().next());
+		out.getIdentifier().get(0).getType().setValueAsEnum(IdentifierTypeCodesEnum.MR);
+		assertEquals("MR", out.getIdentifier().get(0).getType().getCoding().get(0).getCode());
+		assertEquals("http://hl7.org/fhir/v2/0203", out.getIdentifier().get(0).getType().getCoding().get(0).getSystem());
+	}
+
+	@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;
+	}
+
 	@Test
 	public void testSerialization() throws Exception {
-		String input = IOUtils.toString(ModelSerializationTest.class.getResourceAsStream("/diagnosticreport-examples-lab-text(72ac8493-52ac-41bd-8d5d-7258c289b5ea).xml"));
+		String input = IOUtils.toString(ModelSerializationDstu2Test.class.getResourceAsStream("/diagnosticreport-examples-lab-text(72ac8493-52ac-41bd-8d5d-7258c289b5ea).xml"));
 
 		Bundle parsed = ourCtx.newXmlParser().parseResource(Bundle.class, input);
 		testIsSerializable(parsed);
@@ -44,31 +96,4 @@ public class ModelSerializationTest {
 		testIsSerializable(patient);
 	}
 
-	private void testIsSerializable(IBaseResource 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));
-
-	}
-
-	/**
-	 * Verify that MaritalStatusCodeEnum (and, by extension, BoundCodeableConcepts in general) are serializable.
-	 * Author: Nick Peterson (nrpeterson@gmail.com)
-	 */
-	@Test
-	public void testBoundCodeableConceptSerialization() {
-		MaritalStatusCodesEnum maritalStatus = MaritalStatusCodesEnum.M;
-		byte[] bytes = SerializationUtils.serialize(maritalStatus);
-		assertTrue(bytes.length > 0);
-
-		MaritalStatusCodesEnum deserialized = SerializationUtils.deserialize(bytes);
-		assertEquals(maritalStatus.getCode(), deserialized.getCode());
-		assertEquals(maritalStatus.getSystem(), deserialized.getSystem());
-	}
-
 }

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/Enumeration.java

@@ -1,5 +1,10 @@
 package org.hl7.fhir.dstu3.model;
 
+import java.io.Externalizable;
+import java.io.IOException;
+import java.io.ObjectInput;
+import java.io.ObjectOutput;
+
 import org.hl7.fhir.instance.model.api.IBaseEnumeration;
 
 import ca.uhn.fhir.model.api.annotation.DatatypeDef;
@@ -38,11 +43,20 @@ POSSIBILITY OF SUCH DAMAGE.
  * 
  */
 @DatatypeDef(name = "code", isSpecialization = true)
-public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements IBaseEnumeration<T> {
+public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements IBaseEnumeration<T>, Externalizable {
 
 	private static final long serialVersionUID = 1L;
-	private final EnumFactory<T> myEnumFactory;
+	private EnumFactory<T> myEnumFactory;
 
+	/**
+	 * Constructor
+	 * @deprecated This no-arg constructor is provided for serialization only - Do not use
+	 */
+	@Deprecated
+	public Enumeration() {
+		// nothing
+	}
+	
 	/**
 	 * Constructor
 	 */
@@ -100,4 +114,18 @@ public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements
 		}
 		return null;
 	}
+	
+	@SuppressWarnings("unchecked")
+	@Override
+	public void readExternal(ObjectInput theIn) throws IOException, ClassNotFoundException {
+		myEnumFactory = (EnumFactory<T>) theIn.readObject();
+		super.readExternal(theIn);
+	}
+
+	@Override
+	public void writeExternal(ObjectOutput theOut) throws IOException {
+		theOut.writeObject(myEnumFactory);
+		super.writeExternal(theOut);
+	}
+
 }

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/PrimitiveType.java

@@ -1,5 +1,10 @@
 package org.hl7.fhir.dstu3.model;
 
+import java.io.Externalizable;
+import java.io.IOException;
+import java.io.ObjectInput;
+import java.io.ObjectOutput;
+
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
@@ -8,64 +13,18 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import ca.uhn.fhir.model.api.IElement;
 
-public abstract class PrimitiveType<T> extends Type implements IPrimitiveType<T>, IBaseHasExtensions, IElement {
+public abstract class PrimitiveType<T> extends Type implements IPrimitiveType<T>, IBaseHasExtensions, IElement, Externalizable {
 
 	private static final long serialVersionUID = 3L;
 
 	private T myCoercedValue;
 	private String myStringValue;
 
-	public T getValue() {
-		return myCoercedValue;
-	}
-
 	public String asStringValue() {
 		return myStringValue;
 	}
 
-	@Override
+	public abstract Type copy();
-	public int hashCode() {
-		return new HashCodeBuilder().append(getValue()).toHashCode();
-	}
-
-	public PrimitiveType<T> setValue(T theValue) {
-		myCoercedValue = theValue;
-		updateStringValue();
-		return this;
-	}
-
-	protected void updateStringValue() {
-		if (myCoercedValue == null) {
-			myStringValue = null;
-		} else {
-			// NB this might be null
-			myStringValue = encode(myCoercedValue);
-		}
-	}
-
-	@Override
-	public boolean isEmpty() {
-		return super.isEmpty() && StringUtils.isBlank(getValueAsString());
-	}
-
-	public void fromStringValue(String theValue) {
-		if (theValue == null) {
-			myCoercedValue = null;
-		} else {
-			// NB this might be null
-			myCoercedValue = parse(theValue);
-		}
-		myStringValue = theValue;
-	}
-
-	/**
-	 * 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);
 
 	/**
 	 * Subclasses must override to convert a "coerced" value into an encoded one.
@@ -76,37 +35,6 @@ public abstract class PrimitiveType<T> extends Type implements IPrimitiveType<T>
 	 */
 	protected abstract String encode(T theValue);
 
-	public boolean isPrimitive() {
-		return true;
-	}
-	
-	public String primitiveValue() {
-		return asStringValue();
-	}
-
-	@Override
-	public String toString() {
-		return getClass().getSimpleName() + "[" + asStringValue() + "]";
-	}
-
-	public boolean hasValue() {
-  	  return !StringUtils.isBlank(getValueAsString());
-	}
-
-	public String getValueAsString() {
-		return asStringValue();
-	}
-
-	public void setValueAsString(String theValue) {
-		fromStringValue(theValue);
-	}
-
-	protected Type typedCopy() {
-		return copy();
-	}
-
-	public abstract Type copy();
-
 	@Override
 	public boolean equalsDeep(Base obj) {
 		if (!super.equalsDeep(obj))
@@ -141,4 +69,92 @@ public abstract class PrimitiveType<T> extends Type implements IPrimitiveType<T>
 		return b.isEquals();
 	}
 
+	public void fromStringValue(String theValue) {
+		if (theValue == null) {
+			myCoercedValue = null;
+		} else {
+			// NB this might be null
+			myCoercedValue = parse(theValue);
+		}
+		myStringValue = theValue;
+	}
+
+	public T getValue() {
+		return myCoercedValue;
+	}
+
+	public String getValueAsString() {
+		return asStringValue();
+	}
+
+	@Override
+	public int hashCode() {
+		return new HashCodeBuilder().append(getValue()).toHashCode();
+	}
+
+	public boolean hasValue() {
+  	  return !StringUtils.isBlank(getValueAsString());
+	}
+	
+	@Override
+	public boolean isEmpty() {
+		return super.isEmpty() && StringUtils.isBlank(getValueAsString());
+	}
+
+	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());
+	}
+
 }

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/model/ModelSerializationDstu3Test.java

@@ -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);
+	}
+
+}

src/changes/changes.xml

@@ -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">