Merge branch 'master' of github.com:jamesagnew/hapi-fhir

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TestUtil.java

@@ -20,33 +20,34 @@ package ca.uhn.fhir.util;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.i18n.HapiLocalizer;
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
+import ch.qos.logback.classic.LoggerContext;
+import org.slf4j.LoggerFactory;
+
 import java.lang.reflect.Field;
 import java.lang.reflect.Modifier;
 import java.util.Arrays;
 import java.util.Locale;
 import java.util.TimeZone;
 
-import org.slf4j.LoggerFactory;
+import static org.apache.commons.lang3.StringUtils.defaultString;
-
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.i18n.HapiLocalizer;
-import ch.qos.logback.classic.Level;
-import ch.qos.logback.classic.Logger;
-import ch.qos.logback.classic.LoggerContext;
 
 public class TestUtil {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestUtil.class);
 
 	/**
 	 * <b>THIS IS FOR UNIT TESTS ONLY - DO NOT CALL THIS METHOD FROM USER CODE</b>
-	 * 
+	 * <p>
 	 * When we run the unit tests in cobertura, JUnit doesn't seem to clean up static fields which leads to
 	 * tons of memory being used by the end and the JVM crashes in Travis. Manually clearing all of the
 	 * static fields seems to solve this.
 	 */
 	public static void clearAllStaticFieldsForUnitTest() {
 		HapiLocalizer.setOurFailOnMissingMessage(true);
-		
+
 		Class<?> theType;
 		try {
 			throw new Exception();
@@ -104,7 +105,7 @@ public class TestUtil {
 	 * environment
 	 */
 	public static void randomizeLocale() {
-		Locale[] availableLocales = { Locale.CANADA, Locale.GERMANY, Locale.TAIWAN };
+		Locale[] availableLocales = {Locale.CANADA, Locale.GERMANY, Locale.TAIWAN};
 		Locale.setDefault(availableLocales[(int) (Math.random() * availableLocales.length)]);
 		ourLog.info("Tests are running in locale: " + Locale.getDefault().getDisplayName());
 		if (Math.random() < 0.5) {
@@ -116,10 +117,19 @@ public class TestUtil {
 			System.setProperty("file.encoding", "UTF-8");
 			System.setProperty("line.separator", "\n");
 		}
-		String availableTimeZones[] = { "GMT+08:00", "GMT-05:00", "GMT+00:00", "GMT+03:30" };
+		String availableTimeZones[] = {"GMT+08:00", "GMT-05:00", "GMT+00:00", "GMT+03:30"};
 		String timeZone = availableTimeZones[(int) (Math.random() * availableTimeZones.length)];
 		TimeZone.setDefault(TimeZone.getTimeZone(timeZone));
 		ourLog.info("Tests are using time zone: {}", TimeZone.getDefault().getID());
 	}
 
+	/**
+	 * <b>THIS IS FOR UNIT TESTS ONLY - DO NOT CALL THIS METHOD FROM USER CODE</b>
+	 * <p>
+	 * Strip \r chars from a string to account for line ending platform differences
+	 */
+	public static String stripReturns(String theString) {
+		return defaultString(theString).replace("\r", "");
+	}
+
 }

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/model/BackboneElement.java

@@ -159,6 +159,7 @@ public abstract class BackboneElement extends Element implements IBaseBackboneEl
       public abstract BackboneElement copy();
 
       public void copyValues(BackboneElement dst) {
+        super.copyValues(dst);
         if (modifierExtension != null) {
           dst.modifierExtension = new ArrayList<Extension>();
           for (Extension i : modifierExtension)

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/model/DomainResource.java

@@ -340,6 +340,7 @@ public abstract class DomainResource extends Resource implements IBaseHasExtensi
       public abstract DomainResource copy();
 
       public void copyValues(DomainResource dst) {
+        super.copyValues(dst);
         dst.text = text == null ? null : text.copy();
         if (contained != null) {
           dst.contained = new ArrayList<Resource>();

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/model/BackboneElementDstu2_1Test.java

@@ -0,0 +1,26 @@
+package ca.uhn.fhir.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.hl7.fhir.dstu2016may.model.BackboneElement;
+import org.hl7.fhir.dstu2016may.model.Patient.PatientCommunicationComponent;
+import org.junit.Test;
+
+public class BackboneElementDstu2_1Test {
+    /**
+     * Ensuring that IDs of subtypes of BackboneElement get copied when
+     * the {@link org.hl7.fhir.dstu2016may.model.BackboneElement#copy()} method is called
+     */
+    @Test
+    public void testPatientCommunicationComponentIdCopy() {
+        PatientCommunicationComponent pcc1 = new PatientCommunicationComponent();
+        pcc1.setId("1001");
+
+        PatientCommunicationComponent copiedPcc = pcc1.copy();
+        String copiedPccID = copiedPcc.getIdElement().getIdPart();
+
+        assertTrue(copiedPcc instanceof BackboneElement); // Just making sure this assumption still holds up, otherwise this test isn't very useful
+        assertEquals("1001", copiedPccID);
+    }
+}

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/model/DomainResourceDstu2_1Test.java

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.hl7.fhir.dstu2016may.model.DomainResource;
+import org.hl7.fhir.dstu2016may.model.Narrative;
+import org.hl7.fhir.dstu2016may.model.Patient;
+import org.junit.Test;
+
+public class DomainResourceDstu2_1Test {
+    /**
+     * Ensuring that Ensuring that fields defined in {@link org.hl7.fhir.dstu2016may.model.DomainResource} and {@link org.hl7.fhir.dstu2016may.model.Resource}
+     * get copied when the {@link org.hl7.fhir.dstu2016may.model.DomainResource#copy()} method is called
+     */
+    @Test
+    public void testPatientCopy() {
+       Patient p1 = new Patient();
+       p1.setId("1001");
+       p1.setText(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL));
+
+       Patient copiedPatient = p1.copy();
+       String copiedPatientID = copiedPatient.getIdElement().getIdPart();
+       Narrative.NarrativeStatus copiedPatientTextStatus = copiedPatient.getText().getStatus();
+
+       assertTrue(copiedPatient instanceof DomainResource); // Just making sure this assumption still holds up, otherwise this test isn't very useful
+       assertEquals("1001", copiedPatientID);
+       assertEquals(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL).getStatus(), copiedPatientTextStatus);
+    }
+}

hapi-fhir-structures-dstu3/src/test/java/org/hl7/fhir/dstu3/model/BackboneElementDstu3Test.java

@@ -0,0 +1,25 @@
+package org.hl7.fhir.dstu3.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.hl7.fhir.dstu3.model.Patient.PatientCommunicationComponent;
+import org.junit.Test;
+
+public class BackboneElementDstu3Test {
+    /**
+     * Ensuring that IDs of subtypes of BackboneElement get copied when
+     * the {@link BackboneElement#copy()} method is called
+     */
+    @Test
+    public void testPatientCommunicationComponentCopy() {
+        PatientCommunicationComponent pcc1 = new PatientCommunicationComponent();
+        pcc1.setId("1001");
+
+        PatientCommunicationComponent copiedPcc = pcc1.copy();
+        String copiedPccID = copiedPcc.getId();
+
+       assertTrue(copiedPcc instanceof BackboneElement); // Just making sure this assumption still holds up, otherwise this test isn't very useful
+       assertEquals("1001", copiedPccID);
+    }
+}

hapi-fhir-structures-dstu3/src/test/java/org/hl7/fhir/dstu3/model/DomainResourceDstu3Test.java

@@ -0,0 +1,27 @@
+package org.hl7.fhir.dstu3.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.Test;
+
+public class DomainResourceDstu3Test {
+    /**
+     * Ensuring that fields defined in {@link DomainResource} and {@link Resource}
+     * get copied when the {@link DomainResource#copy()} method is called
+     */
+    @Test
+    public void testPatientCopy() {
+       Patient p1 = new Patient();
+       p1.setId("1001");
+       p1.setText(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL));
+
+       Patient copiedPatient = p1.copy();
+       String copiedPatientID = copiedPatient.getIdElement().getIdPart();
+       Narrative.NarrativeStatus copiedPatientTextStatus = copiedPatient.getText().getStatus();
+
+       assertTrue(copiedPatient instanceof DomainResource); // Just making sure this assumption still holds up, otherwise this test isn't very useful
+       assertEquals("1001", copiedPatientID);
+       assertEquals(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL).getStatus(), copiedPatientTextStatus);
+    }
+}

hapi-fhir-structures-dstu3/src/test/java/org/hl7/fhir/dstu3/model/MetadataResourceDstu3Test.java

@@ -0,0 +1,29 @@
+package org.hl7.fhir.dstu3.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import org.junit.Test;
+
+public class MetadataResourceDstu3Test {
+    /**
+     * Ensuring that fields defined in {@link MetadataResource}, {@link DomainResource}, and {@link Resource}
+     * get copied when the {@link MetadataResource#copy()} method is called
+     */
+    @Test
+    public void testCodeSystemCopy() {
+        CodeSystem codeSystem1 = new CodeSystem();
+        codeSystem1.setId("1001");
+        codeSystem1.setName("Name123");
+        codeSystem1.setText(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL));
+
+        CodeSystem copiedCodeSystem = codeSystem1.copy();
+        String copiedCodeSystemID = copiedCodeSystem.getId();
+        String copiedCodeSystemName = copiedCodeSystem.getName();
+        Narrative.NarrativeStatus copiedCodeSystemTextStatus = copiedCodeSystem.getText().getStatus();
+
+        assertTrue(copiedCodeSystem instanceof MetadataResource); // Just making sure this assumption still holds up, otherwise this test isn't very useful
+        assertEquals("1001", copiedCodeSystemID);
+        assertEquals("Name123", copiedCodeSystemName);
+        assertEquals(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL).getStatus(), copiedCodeSystemTextStatus);
+    }
+}

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/model/BackboneElement.java

@@ -128,6 +128,7 @@ public abstract class BackboneElement extends Element implements IBaseBackboneEl
       public abstract BackboneElement copy();
 
       public void copyValues(BackboneElement dst) {
+        super.copyValues(dst);
         if (modifierExtension != null) {
           dst.modifierExtension = new ArrayList<Extension>();
           for (Extension i : modifierExtension)

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/model/DomainResource.java

@@ -265,6 +265,7 @@ public abstract class DomainResource extends Resource implements IBaseHasExtensi
       public abstract DomainResource copy();
 
       public void copyValues(DomainResource dst) {
+        super.copyValues(dst);
         dst.text = text == null ? null : text.copy();
         if (contained != null) {
           dst.contained = new ArrayList<Resource>();

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/model/BackboneElementHL7_Dstu2Test.java

@@ -0,0 +1,26 @@
+package ca.uhn.fhir.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.hl7.fhir.instance.model.BackboneElement;
+import org.hl7.fhir.instance.model.Patient.PatientCommunicationComponent;
+import org.junit.Test;
+
+public class BackboneElementHL7_Dstu2Test {
+    /**
+     * Ensuring that IDs of subtypes of BackboneElement get copied when
+     * the {@link org.hl7.fhir.instance.model.BackboneElement#copy()} method is called
+     */
+    @Test
+    public void testPatientCommunicationComponentIdCopy() {
+        PatientCommunicationComponent pcc1 = new PatientCommunicationComponent();
+        pcc1.setId("1001");
+
+        PatientCommunicationComponent copiedPcc = pcc1.copy();
+        String copiedPccID = copiedPcc.getIdElement().getIdPart();
+
+        assertTrue(copiedPcc instanceof BackboneElement); // Just making sure this assumption still holds up, otherwise this test isn't very useful
+        assertEquals("1001", copiedPccID);
+    }
+}

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/model/DomainResourceHL7_Dstu2Test.java

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.hl7.fhir.instance.model.DomainResource;
+import org.hl7.fhir.instance.model.Narrative;
+import org.hl7.fhir.instance.model.Patient;
+import org.junit.Test;
+
+public class DomainResourceHL7_Dstu2Test {
+    /**
+     * Ensuring that fields defined in {@link org.hl7.fhir.instance.model.DomainResource} and {@link org.hl7.fhir.instance.model.Resource}
+     * the {@link org.hl7.fhir.instance.model.DomainResource#copy()} method is called
+     */
+    @Test
+    public void testPatientCopy() {
+        Patient p1 = new Patient();
+        p1.setId("1001");
+        p1.setText(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL));
+
+        Patient copiedPatient = p1.copy();
+        String copiedPatientID = copiedPatient.getIdElement().getIdPart();
+        Narrative.NarrativeStatus copiedPatientTextStatus = copiedPatient.getText().getStatus();
+
+        assertTrue(copiedPatient instanceof DomainResource); // Just making sure this assumption still holds up, otherwise this test isn't very useful
+        assertEquals("1001", copiedPatientID);
+        assertEquals(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL).getStatus(), copiedPatientTextStatus);
+    }
+}

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/GraphQLR4ProviderTest.java

@@ -22,7 +22,6 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.hapi.rest.server.GraphQLProvider;
 import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.utils.GraphQLEngine;
 import org.hl7.fhir.utilities.graphql.Argument;
 import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
 import org.hl7.fhir.utilities.graphql.ReferenceResolution;
@@ -37,8 +36,7 @@ import java.util.List;
 import java.util.concurrent.TimeUnit;
 
 import static org.hamcrest.Matchers.startsWith;
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.*;
-import static org.junit.Assert.assertThat;
 
 public class GraphQLR4ProviderTest {
 
@@ -48,6 +46,121 @@ public class GraphQLR4ProviderTest {
 	private static int ourPort;
 	private static Server ourServer;
 
+	@Before
+	public void before() {
+		//nothing
+	}
+
+	@Test
+	public void testGraphInstance() throws Exception {
+		String query = "{name{family,given}}";
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/123/$graphql?query=" + UrlUtil.escape(query));
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(200, status.getStatusLine().getStatusCode());
+
+			assertEquals(TestUtil.stripReturns("{" +
+				"  \"name\":[{" +
+				"    \"family\":\"FAMILY\"," +
+				"    \"given\":[\"GIVEN1\",\"GIVEN2\"]" +
+				"  },{" +
+				"    \"given\":[\"GivenOnly1\",\"GivenOnly2\"]" +
+				"  }]" +
+				"}"), TestUtil.stripReturns(responseContent));
+			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
+
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
+	@Test
+	public void testGraphInstanceWithFhirpath() throws Exception {
+		String query = "{name(fhirpath:\"family.exists()\"){text,given,family}}";
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/123/$graphql?query=" + UrlUtil.escape(query));
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(200, status.getStatusLine().getStatusCode());
+
+			assertEquals(TestUtil.stripReturns("{\n" +
+				"  \"name\":[{\n" +
+				"    \"given\":[\"GIVEN1\",\"GIVEN2\"],\n" +
+				"    \"family\":\"FAMILY\"\n" +
+				"  }]\n" +
+				"}"), TestUtil.stripReturns(responseContent));
+			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
+
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
+	@Test
+	public void testGraphSystemInstance() throws Exception {
+		String query = "{Patient(id:123){id,name{given,family}}}";
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escape(query));
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(200, status.getStatusLine().getStatusCode());
+
+			assertEquals(TestUtil.stripReturns("{\n" +
+				"  \"Patient\":{\n" +
+				"    \"name\":[{\n" +
+				"      \"given\":[\"GIVEN1\",\"GIVEN2\"],\n" +
+				"      \"family\":\"FAMILY\"\n" +
+				"    },{\n" +
+				"      \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
+				"    }]\n" +
+				"  }\n" +
+				"}"), TestUtil.stripReturns(responseContent));
+			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
+
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
+	@Test
+	public void testGraphSystemList() throws Exception {
+		String query = "{PatientList(name:\"pet\"){name{family,given}}}";
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escape(query));
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(200, status.getStatusLine().getStatusCode());
+
+			assertEquals(TestUtil.stripReturns("{\n" +
+				"  \"PatientList\":[{\n" +
+				"    \"name\":[{\n" +
+				"      \"family\":\"pet\",\n" +
+				"      \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
+				"    },{\n" +
+				"      \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
+				"    }]\n" +
+				"  },{\n" +
+				"    \"name\":[{\n" +
+				"      \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
+				"    }]\n" +
+				"  }]\n" +
+				"}"), TestUtil.stripReturns(responseContent));
+			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
+
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() throws Exception {
 		ourServer.stop();
@@ -79,121 +192,6 @@ public class GraphQLR4ProviderTest {
 
 	}
 
-	@Before
-	public void before() {
-		//nothing
-	}
-
-	@Test
-	public void testGraphInstance() throws Exception {
-		String query = "{name{family,given}}";
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/123/$graphql?query=" + UrlUtil.escape(query));
-		CloseableHttpResponse status = ourClient.execute(httpGet);
-		try {
-			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
-			ourLog.info(responseContent);
-			assertEquals(200, status.getStatusLine().getStatusCode());
-
-			assertEquals("{" +
-				"  \"name\":[{" +
-				"    \"family\":\"FAMILY\"," +
-				"    \"given\":[\"GIVEN1\",\"GIVEN2\"]" +
-				"  },{" +
-				"    \"given\":[\"GivenOnly1\",\"GivenOnly2\"]" +
-				"  }]" +
-				"}", responseContent.replace("\n", "").replace("\r", ""));
-			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
-
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
-		}
-
-	}
-
-	@Test
-	public void testGraphSystemInstance() throws Exception {
-		String query = "{Patient(id:123){id,name{given,family}}}";
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escape(query));
-		CloseableHttpResponse status = ourClient.execute(httpGet);
-		try {
-			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
-			ourLog.info(responseContent);
-			assertEquals(200, status.getStatusLine().getStatusCode());
-
-			assertEquals("{\n" +
-				"  \"Patient\":{\n" +
-				"    \"name\":[{\n" +
-				"      \"given\":[\"GIVEN1\",\"GIVEN2\"],\n" +
-				"      \"family\":\"FAMILY\"\n" +
-				"    },{\n" +
-				"      \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
-				"    }]\n" +
-				"  }\n" +
-				"}", responseContent);
-			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
-
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
-		}
-
-	}
-
-	@Test
-	public void testGraphSystemList() throws Exception {
-		String query = "{PatientList(name:\"pet\"){name{family,given}}}";
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escape(query));
-		CloseableHttpResponse status = ourClient.execute(httpGet);
-		try {
-			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
-			ourLog.info(responseContent);
-			assertEquals(200, status.getStatusLine().getStatusCode());
-
-			assertEquals("{\n" +
-				"  \"PatientList\":[{\n" +
-				"    \"name\":[{\n" +
-				"      \"family\":\"pet\",\n" +
-				"      \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
-				"    },{\n" +
-				"      \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
-				"    }]\n" +
-				"  },{\n" +
-				"    \"name\":[{\n" +
-				"      \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
-				"    }]\n" +
-				"  }]\n" +
-				"}", responseContent);
-			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
-
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
-		}
-
-	}
-
-	@Test
-	public void testGraphInstanceWithFhirpath() throws Exception {
-		String query = "{name(fhirpath:\"family.exists()\"){text,given,family}}";
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/123/$graphql?query=" + UrlUtil.escape(query));
-		CloseableHttpResponse status = ourClient.execute(httpGet);
-		try {
-			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
-			ourLog.info(responseContent);
-			assertEquals(200, status.getStatusLine().getStatusCode());
-
-			assertEquals("{\n" +
-				"  \"name\":[{\n" +
-				"    \"given\":[\"GIVEN1\",\"GIVEN2\"],\n" +
-				"    \"family\":\"FAMILY\"\n" +
-				"  }]\n" +
-				"}", responseContent);
-			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), startsWith("application/json"));
-
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
-		}
-
-	}
-
 	public static class DummyPatientResourceProvider implements IResourceProvider {
 
 		@Override
@@ -219,31 +217,6 @@ public class GraphQLR4ProviderTest {
 	}
 
 	private static class MyStorageServices implements IGraphQLStorageServices<Resource, Reference, Bundle> {
-		@Override
-		public ReferenceResolution<Resource> lookup(Object theAppInfo, Resource theContext, Reference theReference) throws FHIRException {
-			ourLog.info("lookup from {} to {}", theContext.getIdElement().getValue(), theReference.getReference());
-			return null;
-		}
-
-		@Override
-		public Resource lookup(Object theAppInfo, String theType, String theId) throws FHIRException {
-			ourLog.info("lookup {}/{}", theType, theId);
-
-			if (theType.equals("Patient") && theId.equals("123")) {
-				Patient p = new Patient();
-				p.addName()
-					.setFamily("FAMILY")
-					.addGiven("GIVEN1")
-					.addGiven("GIVEN2");
-				p.addName()
-					.addGiven("GivenOnly1")
-					.addGiven("GivenOnly2");
-				return p;
-			}
-
-			return null;
-		}
-
 		@Override
 		public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<Resource> theMatches) throws FHIRException {
 			ourLog.info("listResources of {} - {}", theType, theSearchParams);
@@ -271,6 +244,31 @@ public class GraphQLR4ProviderTest {
 			}
 		}
 
+		@Override
+		public Resource lookup(Object theAppInfo, String theType, String theId) throws FHIRException {
+			ourLog.info("lookup {}/{}", theType, theId);
+
+			if (theType.equals("Patient") && theId.equals("123")) {
+				Patient p = new Patient();
+				p.addName()
+					.setFamily("FAMILY")
+					.addGiven("GIVEN1")
+					.addGiven("GIVEN2");
+				p.addName()
+					.addGiven("GivenOnly1")
+					.addGiven("GivenOnly2");
+				return p;
+			}
+
+			return null;
+		}
+
+		@Override
+		public ReferenceResolution<Resource> lookup(Object theAppInfo, Resource theContext, Reference theReference) throws FHIRException {
+			ourLog.info("lookup from {} to {}", theContext.getIdElement().getValue(), theReference.getReference());
+			return null;
+		}
+
 		@Override
 		public Bundle search(Object theAppInfo, String theType, List<Argument> theSearchParams) throws FHIRException {
 			ourLog.info("search on {} - {}", theType, theSearchParams);

hapi-fhir-structures-r4/src/test/java/org/hl7/fhir/r4/model/BackboneElementR4Test.java

@@ -0,0 +1,25 @@
+package org.hl7.fhir.r4.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.hl7.fhir.r4.model.Patient.PatientCommunicationComponent;
+import org.junit.Test;
+
+public class BackboneElementR4Test {
+    /**
+     * Ensuring that IDs of subtypes of BackboneElement get copied when
+     * the {@link BackboneElement#copy()} method is called
+     */
+    @Test
+    public void testPatientCommunicationComponentCopy() {
+        PatientCommunicationComponent pcc1 = new PatientCommunicationComponent();
+        pcc1.setId("1001");
+
+        PatientCommunicationComponent copiedPcc = pcc1.copy();
+        String copiedPccID = copiedPcc.getId();
+
+        assertTrue(copiedPcc instanceof BackboneElement); // Just making sure this assumption still holds up, otherwise this test isn't very useful
+        assertEquals("1001", copiedPccID);
+    }
+}

hapi-fhir-structures-r4/src/test/java/org/hl7/fhir/r4/model/DomainResourceR4Test.java

@@ -0,0 +1,26 @@
+package org.hl7.fhir.r4.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import org.junit.Test;
+
+public class DomainResourceR4Test {
+    /**
+     * Ensuring that fields defined in {@link DomainResource} and {@link Resource}
+     * get copied when the {@link DomainResource#copy()} method is called
+     */
+    @Test
+    public void testPatientCopy() {
+       Patient p1 = new Patient();
+       p1.setId("1001");
+       p1.setText(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL));
+
+       Patient copiedPatient = p1.copy();
+       String copiedPatientID = copiedPatient.getIdElement().getIdPart();
+       Narrative.NarrativeStatus copiedPatientTextStatus = copiedPatient.getText().getStatus();
+
+       assertTrue(copiedPatient instanceof DomainResource); // Just making sure this assumption still holds up, otherwise this test isn't very useful
+       assertEquals("1001", copiedPatientID);
+       assertEquals(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL).getStatus(), copiedPatientTextStatus);
+    }
+}

hapi-fhir-structures-r4/src/test/java/org/hl7/fhir/r4/model/MetadataResourceR4Test.java

@@ -0,0 +1,29 @@
+package org.hl7.fhir.r4.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import org.junit.Test;
+
+public class MetadataResourceR4Test {
+    /**
+     * Ensuring that fields defined in {@link MetadataResource}, {@link DomainResource}, and {@link Resource}
+     * get copied when the {@link MetadataResource#copy()} method is called
+     */
+    @Test
+    public void testCodeSystemCopy() {
+        CodeSystem codeSystem1 = new CodeSystem();
+        codeSystem1.setId("1001");
+        codeSystem1.setName("Name123");
+        codeSystem1.setText(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL));
+
+        CodeSystem copiedCodeSystem = codeSystem1.copy();
+        String copiedCodeSystemID = copiedCodeSystem.getId();
+        String copiedCodeSystemName = copiedCodeSystem.getName();
+        Narrative.NarrativeStatus copiedCodeSystemTextStatus = copiedCodeSystem.getText().getStatus();
+
+        assertTrue(copiedCodeSystem instanceof MetadataResource); // Just making sure this assumption still holds up, otherwise this test isn't very useful
+        assertEquals("1001", copiedCodeSystemID);
+        assertEquals("Name123", copiedCodeSystemName);
+        assertEquals(new Narrative().setStatus(Narrative.NarrativeStatus.ADDITIONAL).getStatus(), copiedCodeSystemTextStatus);
+    }
+}

hapi-fhir-validation/src/test/java/ca/uhn/fhir/rest/server/GraphQLDstu3ProviderTest.java

@@ -48,39 +48,6 @@ public class GraphQLDstu3ProviderTest {
 	private static int ourPort;
 	private static Server ourServer;
 
-	@AfterClass
-	public static void afterClassClearContext() throws Exception {
-		ourServer.stop();
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
-
-	@BeforeClass
-	public static void beforeClass() throws Exception {
-		ourPort = PortUtil.findFreePort();
-		ourServer = new Server(ourPort);
-
-
-
-		ServletHandler proxyHandler = new ServletHandler();
-		RestfulServer servlet = new RestfulServer(ourCtx);
-		servlet.setDefaultResponseEncoding(EncodingEnum.JSON);
-		servlet.setPagingProvider(new FifoMemoryPagingProvider(10));
-
-		servlet.registerProvider(new DummyPatientResourceProvider());
-		MyStorageServices storageServices = new MyStorageServices();
-		servlet.registerProvider(new GraphQLProviderDstu3(ourCtx, new DefaultProfileValidationSupport(), storageServices));
-		ServletHolder servletHolder = new ServletHolder(servlet);
-		proxyHandler.addServletWithMapping(servletHolder, "/*");
-		ourServer.setHandler(proxyHandler);
-		ourServer.start();
-
-		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
-		HttpClientBuilder builder = HttpClientBuilder.create();
-		builder.setConnectionManager(connectionManager);
-		ourClient = builder.build();
-
-	}
-
 	@Before
 	public void before() {
 		//nothing
@@ -97,76 +64,14 @@ public class GraphQLDstu3ProviderTest {
 			ourLog.info(responseContent);
 			assertEquals(200, status.getStatusLine().getStatusCode());
 
-			assertEquals("{\n" +
+			assertEquals(TestUtil.stripReturns("{\n" +
 				"  \"name\":[{\n" +
 				"    \"family\":[\"FAMILY\"],\n" +
 				"    \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
 				"  },{\n" +
 				"    \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
 				"  }]\n" +
-				"}", responseContent);
+				"}"), TestUtil.stripReturns(responseContent));
-			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), Matchers.startsWith("application/json"));
-
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
-		}
-
-	}
-
-	@Test
-	@org.junit.Ignore
-	public void testGraphSystemInstance() throws Exception {
-		String query = "{Patient(id:123){id,name{given,family}}}";
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escape(query));
-		CloseableHttpResponse status = ourClient.execute(httpGet);
-		try {
-			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
-			ourLog.info(responseContent);
-			assertEquals(200, status.getStatusLine().getStatusCode());
-
-			assertEquals("{\n" +
-				"  \"Patient\":{\n" +
-				"    \"name\":[{\n" +
-				"      \"given\":[\"GIVEN1\",\"GIVEN2\"],\n" +
-				"      \"family\":[\"FAMILY\"]\n" +
-				"    },{\n" +
-				"      \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
-				"    }]\n" +
-				"  }\n" +
-				"}", responseContent);
-			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), Matchers.startsWith("application/json"));
-
-		} finally {
-			IOUtils.closeQuietly(status.getEntity().getContent());
-		}
-
-	}
-
-	@Test
-	@Ignore
-	public void testGraphSystemList() throws Exception {
-		String query = "{PatientList(name:\"pet\"){name{family,given}}}";
-		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escape(query));
-		CloseableHttpResponse status = ourClient.execute(httpGet);
-		try {
-			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
-			ourLog.info(responseContent);
-			assertEquals(200, status.getStatusLine().getStatusCode());
-
-			assertEquals("{\n" +
-				"  \"PatientList\":[{\n" +
-				"    \"name\":[{\n" +
-				"      \"family\":[\"pet\"],\n" +
-				"      \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
-				"    },{\n" +
-				"      \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
-				"    }]\n" +
-				"  },{\n" +
-				"    \"name\":[{\n" +
-				"      \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
-				"    }]\n" +
-				"  }]\n" +
-				"}", responseContent);
 			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), Matchers.startsWith("application/json"));
 
 		} finally {
@@ -186,12 +91,12 @@ public class GraphQLDstu3ProviderTest {
 			ourLog.info(responseContent);
 			assertEquals(200, status.getStatusLine().getStatusCode());
 
-			assertEquals("{\n" +
+			assertEquals(TestUtil.stripReturns("{\n" +
 				"  \"name\":[{\n" +
 				"    \"given\":[\"GIVEN1\",\"GIVEN2\"],\n" +
 				"    \"family\":[\"FAMILY\"]\n" +
 				"  }]\n" +
-				"}", responseContent);
+				"}"), TestUtil.stripReturns(responseContent));
 			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), Matchers.startsWith("application/json"));
 
 		} finally {
@@ -200,6 +105,100 @@ public class GraphQLDstu3ProviderTest {
 
 	}
 
+	@Test
+	@org.junit.Ignore
+	public void testGraphSystemInstance() throws Exception {
+		String query = "{Patient(id:123){id,name{given,family}}}";
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escape(query));
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(200, status.getStatusLine().getStatusCode());
+
+			assertEquals(TestUtil.stripReturns("{\n" +
+				"  \"Patient\":{\n" +
+				"    \"name\":[{\n" +
+				"      \"given\":[\"GIVEN1\",\"GIVEN2\"],\n" +
+				"      \"family\":[\"FAMILY\"]\n" +
+				"    },{\n" +
+				"      \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
+				"    }]\n" +
+				"  }\n" +
+				"}"), TestUtil.stripReturns(responseContent));
+			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), Matchers.startsWith("application/json"));
+
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
+	@Test
+	@Ignore
+	public void testGraphSystemList() throws Exception {
+		String query = "{PatientList(name:\"pet\"){name{family,given}}}";
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/$graphql?query=" + UrlUtil.escape(query));
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(200, status.getStatusLine().getStatusCode());
+
+			assertEquals(TestUtil.stripReturns("{\n" +
+				"  \"PatientList\":[{\n" +
+				"    \"name\":[{\n" +
+				"      \"family\":[\"pet\"],\n" +
+				"      \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
+				"    },{\n" +
+				"      \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
+				"    }]\n" +
+				"  },{\n" +
+				"    \"name\":[{\n" +
+				"      \"given\":[\"GivenOnlyB1\",\"GivenOnlyB2\"]\n" +
+				"    }]\n" +
+				"  }]\n" +
+				"}"), TestUtil.stripReturns(responseContent));
+			assertThat(status.getFirstHeader(Constants.HEADER_CONTENT_TYPE).getValue(), Matchers.startsWith("application/json"));
+
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		ourServer.stop();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer(ourCtx);
+		servlet.setDefaultResponseEncoding(EncodingEnum.JSON);
+		servlet.setPagingProvider(new FifoMemoryPagingProvider(10));
+
+		servlet.registerProvider(new DummyPatientResourceProvider());
+		MyStorageServices storageServices = new MyStorageServices();
+		servlet.registerProvider(new GraphQLProviderDstu3(ourCtx, new DefaultProfileValidationSupport(), storageServices));
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
 	public static class DummyPatientResourceProvider implements IResourceProvider {
 
 		@Override
@@ -225,31 +224,6 @@ public class GraphQLDstu3ProviderTest {
 	}
 
 	private static class MyStorageServices implements IGraphQLStorageServices<Resource, Reference, Bundle> {
-		@Override
-		public ReferenceResolution<Resource> lookup(Object theAppInfo, Resource theContext, Reference theReference) throws FHIRException {
-			ourLog.info("lookup from {} to {}", theContext.getIdElement().getValue(), theReference.getReference());
-			return null;
-		}
-
-		@Override
-		public Resource lookup(Object theAppInfo, String theType, String theId) throws FHIRException {
-			ourLog.info("lookup {}/{}", theType, theId);
-
-			if (theType.equals("Patient") && theId.equals("123")) {
-				Patient p = new Patient();
-				p.addName()
-					.setFamily("FAMILY")
-					.addGiven("GIVEN1")
-					.addGiven("GIVEN2");
-				p.addName()
-					.addGiven("GivenOnly1")
-					.addGiven("GivenOnly2");
-				return p;
-			}
-
-			return null;
-		}
-
 		@Override
 		public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<Resource> theMatches) throws FHIRException {
 			ourLog.info("listResources of {} - {}", theType, theSearchParams);
@@ -277,6 +251,31 @@ public class GraphQLDstu3ProviderTest {
 			}
 		}
 
+		@Override
+		public Resource lookup(Object theAppInfo, String theType, String theId) throws FHIRException {
+			ourLog.info("lookup {}/{}", theType, theId);
+
+			if (theType.equals("Patient") && theId.equals("123")) {
+				Patient p = new Patient();
+				p.addName()
+					.setFamily("FAMILY")
+					.addGiven("GIVEN1")
+					.addGiven("GIVEN2");
+				p.addName()
+					.addGiven("GivenOnly1")
+					.addGiven("GivenOnly2");
+				return p;
+			}
+
+			return null;
+		}
+
+		@Override
+		public ReferenceResolution<Resource> lookup(Object theAppInfo, Resource theContext, Reference theReference) throws FHIRException {
+			ourLog.info("lookup from {} to {}", theContext.getIdElement().getValue(), theReference.getReference());
+			return null;
+		}
+
 		@Override
 		public Bundle search(Object theAppInfo, String theType, List<Argument> theSearchParams) throws FHIRException {
 			ourLog.info("search on {} - {}", theType, theSearchParams);

src/changes/changes.xml

@@ -166,6 +166,10 @@
 				being acceptable for CORS requests in CorsInterceptor, CLI, and JPA Example.
 				Thanks to Patrick Werner for the pull request!
 			</action>
+			<action type="fix" issue="725">
+				DSTU2-hl7org and DSTU2.1 structures did not copy resource IDs when invoking 
+				copyValues(). Thanks to Clayton Bodendein for the pull request!
+			</action>
 		</release>
 		<release version="3.0.0" date="2017-09-27">
 			<action type="add">