Fix #113 - Handle contained resources with non-local IDs

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java

@@ -20,7 +20,7 @@ package ca.uhn.fhir.parser;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isBlank;
 
 import java.io.IOException;
 import java.io.Reader;
@@ -47,7 +47,6 @@ import org.hl7.fhir.instance.model.api.IReference;
 import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
 import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
-import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
@@ -62,6 +61,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
 
 public abstract class BaseParser implements IParser {
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
 	private ContainedResources myContainedResources;
 	private FhirContext myContext;
 	private boolean mySuppressNarratives;
@@ -80,6 +80,9 @@ public abstract class BaseParser implements IParser {
 			for (IResource next : containedResources) {
 				String nextId = next.getId().getValue();
 				if (StringUtils.isNotBlank(nextId)) {
+					if (!nextId.startsWith("#")) {
+						nextId = '#' + nextId;
+					}
 					allIds.add(nextId);
 					if (existingIdToContainedResource == null) {
 						existingIdToContainedResource = new HashMap<String, IBaseResource>();
@@ -119,7 +122,7 @@ public abstract class BaseParser implements IParser {
 					if (existingIdToContainedResource != null) {
 						IBaseResource potentialTarget = existingIdToContainedResource.remove(next.getReference().getValue());
 						if (potentialTarget != null) {
-							theContained.addContained(potentialTarget);
+							theContained.addContained(next.getReference(), potentialTarget);
 							containResourcesForEncoding(theContained, potentialTarget, theTarget);
 						}
 					}
@@ -387,6 +390,11 @@ public abstract class BaseParser implements IParser {
 			myResources.add(theResource);
 		}
 
+		public void addContained(IdDt theId, IBaseResource theResource) {
+			myResourceToId.put(theResource, theId);
+			myResources.add(theResource);
+		}
+
 		public List<IBaseResource> getContainedResources() {
 			return myResources;
 		}

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java

@@ -104,6 +104,10 @@ import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.util.ElementUtil;
 import ca.uhn.fhir.util.UrlUtil;
 
+/**
+ * This class is the FHIR JSON parser/encoder. Users should not interact with this
+ * class directly, but should use {@link FhirContext#newJsonParser()} to get an instance.
+ */
 public class JsonParser extends BaseParser implements IParser {
 
 	private static final Set<String> BUNDLE_TEXTNODE_CHILDREN_DSTU1;

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java

@@ -20,14 +20,15 @@ package ca.uhn.fhir.parser;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.defaultString;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.io.IOException;
 import java.io.Reader;
 import java.io.StringWriter;
 import java.io.Writer;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
@@ -49,8 +50,8 @@ import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.IBase;
 import org.hl7.fhir.instance.model.IBaseResource;
 import org.hl7.fhir.instance.model.IPrimitiveType;
-import org.hl7.fhir.instance.model.api.IBaseBinary;
 import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseBinary;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseExtension;
 import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
@@ -91,7 +92,12 @@ import ca.uhn.fhir.util.NonPrettyPrintWriterWrapper;
 import ca.uhn.fhir.util.PrettyPrintWriterWrapper;
 import ca.uhn.fhir.util.XmlUtil;
 
+/**
+ * This class is the FHIR XML parser/encoder. Users should not interact with this
+ * class directly, but should use {@link FhirContext#newXmlParser()} to get an instance.
+ */
 public class XmlParser extends BaseParser implements IParser {
+	
 	static final String ATOM_NS = "http://www.w3.org/2005/Atom";
 	static final String FHIR_NS = "http://hl7.org/fhir";
 	static final String OPENSEARCH_NS = "http://a9.com/-/spec/opensearch/1.1/";

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserTest.java

@@ -20,11 +20,14 @@ import org.junit.Test;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.ExtensionDt;
+import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
 import ca.uhn.fhir.model.api.Tag;
 import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
+import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
+import ca.uhn.fhir.model.dstu2.composite.ContainedDt;
 import ca.uhn.fhir.model.dstu2.composite.DurationDt;
 import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
 import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
@@ -32,6 +35,7 @@ import ca.uhn.fhir.model.dstu2.resource.AllergyIntolerance;
 import ca.uhn.fhir.model.dstu2.resource.Binary;
 import ca.uhn.fhir.model.dstu2.resource.Composition;
 import ca.uhn.fhir.model.dstu2.resource.Encounter;
+import ca.uhn.fhir.model.dstu2.resource.Medication;
 import ca.uhn.fhir.model.dstu2.resource.MedicationPrescription;
 import ca.uhn.fhir.model.dstu2.resource.Organization;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
@@ -53,6 +57,160 @@ public class XmlParserTest {
 		XMLUnit.setIgnoreWhitespace(true);
 	}
 
+	/**
+	 * See #113
+	 */
+	@Test
+	public void testEncodeContainedResources() {
+		
+		MedicationPrescription medicationPrescript = new MedicationPrescription();
+		
+		String medId = "123";
+		CodeableConceptDt codeDt = new CodeableConceptDt("urn:sys", "code1");
+
+		// Adding medication to Contained.
+		Medication medResource = new Medication();
+		medResource.setCode(codeDt);
+		medResource.setId("#" + String.valueOf(medId));
+		ArrayList<IResource> medResList = new ArrayList<IResource>();
+		medResList.add(medResource);
+		ContainedDt medContainedDt = new ContainedDt();
+		medContainedDt.setContainedResources(medResList);
+		medicationPrescript.setContained(medContainedDt);
+
+		// Medication reference. This should point to the contained resource.
+		ResourceReferenceDt medRefDt = new ResourceReferenceDt("#" + medId);
+		medRefDt.setDisplay("MedRef");
+		medicationPrescript.setMedication(medRefDt);
+		
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String encoded = p.encodeResourceToString(medicationPrescript);
+		ourLog.info(encoded);
+		
+		//@formatter:on
+		assertThat(encoded, stringContainsInOrder(
+			"<MedicationPrescription xmlns=\"http://hl7.org/fhir\">",
+			"<contained>", 
+			"<Medication xmlns=\"http://hl7.org/fhir\">", 
+			"<id value=\"123\"/>", 
+			"<code>", 
+			"<coding>", 
+			"<system value=\"urn:sys\"/>", 
+			"<code value=\"code1\"/>", 
+			"</coding>", 
+			"</code>", 
+			"</Medication>", 
+			"</contained>", 
+			"<medication>", 
+			"<reference value=\"#123\"/>", 
+			"<display value=\"MedRef\"/>", 
+			"</medication>", 
+			"</MedicationPrescription>"));
+		//@formatter:off
+
+	}
+	
+	/**
+	 * See #113
+	 */
+	@Test
+	public void testEncodeContainedResourcesManualContainUsingNonLocalId() {
+		
+		MedicationPrescription medicationPrescript = new MedicationPrescription();
+		
+		String medId = "123";
+		CodeableConceptDt codeDt = new CodeableConceptDt("urn:sys", "code1");
+
+		// Adding medication to Contained.
+		Medication medResource = new Medication();
+		medResource.setCode(codeDt);
+		medResource.setId(String.valueOf(medId)); // ID does not start with '#'
+		ArrayList<IResource> medResList = new ArrayList<IResource>();
+		medResList.add(medResource);
+		ContainedDt medContainedDt = new ContainedDt();
+		medContainedDt.setContainedResources(medResList);
+		medicationPrescript.setContained(medContainedDt);
+
+		// Medication reference. This should point to the contained resource.
+		ResourceReferenceDt medRefDt = new ResourceReferenceDt("#" + medId);
+		medRefDt.setDisplay("MedRef");
+		medicationPrescript.setMedication(medRefDt);
+		
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String encoded = p.encodeResourceToString(medicationPrescript);
+		ourLog.info(encoded);
+		
+		//@formatter:on
+		assertThat(encoded, stringContainsInOrder(
+			"<MedicationPrescription xmlns=\"http://hl7.org/fhir\">",
+			"<contained>", 
+			"<Medication xmlns=\"http://hl7.org/fhir\">", 
+			"<id value=\"123\"/>", 
+			"<code>", 
+			"<coding>", 
+			"<system value=\"urn:sys\"/>", 
+			"<code value=\"code1\"/>", 
+			"</coding>", 
+			"</code>", 
+			"</Medication>", 
+			"</contained>", 
+			"<medication>", 
+			"<reference value=\"#123\"/>", 
+			"<display value=\"MedRef\"/>", 
+			"</medication>", 
+			"</MedicationPrescription>"));
+		//@formatter:off
+
+	}
+
+	/**
+	 * See #113
+	 */
+	@Test
+	public void testEncodeContainedResourcesAutomatic() {
+		
+		MedicationPrescription medicationPrescript = new MedicationPrescription();
+		String nameDisp = "MedRef";
+		CodeableConceptDt codeDt = new CodeableConceptDt("urn:sys", "code1");
+		
+		// Adding medication to Contained.
+		Medication medResource = new Medication();
+		// No ID set
+		medResource.setCode(codeDt);
+
+		// Medication reference. This should point to the contained resource.
+		ResourceReferenceDt medRefDt = new ResourceReferenceDt();
+		medRefDt.setDisplay(nameDisp);
+		// Resource reference set, but no ID
+		medRefDt.setResource(medResource);
+		medicationPrescript.setMedication(medRefDt);
+		
+		IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
+		String encoded = p.encodeResourceToString(medicationPrescript);
+		ourLog.info(encoded);
+		
+		//@formatter:on
+		assertThat(encoded, stringContainsInOrder(
+			"<MedicationPrescription xmlns=\"http://hl7.org/fhir\">",
+			"<contained>", 
+			"<Medication xmlns=\"http://hl7.org/fhir\">", 
+			"<id value=\"1\"/>", 
+			"<code>", 
+			"<coding>", 
+			"<system value=\"urn:sys\"/>", 
+			"<code value=\"code1\"/>", 
+			"</coding>", 
+			"</code>", 
+			"</Medication>", 
+			"</contained>", 
+			"<medication>", 
+			"<reference value=\"#1\"/>", 
+			"<display value=\"MedRef\"/>", 
+			"</medication>", 
+			"</MedicationPrescription>"));
+		//@formatter:off
+	}
+
 	@Test
 	public void testEncodeAndParseSecurityLabels() {
 		Patient p = new Patient();