Fix unit test

hapi-fhir-android/dependency-reduced-pom.xml

@@ -55,6 +55,7 @@
                   <include>org.glassfish:javax.json</include>
                   <include>org.codehaus.woodstox:woodstox-core-asl</include>
                   <include>javax.xml.stream:stax-api</include>
+                  <include>javax.servlet:javax.servlet-api</include>
                   <include>org.codehaus.woodstox:stax2-api</include>
                   <include>org.slf4j:slf4j*</include>
                   <include>org.apache.commons:*</include>
@@ -128,12 +129,6 @@
       <version>4.3.6</version>
       <scope>compile</scope>
     </dependency>
-    <dependency>
-      <groupId>javax.servlet</groupId>
-      <artifactId>javax.servlet-api</artifactId>
-      <version>3.1.0</version>
-      <scope>compile</scope>
-    </dependency>
     <dependency>
       <groupId>junit</groupId>
       <artifactId>junit</artifactId>

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

@@ -1,15 +1,7 @@
 package ca.uhn.fhir.parser;
 
-import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.*;
-import static org.hamcrest.Matchers.not;
+import static org.junit.Assert.*;
-import static org.hamcrest.Matchers.stringContainsInOrder;
-import static org.junit.Assert.assertArrayEquals;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.assertTrue;
 
 import java.io.IOException;
 import java.io.InputStreamReader;
@@ -84,6 +76,43 @@ public class XmlParserTest {
 	private static FhirContext ourCtx;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserTest.class);
 
+	/**
+	 * see #144 and #146
+	 */
+	@Test
+	public void testParseContained() {
+
+		FhirContext c = FhirContext.forDstu1();
+		IParser parser = c.newXmlParser().setPrettyPrint(true);
+
+		Observation o = new Observation();
+		o.getName().setText("obs text");
+
+		Patient p = new Patient();
+		p.addName().addFamily("patient family");
+		o.getSubject().setResource(p);
+		
+		String enc = parser.encodeResourceToString(o);
+		ourLog.info(enc);
+		
+		//@formatter:off
+		assertThat(enc, stringContainsInOrder(
+			"<Observation xmlns=\"http://hl7.org/fhir\">",
+			"<contained>",
+			"<Patient xmlns=\"http://hl7.org/fhir\" id=\"1\">",
+			"</contained>",
+			"<reference value=\"#1\"/>"
+			));
+		//@formatter:on
+		
+		o = parser.parseResource(Observation.class, enc);
+		assertEquals("obs text", o.getName().getText().getValue());
+		
+		assertNotNull(o.getSubject().getResource());
+		p = (Patient) o.getSubject().getResource();
+		assertEquals("patient family", p.getNameFirstRep().getFamilyAsSingleString());
+	}
+
 	@Test
 	public void testComposition() {
 

hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2/Dstu2BundleFactory.java

@@ -252,11 +252,11 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 
 			if (searchId != null) {
 				if (theOffset + numToReturn < theResult.size()) {
-					myBundle.addLink().setRelation(Constants.LINK_NEXT).setUrl(RestfulServerUtils.createPagingLink(theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint));
+					myBundle.addLink().setRelation(Constants.LINK_NEXT).setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint));
 				}
 				if (theOffset > 0) {
 					int start = Math.max(0, theOffset - limit);
-					myBundle.addLink().setRelation(Constants.LINK_PREVIOUS).setUrl(RestfulServerUtils.createPagingLink(theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint));
+					myBundle.addLink().setRelation(Constants.LINK_PREVIOUS).setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint));
 				}
 			}
 		}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java

@@ -6,14 +6,15 @@ import static org.junit.Assert.*;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Observable;
 
 import net.sf.json.JSON;
 import net.sf.json.JSONSerializer;
 import net.sf.json.JsonConfig;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.hamcrest.Matchers;
+import org.junit.Assert;
 import org.junit.Test;
 
 import ca.uhn.fhir.context.ConfigurationException;
@@ -28,19 +29,23 @@ import ca.uhn.fhir.model.base.composite.BaseCodingDt;
 import ca.uhn.fhir.model.dstu2.composite.CodingDt;
 import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
 import ca.uhn.fhir.model.dstu2.resource.Binary;
+import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
+import ca.uhn.fhir.model.dstu2.resource.Medication;
 import ca.uhn.fhir.model.dstu2.resource.MedicationPrescription;
 import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.dstu2.resource.QuestionnaireAnswers;
 import ca.uhn.fhir.model.dstu2.valueset.IdentifierUseEnum;
+import ca.uhn.fhir.model.dstu2.valueset.ObservationReliabilityEnum;
+import ca.uhn.fhir.model.dstu2.valueset.ObservationStatusEnum;
 import ca.uhn.fhir.model.primitive.DateDt;
 import ca.uhn.fhir.model.primitive.DateTimeDt;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 
-public class JsonParserTest {
+public class JsonParserDstu2Test {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserTest.class);
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserDstu2Test.class);
 	private static final FhirContext ourCtx = FhirContext.forDstu2();
 
 	@Test
@@ -54,6 +59,54 @@ public class JsonParserTest {
 		assertEquals("{\"resourceType\":\"Binary\",\"id\":\"11\",\"meta\":{\"versionId\":\"22\"},\"contentType\":\"foo\",\"content\":\"AQIDBA==\"}", val);
 	}
 
+	/**
+	 * See #144 and #146
+	 */
+	@Test
+	public void testReportSerialize() {
+
+		ReportObservation obsv = new ReportObservation();
+		obsv.getCode().addCoding().setCode("name");
+		obsv.setValue(new StringDt("value test"));
+		obsv.setStatus(ObservationStatusEnum.FINAL);
+		obsv.setReliability(ObservationReliabilityEnum.OK);
+		obsv.addIdentifier().setSystem("System").setValue("id value");
+		
+		DiagnosticReport report = new DiagnosticReport();
+		report.getContained().getContainedResources().add(obsv);
+		report.addResult().setResource(obsv);
+
+		IParser parser = new FhirContext().newXmlParser().setPrettyPrint(true);
+		String message = parser.encodeResourceToString(report);
+		ourLog.info(message);
+		Assert.assertThat(message, containsString("contained"));
+	}
+
+	/**
+	 * See #144 and #146
+	 */
+	@Test
+	public void testReportSerializeWithMatchingId() {
+
+		ReportObservation obsv = new ReportObservation();
+		obsv.getCode().addCoding().setCode("name");
+		obsv.setValue(new StringDt("value test"));
+		obsv.setStatus(ObservationStatusEnum.FINAL);
+		obsv.setReliability(ObservationReliabilityEnum.OK);
+		obsv.addIdentifier().setSystem("System").setValue("id value");
+		
+		DiagnosticReport report = new DiagnosticReport();
+		report.getContained().getContainedResources().add(obsv);
+		
+		obsv.setId("#123");
+		report.addResult().setReference("#123");
+
+		IParser parser = new FhirContext().newXmlParser().setPrettyPrint(true);
+		String message = parser.encodeResourceToString(report);
+		ourLog.info(message);
+		Assert.assertThat(message, containsString("contained"));
+	}
+
 	/**
 	 * see #144 and #146
 	 */
@@ -69,10 +122,10 @@ public class JsonParserTest {
 		Patient p = new Patient();
 		p.addName().addFamily("patient family");
 		o.getSubject().setResource(p);
-		
+
 		String enc = parser.encodeResourceToString(o);
 		ourLog.info(enc);
-		
+
 		//@formatter:off
 		assertThat(enc, stringContainsInOrder(
 			"\"resourceType\":\"Observation\"",
@@ -82,10 +135,10 @@ public class JsonParserTest {
 			"\"reference\":\"#1\""
 			));
 		//@formatter:on
-		
+
 		o = parser.parseResource(Observation.class, enc);
 		assertEquals("obs text", o.getCode().getText());
-		
+
 		assertNotNull(o.getSubject().getResource());
 		p = (Patient) o.getSubject().getResource();
 		assertEquals("patient family", p.getNameFirstRep().getFamilyAsSingleString());
@@ -217,7 +270,7 @@ public class JsonParserTest {
 	 */
 	@Test
 	public void testEncodeBundleWithDeletedEntry() throws ConfigurationException, DataFormatException, IOException {
-		Bundle b = ourCtx.newXmlParser().parseBundle(IOUtils.toString(JsonParserTest.class.getResourceAsStream("/xml-bundle.xml")));
+		Bundle b = ourCtx.newXmlParser().parseBundle(IOUtils.toString(JsonParserDstu2Test.class.getResourceAsStream("/xml-bundle.xml")));
 		String val = ourCtx.newJsonParser().encodeBundleToString(b);
 
 		ourLog.info(val);
@@ -417,7 +470,7 @@ public class JsonParserTest {
 
 	@Test
 	public void testParseAndEncodeBundle() throws Exception {
-		String content = IOUtils.toString(JsonParserTest.class.getResourceAsStream("/bundle-example.json"));
+		String content = IOUtils.toString(JsonParserDstu2Test.class.getResourceAsStream("/bundle-example.json"));
 
 		Bundle parsed = ourCtx.newJsonParser().parseBundle(content);
 		assertEquals("http://example.com/base/Bundle/example/_history/1", parsed.getId().getValue());
@@ -437,6 +490,10 @@ public class JsonParserTest {
 		assertEquals("2014-08-16T05:31:17Z", ResourceMetadataKeyEnum.UPDATED.get(p).getValueAsString());
 		assertEquals("http://example.com/base/MedicationPrescription/3123/_history/1", p.getId().getValue());
 
+		Medication m = (Medication) parsed.getEntries().get(1).getResource();
+		assertEquals("http://example.com/base/Medication/example", m.getId().getValue());
+		assertSame(p.getMedication().getResource(), m);
+		
 		String reencoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeBundleToString(parsed);
 		ourLog.info(reencoded);
 
@@ -457,7 +514,7 @@ public class JsonParserTest {
 
 	@Test
 	public void testParseAndEncodeBundleOldStyle() throws Exception {
-		String content = IOUtils.toString(JsonParserTest.class.getResourceAsStream("/bundle-transaction.json"));
+		String content = IOUtils.toString(JsonParserDstu2Test.class.getResourceAsStream("/bundle-transaction.json"));
 
 		Bundle parsed = ourCtx.newJsonParser().parseBundle(content);
 		// assertEquals("http://example.com/base/Bundle/example/_history/1", parsed.getId().getValue());
@@ -502,7 +559,7 @@ public class JsonParserTest {
 
 	@Test
 	public void testParseAndEncodeBundleNewStyle() throws Exception {
-		String content = IOUtils.toString(JsonParserTest.class.getResourceAsStream("/bundle-example.json"));
+		String content = IOUtils.toString(JsonParserDstu2Test.class.getResourceAsStream("/bundle-example.json"));
 
 		ca.uhn.fhir.model.dstu2.resource.Bundle parsed = ourCtx.newJsonParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, content);
 		assertEquals("http://example.com/base/Bundle/example/_history/1", parsed.getId().getValue());

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

@@ -0,0 +1,111 @@
+package ca.uhn.fhir.parser;
+
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+import ca.uhn.fhir.model.dstu2.resource.Observation;
+import ca.uhn.fhir.model.primitive.BooleanDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.util.ElementUtil;
+
+@ResourceDef(name = "Observation", id = "reportobservation")
+public class ReportObservation extends Observation {
+
+	/**
+	 * Each extension is defined in a field. Any valid HAPI Data Type can be used for the field type. Note that the
+	 * [name=""] attribute in the @Child annotation needs to match the name for the bean accessor and mutator methods.
+	 */
+	@Child(name = "mandatory", order = 0)
+	@Extension(url = "#mandatory", definedLocally = true, isModifier = false)
+	@Description(shortDefinition = "The report observation is mandatory or not")
+	private BooleanDt mandatory;
+
+	@Child(name = "readOnly", order = 1)
+	@Extension(url = "#readOnly", definedLocally = true, isModifier = false)
+	@Description(shortDefinition = "The report observation is read only or not")
+	private BooleanDt readOnly;
+
+	@Child(name = "defaultCursor", order = 2)
+	@Extension(url = "#defaultCursor", definedLocally = true, isModifier = false)
+	@Description(shortDefinition = "The report observation is default cursor or not")
+	private BooleanDt defaultCursor;
+
+	@Child(name = "sectionContentId", order = 3)
+	@Extension(url = "#sectionContentId", definedLocally = true, isModifier = false)
+	@Description(shortDefinition = "The primary key of the report section content")
+	private StringDt sectionContentId;
+
+	/**
+	 * It is important to override the isEmpty() method, adding a check for any newly added fields.
+	 */
+	@Override
+	public boolean isEmpty() {
+		return super.isEmpty() && ElementUtil.isEmpty(mandatory, readOnly, defaultCursor, sectionContentId);
+	}
+
+	/********
+	 * Accessors and mutators follow
+	 *
+	 * IMPORTANT: Each extension is required to have an getter/accessor and a stter/mutator. You are highly recommended
+	 * to create getters which create instances if they do not already exist, since this is how the rest of the HAPI
+	 * FHIR API works.
+	 ********/
+
+	/** Getter for mandatory */
+	public BooleanDt getMandatory() {
+		if (mandatory == null) {
+			mandatory = new BooleanDt(false);
+		}
+		return mandatory;
+	}
+
+	/** Setter for mandatory */
+	public ReportObservation setMandatory(Boolean isMandatory) {
+		mandatory = new BooleanDt(isMandatory);
+		return this;
+	}
+
+	/** Getter for readOnly */
+	public BooleanDt getReadOnly() {
+		if (readOnly == null) {
+			readOnly = new BooleanDt(false);
+		}
+		return readOnly;
+	}
+
+	/** Setter for readOnly */
+	public ReportObservation setReadOnly(Boolean isReadOnly) {
+		readOnly = new BooleanDt(isReadOnly);
+		return this;
+	}
+
+	/** Getter for defaultCursor */
+	public BooleanDt getDefaultCursor() {
+		if (defaultCursor == null) {
+			defaultCursor = new BooleanDt(false);
+		}
+		return defaultCursor;
+	}
+
+	/** Setter for defaultCursor */
+	public ReportObservation setDefaultCursor(Boolean isDefaultCursor) {
+		defaultCursor = new BooleanDt(isDefaultCursor);
+		return this;
+	}
+
+	/** Getter for sectionContentId */
+	public StringDt getSectionContentId() {
+		if (sectionContentId == null) {
+			sectionContentId = new StringDt();
+		}
+		return sectionContentId;
+	}
+
+	/** Setter for sectionContentId */
+	public ReportObservation setSectionContentId(String sectionContentId) {
+		this.sectionContentId = new StringDt(sectionContentId);
+		return this;
+	}
+
+}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java

@@ -43,8 +43,8 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 
-public class XmlParserTest {
+public class XmlParserDstu2Test {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserTest.class);
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserDstu2Test.class);
 	private static final FhirContext ourCtx = FhirContext.forDstu2();
 
 	@BeforeClass
@@ -384,7 +384,7 @@ public class XmlParserTest {
 
 	@Test
 	public void testParseAndEncodeBundle() throws Exception {
-		String content = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/bundle-example.xml"));
+		String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
 
 		Bundle parsed = ourCtx.newXmlParser().parseBundle(content);
 		assertEquals("http://example.com/base/Bundle/example/_history/1", parsed.getId().getValue());
@@ -415,7 +415,7 @@ public class XmlParserTest {
 
 	@Test
 	public void testParseAndEncodeBundleNewStyle() throws Exception {
-		String content = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/bundle-example.xml"));
+		String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
 
 		IParser newXmlParser = ourCtx.newXmlParser();
 		ca.uhn.fhir.model.dstu2.resource.Bundle parsed = newXmlParser.parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, content);