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

README.md

@@ -7,7 +7,7 @@ HAPI FHIR - Java API for HL7 FHIR Clients and Servers
 [![Coverage Status](https://coveralls.io/repos/jamesagnew/hapi-fhir/badge.svg?branch=master&service=github)](https://coveralls.io/github/jamesagnew/hapi-fhir?branch=master)
 [![Maven Central](https://maven-badges.herokuapp.com/maven-central/ca.uhn.hapi.fhir/hapi-fhir-base/badge.svg)](http://search.maven.org/#search|ga|1|ca.uhn.hapi.fhir)
 [![Dependency Status](https://www.versioneye.com/user/projects/55e1d0d9c6d8f2001c00043e/badge.svg?style=flat)](https://www.versioneye.com/user/projects/55e1d0d9c6d8f2001c00043e)
-[![License](https://img.shields.io/badge/license-apache%202.0-ff69b4.svg)](https://github.com/jamesagnew/hapi-fhir/blob/master/LICENSE.txt)
+[![License](https://img.shields.io/badge/license-apache%202.0-ff69b4.svg)](http://jamesagnew.github.io/hapi-fhir/license.html)
 
 Complete project documentation is available here:
 http://jamesagnew.github.io/hapi-fhir/

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/interceptor/LoggingInterceptor.java

@@ -152,7 +152,7 @@ public void interceptResponse(HttpResponse theResponse) throws IOException {
 				throw new InternalErrorException(e);
 			}
 
-			myLog.info("Client response body:\n{}", new String(bytes));
+			myLog.info("Client response body:\n{}", new String(bytes, "UTF-8"));
 			theResponse.setEntity(new MyEntityWrapper(respEntity, bytes));
 			} else {
 				myLog.info("Client response body: (none)");

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

@@ -50,7 +50,6 @@
 import org.codehaus.stax2.io.EscapingWriterFactory;
 
 import com.ctc.wstx.api.WstxInputProperties;
-import com.ctc.wstx.stax.WstxInputFactory;
 import com.ctc.wstx.stax.WstxOutputFactory;
 
 /**
@@ -1550,6 +1549,7 @@ private static XMLInputFactory getOrCreateInputFactory() throws FactoryConfigura
 		if (ourInputFactory == null) {
 
 			try {
+				// Detect if we're running with the Android lib, and force repackaged Woodstox to be used
 				Class.forName("ca.uhn.fhir.repackage.javax.xml.stream.XMLInputFactory");
 				System.setProperty("javax.xml.stream.XMLInputFactory", "com.ctc.wstx.stax.WstxInputFactory");
 			} catch (ClassNotFoundException e) {
@@ -1589,6 +1589,7 @@ private static XMLOutputFactory getOrCreateOutputFactory() throws FactoryConfigu
 		if (ourOutputFactory == null) {
 
 			try {
+				// Detect if we're running with the Android lib, and force repackaged Woodstox to be used
 				Class.forName("ca.uhn.fhir.repackage.javax.xml.stream.XMLOutputFactory");
 				System.setProperty("javax.xml.stream.XMLOutputFactory", "com.ctc.wstx.stax.WstxOutputFactory");
 			} catch (ClassNotFoundException e) {
@@ -1708,7 +1709,7 @@ public static class MyEscaper implements EscapingWriterFactory {
 
 		@Override
 		public Writer createEscapingWriterFor(OutputStream theOut, String theEnc) throws UnsupportedEncodingException {
-			return createEscapingWriterFor(new OutputStreamWriter(theOut), theEnc);
+			return createEscapingWriterFor(new OutputStreamWriter(theOut, theEnc), theEnc);
 		}
 
 		@Override

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/SchemaBaseValidator.java

@@ -38,6 +38,7 @@
 import javax.xml.validation.SchemaFactory;
 import javax.xml.validation.Validator;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.input.BOMInputStream;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.w3c.dom.ls.LSInput;
@@ -203,6 +204,7 @@ public LSInput resolveResource(String theType, String theNamespaceURI, String th
 
 				InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase);
 				if (baseIs == null) {
+					IOUtils.closeQuietly(baseIs);
 					throw new InternalErrorException("Schema file not found: " + pathToBase);
 				}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/SchematronBaseValidator.java

@@ -28,6 +28,7 @@
 
 import javax.xml.transform.stream.StreamSource;
 
+import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.oclc.purl.dsdl.svrl.SchematronOutputType;
 
@@ -120,12 +121,14 @@ private ISchematronResource getSchematronAndCache(IValidationContext<IBaseResour
 				return retVal;
 			}
 
-			String pathToBase = myCtx.getVersion().getPathToSchemaDefinitions() + '/' + theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getName().toLowerCase()
-					+ ".sch";
+			String pathToBase = myCtx.getVersion().getPathToSchemaDefinitions() + '/' + theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getName().toLowerCase() + ".sch";
 			InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase);
-			if (baseIs == null) {
-				throw new InternalErrorException("No schematron found for resource type: "
-						+ theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getImplementingClass().getCanonicalName());
+			try {
+				if (baseIs == null) {
+					throw new InternalErrorException("No schematron found for resource type: " + theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getImplementingClass().getCanonicalName());
+				}
+			} finally {
+				IOUtils.closeQuietly(baseIs);
 			}
 
 			retVal = SchematronResourceSCH.fromClassPath(pathToBase);

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

@@ -160,7 +160,7 @@ public Conformance getServerConformance(HttpServletRequest theRequest) {
 
 		retVal.setPublisher(myPublisher);
 		retVal.setDate(DateTimeDt.withCurrentTime());
-		retVal.setFhirVersion("0.5.0"); // TODO: pull from model
+		retVal.setFhirVersion("1.0.0"); // TODO: pull from model
 		retVal.setAcceptUnknown(UnknownContentCodeEnum.UNKNOWN_EXTENSIONS); // TODO: make this configurable - this is a fairly big effort since the parser
 		// needs to be modified to actually allow it
 

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/conf/ServerConformanceProvider.java

@@ -166,7 +166,7 @@ public Conformance getServerConformance(HttpServletRequest theRequest) {
 
     retVal.setPublisher(myPublisher);
     retVal.setDate(new Date());
-    retVal.setFhirVersion("0.5.0"); // TODO: pull from model
+    retVal.setFhirVersion("1.0.0"); // TODO: pull from model
     retVal.setAcceptUnknown(UnknownContentCode.EXTENSIONS); // TODO: make this configurable - this is a fairly big effort since the parser
     // needs to be modified to actually allow it
 

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/validation/InstanceValidator.java

@@ -890,7 +890,7 @@ private void checkDeclaredProfiles(List<ValidationMessage> errors, WrapperElemen
         String p = stack.addToLiteralPath("meta", "profile", ":"+Integer.toString(i));
         if (rule(errors, IssueType.INVALID, element.line(), element.col(), p, !Utilities.noString(ref), "StructureDefinition reference invalid")) {
           StructureDefinition pr = context.fetchResource(StructureDefinition.class, ref);
-          if (warning(errors, IssueType.INVALID, element.line(), element.col(), p, pr != null, "StructureDefinition reference could not be resolved")) {
+          if (warning(errors, IssueType.INVALID, element.line(), element.col(), p, pr != null, "StructureDefinition reference \"{0}\" could not be resolved", ref)) {
             if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), p, pr.hasSnapshot(), "StructureDefinition has no snapshot - validation is against the snapshot, so it must be provided")) {
               validateElement(errors, pr, pr.getSnapshot().getElement().get(0), null, null, element, element.getName(), stack);
             }

hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/validation/FhirInstanceValidatorTest.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.validation;
 
+import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.greaterThan;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
@@ -8,6 +9,7 @@
 import static org.mockito.Mockito.when;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.hl7.fhir.instance.model.CodeType;
@@ -23,6 +25,8 @@
 import org.mockito.stubbing.Answer;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.primitive.IdDt;
 
 public class FhirInstanceValidatorTest {
 
@@ -120,26 +124,63 @@ private List<SingleValidationMessage> logResultsAndReturnNonInformationalOnes(Va
   }
 
   @Test
-  public void testValidateJsonResource() {
-    // @formatter:off
-    String input = "{" + "\"resourceType\":\"Patient\"," + "\"id\":\"123\"" + "}";
-    // @formatter:on
+  public void testValidateRawJsonResource() {
+    //@formatter:off
+    String input = 
+        "{" + 
+        "\"resourceType\":\"Patient\"," + 
+        "\"id\":\"123\"" + 
+        "}";
+    //@formatter:on
 
     ValidationResult output = myVal.validateWithResult(input);
     assertEquals(output.toString(), 0, output.getMessages().size());
   }
 
   @Test
-  public void testValidateJsonResourceBadAttributes() {
+  public void testValidateRawJsonResourceBadAttributes() {
+    //@formatter:off
+    String input = 
+        "{" + 
+        "\"resourceType\":\"Patient\"," + 
+        "\"id\":\"123\"," + 
+        "\"foo\":\"123\"" + 
+        "}";
+    //@formatter:on
+
+    ValidationResult output = myVal.validateWithResult(input);
+    assertEquals(output.toString(), 1, output.getMessages().size());
+    ourLog.info(output.getMessages().get(0).getLocationString());
+    ourLog.info(output.getMessages().get(0).getMessage());
+    assertEquals("/foo", output.getMessages().get(0).getLocationString());
+    assertEquals("Element is unknown or does not match any slice", output.getMessages().get(0).getMessage());
+  }
+
+  @Test
+  public void testValidateRawXmlResource() {
+    //@formatter:off
+    String input = 
+      "<Patient xmlns=\"http://hl7.org/fhir\">" + 
+      "<id value=\"123\"/>" + 
+      "</Patient>";
+    //@formatter:on
+
+    ValidationResult output = myVal.validateWithResult(input);
+    assertEquals(output.toString(), 0, output.getMessages().size());
+  }
+
+  @Test
+  public void testValidateRawXmlResourceBadAttributes() {
     // @formatter:off
-    String input = "{" + "\"resourceType\":\"Patient\"," + "\"id\":\"123\"," + "\"foo\":\"123\"" + "}";
+    String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "<foo value=\"222\"/>"
+        + "</Patient>";
     // @formatter:on
 
     ValidationResult output = myVal.validateWithResult(input);
     assertEquals(output.toString(), 1, output.getMessages().size());
     ourLog.info(output.getMessages().get(0).getLocationString());
     ourLog.info(output.getMessages().get(0).getMessage());
-    assertEquals("/foo", output.getMessages().get(0).getLocationString());
+    assertEquals("/f:Patient/f:foo", output.getMessages().get(0).getLocationString());
     assertEquals("Element is unknown or does not match any slice", output.getMessages().get(0).getMessage());
   }
 
@@ -159,34 +200,42 @@ public void testValidateResourceFailingInvariant() {
   }
 
   @Test
-  public void testValidateResourceWithExampleBindingCodeValidationFailing() {
+  public void testValidateResourceContainingProfileDeclarationDoesntResolve() {
+    addValidConcept("http://loinc.org", "12345");
+
     Observation input = new Observation();
-
-    myInstanceVal.setValidationSupport(myMockSupport);
-
-    input.setStatus(ObservationStatus.FINAL);
+    input.getMeta().addProfile("http://foo/myprofile");
+
     input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
+    input.setStatus(ObservationStatus.FINAL);
 
+    myInstanceVal.setValidationSupport(myMockSupport);
     ValidationResult output = myVal.validateWithResult(input);
     List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
     assertEquals(errors.toString(), 1, errors.size());
-    assertEquals("Unable to validate code \"12345\" in code system \"http://loinc.org\"", errors.get(0).getMessage());
-
+    assertEquals("StructureDefinition reference \"http://foo/myprofile\" could not be resolved", errors.get(0).getMessage());
   }
 
   @Test
-  public void testValidateResourceWithExampleBindingCodeValidationPassing() {
-    Observation input = new Observation();
-
-    myInstanceVal.setValidationSupport(myMockSupport);
+  public void testValidateResourceContainingProfileDeclaration() {
     addValidConcept("http://loinc.org", "12345");
+
+    Observation input = new Observation();
+    input.getMeta().addProfile("http://hl7.org/fhir/StructureDefinition/devicemetricobservation");
 
+    input.addIdentifier().setSystem("http://acme").setValue("12345");
+    input.getEncounter().setReference("http://foo.com/Encounter/9");
     input.setStatus(ObservationStatus.FINAL);
     input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
 
+    myInstanceVal.setValidationSupport(myMockSupport);
     ValidationResult output = myVal.validateWithResult(input);
     List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
-    assertEquals(errors.toString(), 0, errors.size());
+
+    assertThat(errors.toString(), containsString("Element '/f:Observation.subject': minimum required = 1, but only found 0"));
+    assertThat(errors.toString(), containsString("Element encounter @ /f:Observation: max allowed = 0, but found 1"));
+    assertThat(errors.toString(), containsString("Element '/f:Observation.device': minimum required = 1, but only found 0"));
+    assertThat(errors.toString(), containsString(""));
   }
 
   @Test
@@ -213,27 +262,33 @@ public void testValidateResourceWithDefaultValuesetBadCode() {
   }
 
   @Test
-  public void testValidateXmlResource() {
-    // @formatter:off
-    String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "</Patient>";
-    // @formatter:on
+  public void testValidateResourceWithExampleBindingCodeValidationFailing() {
+    Observation input = new Observation();
+
+    myInstanceVal.setValidationSupport(myMockSupport);
+
+    input.setStatus(ObservationStatus.FINAL);
+    input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
 
     ValidationResult output = myVal.validateWithResult(input);
-    assertEquals(output.toString(), 0, output.getMessages().size());
+    List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
+    assertEquals(errors.toString(), 1, errors.size());
+    assertEquals("Unable to validate code \"12345\" in code system \"http://loinc.org\"", errors.get(0).getMessage());
+
   }
 
   @Test
-  public void testValidateXmlResourceBadAttributes() {
-    // @formatter:off
-    String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "<foo value=\"222\"/>"
-        + "</Patient>";
-    // @formatter:on
+  public void testValidateResourceWithExampleBindingCodeValidationPassing() {
+    Observation input = new Observation();
+
+    myInstanceVal.setValidationSupport(myMockSupport);
+    addValidConcept("http://loinc.org", "12345");
+
+    input.setStatus(ObservationStatus.FINAL);
+    input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
 
     ValidationResult output = myVal.validateWithResult(input);
-    assertEquals(output.toString(), 1, output.getMessages().size());
-    ourLog.info(output.getMessages().get(0).getLocationString());
-    ourLog.info(output.getMessages().get(0).getMessage());
-    assertEquals("/f:Patient/f:foo", output.getMessages().get(0).getLocationString());
-    assertEquals("Element is unknown or does not match any slice", output.getMessages().get(0).getMessage());
+    List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
+    assertEquals(errors.toString(), 0, errors.size());
   }
 }

pom.xml

@@ -783,9 +783,11 @@
 								<copy todir="target/site/xref-base">
 									<fileset dir="hapi-fhir-base/target/site/xref" />
 								</copy>
+								<!--
 								<copy todir="target/site/cobertura">
 									<fileset dir="hapi-fhir-cobertura/target/site/cobertura" />
 								</copy>
+								-->
 								<copy todir="target/site">
 									<fileset dir="hapi-fhir-base/target/site" includes="checkstyle.*" />
 								</copy>
@@ -1164,7 +1166,9 @@
 				<module>hapi-fhir-structures-dstu2</module>
 				<module>hapi-fhir-structures-hl7org-dstu2</module>
 				<module>hapi-fhir-jpaserver-base</module>
+				<!-- 
 				<module>hapi-fhir-cobertura</module>
+				-->
 				<module>examples</module>
 			</modules>
 			<reporting>

src/site/site.xml

@@ -137,10 +137,9 @@
 		</menu>
 
 
-		<menu name="Maven Reports" inherit="bottom">
+		<menu name="Reports" inherit="bottom">
 			<item name="Project Developers" href="team-list.html" />
-			<item name="Cobertura (Test Coverage)" href="cobertura/index.html" />
-			<item name="Surefire (Test Status)" href="surefire-report.html" />
+			<item name="Coveralls (Test Coverage)" href="https://coveralls.io/github/jamesagnew/hapi-fhir" />
 			<item name="FindBugs" href="findbugs.html" />
 			<item name="Checkstyle" href="checkstyle.html" />
 		</menu>

src/site/xdoc/index.xml

@@ -24,6 +24,8 @@
 				<a href="https://maven-badges.herokuapp.com/maven-central/ca.uhn.hapi.fhir/hapi-fhir-base/badge.svg"><img src="https://maven-badges.herokuapp.com/maven-central/ca.uhn.hapi.fhir/hapi-fhir-base/badge.svg" alt="Maven Central"/></a>
 				<br/>
 				<a href="https://www.versioneye.com/user/projects/55e1d0d9c6d8f2001c00043e"><img src="https://www.versioneye.com/user/projects/55e1d0d9c6d8f2001c00043e/badge.svg?style=flat" alt="VersionEye"/></a>
+				<br/>
+				<a href="http://jamesagnew.github.io/hapi-fhir/license.html"><img src="https://img.shields.io/badge/license-apache%202.0-ff69b4.svg" alt="Apache 2.0 Licensed"/></a>
 			</p>
 
 			<p>