Fix a few issues found by FindBugs

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 class LoggingInterceptor implements IClientInterceptor {
 				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.XMLOutputFactory2;
 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 @@ public class XmlUtil {
 		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 @@ public class XmlUtil {
 		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 class XmlUtil {
 
 		@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.Schema;
 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 @@ class SchemaBaseValidator implements IValidatorModule {
 
 				InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase);
 				if (baseIs == null) {
+					IOUtils.closeQuietly(baseIs.close());
 					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 java.util.Map;
 
 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 @@ public class SchematronBaseValidator implements IValidatorModule {
 				return retVal;
 			}
 
-			String pathToBase = myCtx.getVersion().getPathToSchemaDefinitions() + '/' + theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getName().toLowerCase()
+			String pathToBase = myCtx.getVersion().getPathToSchemaDefinitions() + '/' + theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getName().toLowerCase() + ".sch";
-					+ ".sch";
 			InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase);
-			if (baseIs == null) {
+			try {
-				throw new InternalErrorException("No schematron found for resource type: "
+				if (baseIs == null) {
-						+ theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getImplementingClass().getCanonicalName());
+					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);

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="Coveralls (Test Coverage)" href="https://coveralls.io/github/jamesagnew/hapi-fhir" />
-			<item name="Surefire (Test Status)" href="surefire-report.html" />
 			<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>