Merge branch 'master' into tinder-for-non-java

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IContextValidationSupport.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.context.support;
 
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2016 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import java.util.List;
 
 import org.hl7.fhir.instance.model.api.IBaseResource;

hapi-fhir-base/src/main/java/ca/uhn/fhir/fluentpath/FluentPathExecutionException.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.fluentpath;
 
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2016 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 
 /**

hapi-fhir-base/src/main/java/ca/uhn/fhir/fluentpath/IFluentPath.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.fluentpath;
 
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2016 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import java.util.List;
 
 import org.hl7.fhir.instance.model.api.IBase;

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

@@ -61,7 +61,7 @@ public class LenientErrorHandler implements IParserErrorHandler {
 	@Override
 	public void incorrectJsonType(IParseLocation theLocation, String theElementName, ValueType theExpected, ValueType theFound) {
 		if (myLogErrors) {
-			ourLog.warn("Found incorrect type for element {} - Expected {} and found {}", theElementName, theExpected.name(), theFound.name());
+			ourLog.warn("Found incorrect type for element {} - Expected {} and found {}", new Object[]{theElementName, theExpected.name(), theFound.name()});
 		}
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/CorsInterceptor.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.rest.server.interceptor;
 
+/*
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2016 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import java.io.IOException;
 
 import javax.servlet.http.HttpServletRequest;

hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/ExampleDataUploader.java

@@ -245,7 +245,7 @@ public class ExampleDataUploader extends BaseCommand {
 				iter.remove();
 			}
 		}
-		
+
 		List<IBaseResource> subResourceList = new ArrayList<IBaseResource>();
 		while (resources.size() > 0) {
 
@@ -253,7 +253,7 @@ public class ExampleDataUploader extends BaseCommand {
 			subResourceList.add(nextAddedResource);
 
 			Set<String> checkedTargets = new HashSet<String>();
-			
+
 			for (int i = 0; i < subResourceList.size(); i++) {
 				IBaseResource nextCandidateSource = subResourceList.get(i);
 				for (ResourceReferenceInfo nextRef : ctx.newTerser().getAllResourceReferences(nextCandidateSource)) {
@@ -276,7 +276,7 @@ public class ExampleDataUploader extends BaseCommand {
 
 					boolean found = false;
 					for (int j = 0; j < resources.size(); j++) {
-						String candidateTarget = resources.get(j).getIdElement().getValue(); 
+						String candidateTarget = resources.get(j).getIdElement().getValue();
 						if (isNotBlank(nextTarget) && nextTarget.equals(candidateTarget)) {
 							ourLog.info("Reflexively adding resource {} to bundle as it is a reference target", nextTarget);
 							subResourceList.add(resources.remove(j));
@@ -287,7 +287,6 @@ public class ExampleDataUploader extends BaseCommand {
 				}
 			}
 
-
 			if (subResourceList.size() < 10 && resources.size() > 0) {
 				subResourceList.add(resources.remove(0));
 				continue;
@@ -357,8 +356,8 @@ public class ExampleDataUploader extends BaseCommand {
 			Entry next = iterator.next();
 
 			// DataElement have giant IDs that seem invalid, need to investigate this..
-			if ("Subscription".equals(next.getResource().getResourceName()) || "DataElement".equals(next.getResource().getResourceName()) || "OperationOutcome".equals(next.getResource().getResourceName())
+			if ("Subscription".equals(next.getResource().getResourceName()) || "DataElement".equals(next.getResource().getResourceName())
-					|| "OperationDefinition".equals(next.getResource().getResourceName())) {
+					|| "OperationOutcome".equals(next.getResource().getResourceName()) || "OperationDefinition".equals(next.getResource().getResourceName())) {
 				ourLog.info("Skipping " + next.getResource().getResourceName() + " example");
 				iterator.remove();
 			} else {
@@ -399,7 +398,7 @@ public class ExampleDataUploader extends BaseCommand {
 				// }
 				nextRef.getResourceReference().setResource(null);
 				String value = nextRef.getResourceReference().getReferenceElement().toUnqualifiedVersionless().getValue();
-				
+
 				if (isNotBlank(value)) {
 					if (!qualIds.contains(value) && !nextRef.getResourceReference().getReferenceElement().isLocal()) {
 						ourLog.info("Discarding unknown reference: {}", value);
@@ -437,8 +436,8 @@ public class ExampleDataUploader extends BaseCommand {
 			BundleEntryComponent next = iterator.next();
 
 			// DataElement have giant IDs that seem invalid, need to investigate this..
-			if ("Subscription".equals(next.getResource().getResourceType()) || "DataElement".equals(next.getResource().getResourceType()) || "OperationOutcome".equals(next.getResource().getResourceType())
+			if ("Subscription".equals(next.getResource().getResourceType()) || "DataElement".equals(next.getResource().getResourceType())
-					|| "OperationDefinition".equals(next.getResource().getResourceType())) {
+					|| "OperationOutcome".equals(next.getResource().getResourceType()) || "OperationDefinition".equals(next.getResource().getResourceType())) {
 				ourLog.info("Skipping " + next.getResource().getResourceType() + " example");
 				iterator.remove();
 			} else {
@@ -479,7 +478,7 @@ public class ExampleDataUploader extends BaseCommand {
 				// }
 				nextRef.getResourceReference().setResource(null);
 				String value = nextRef.getResourceReference().getReferenceElement().toUnqualifiedVersionless().getValue();
-				
+
 				if (isNotBlank(value)) {
 					if (!qualIds.contains(value) && !nextRef.getResourceReference().getReferenceElement().isLocal()) {
 						ourLog.info("Discarding unknown reference: {}", value);
@@ -659,37 +658,41 @@ public class ExampleDataUploader extends BaseCommand {
 
 	private void downloadFileFromInternet(CloseableHttpResponse result, File localFile) throws IOException {
 		FileOutputStream buffer = FileUtils.openOutputStream(localFile);
+		try {
 
-		long maxLength = result.getEntity().getContentLength();
+			long maxLength = result.getEntity().getContentLength();
-		long nextLog = -1;
+			long nextLog = -1;
-		// ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+			// ByteArrayOutputStream buffer = new ByteArrayOutputStream();
-		int nRead;
+			int nRead;
-		byte[] data = new byte[16384];
+			byte[] data = new byte[16384];
-		while ((nRead = result.getEntity().getContent().read(data, 0, data.length)) != -1) {
+			while ((nRead = result.getEntity().getContent().read(data, 0, data.length)) != -1) {
-			buffer.write(data, 0, nRead);
+				buffer.write(data, 0, nRead);
-			long fileSize = FileUtils.sizeOf(localFile);
+				long fileSize = FileUtils.sizeOf(localFile);
-			if (fileSize > nextLog) {
+				if (fileSize > nextLog) {
-				System.err.print("\r" + Ansi.ansi().eraseLine());
+					System.err.print("\r" + Ansi.ansi().eraseLine());
-				System.err.print(FileUtils.byteCountToDisplaySize(fileSize));
+					System.err.print(FileUtils.byteCountToDisplaySize(fileSize));
-				if (maxLength > 0) {
+					if (maxLength > 0) {
-					System.err.print(" [");
+						System.err.print(" [");
-					int stars = (int) (50.0f * ((float) fileSize / (float) maxLength));
+						int stars = (int) (50.0f * ((float) fileSize / (float) maxLength));
-					for (int i = 0; i < stars; i++) {
+						for (int i = 0; i < stars; i++) {
-						System.err.print("*");
+							System.err.print("*");
+						}
+						for (int i = stars; i < 50; i++) {
+							System.err.print(" ");
+						}
+						System.err.print("]");
 					}
-					for (int i = stars; i < 50; i++) {
+					System.err.flush();
-						System.err.print(" ");
+					nextLog += 100000;
-					}
-					System.err.print("]");
 				}
-				System.err.flush();
-				nextLog += 100000;
 			}
-		}
+			buffer.flush();
-		buffer.flush();
 
-		System.err.println();
+			System.err.println();
-		System.err.flush();
+			System.err.flush();
+		} finally {
+			IOUtils.closeQuietly(buffer);
+		}
 	}
 
 }

hapi-fhir-osgi-core/pom.xml

@@ -82,6 +82,18 @@
 
 	<build>
 		<plugins>
+
+<plugin>
+  <groupId>org.apache.maven.plugins</groupId>
+  <artifactId>maven-compiler-plugin</artifactId>
+  <configuration>
+    <excludes>
+      <exclude>**/ca/uhn/fhir/rest/server/interceptor/CorsInterceptor.java</exclude>
+    </excludes>
+  </configuration>
+</plugin>
+
+
 			<plugin>
 				<artifactId>maven-antrun-plugin</artifactId>
 				<executions>

src/changes/changes.xml

@@ -7,7 +7,16 @@
 	</properties>
 	<body>
 		<release version="2.2" date="TBD">
-			<action type="fix">
+			<!--<action type="add">
+				Bump the version of a few dependencies to the
+				latest versions (dependent HAPI modules listed in brackets):
+				<![CDATA[
+					<ul>
+						<li>spring (JPA): 4.3.1 -&gt; 4.3.4</li>
+					</ul>
+				]]>
+			</action>-->
+		<action type="fix">
 				Fix issue in AuthorizationIntetceptor where
 				transactions are blocked even when they
 				should not be
@@ -66,6 +75,10 @@
 				external references (and therefore can't be loaded
 				by the server). Thanks to Hannes Ulrich for reporting!
 			</action>
+			<action type="fix">
+				HAPI FHIR CLI failed to delete a file when uploading
+				example resources while running under Windows.
+			</action>
 		</release>
 		<release version="2.1" date="2016-11-11">
 			<action type="add">