Work on Android

hapi-fhir-android/.classpath

@@ -12,6 +12,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="src" path="src/main/resources"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

hapi-fhir-android/pom.xml

@@ -60,6 +60,30 @@
 			<artifactId>slf4j-android</artifactId>
 			<version>${slf4j_version}</version>
 		</dependency>
+		<!-- <dependency> <groupId>org.codehaus.woodstox</groupId> <artifactId>stax2-api</artifactId> 
+			<version>3.1.4</version> </dependency> -->
+
+		<dependency>
+			<groupId>commons-codec</groupId>
+			<artifactId>commons-codec</artifactId>
+			<version>${commons_codec_version}</version>
+		</dependency>
+		<dependency>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+			<version>${commons_io_version}</version>
+		</dependency>
+
+
+		<!-- Testing -->
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>${junit_version}</version>
+			<scope>test</scope>
+		</dependency>
+		<!-- <dependency> <groupId>commons-io</groupId> <artifactId>commons-io</artifactId> 
+			<version>${commons_io_version}</version> <scope>test</scope> </dependency> -->
 	</dependencies>
 
 	<build>
@@ -71,6 +95,25 @@
 					<skip>true</skip>
 				</configuration>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-failsafe-plugin</artifactId>
+				<version>${maven_failsafe_plugin_version}</version>
+				<configuration>
+					<classpathDependencyScopeExclude>compile+runtime</classpathDependencyScopeExclude>
+					<additionalClasspathElements>
+						<additionalClasspathElement>target/hapi-fhir-android-0.9-SNAPSHOT-shaded.jar</additionalClasspathElement>
+					</additionalClasspathElements>
+				</configuration>
+				<executions>
+					<execution>
+						<goals>
+							<goal>integration-test</goal>
+							<goal>verify</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-shade-plugin</artifactId>
@@ -84,8 +127,11 @@
 						<configuration>
 							<shadedArtifactAttached>true</shadedArtifactAttached>
 							<createDependencyReducedPom>true</createDependencyReducedPom>
+							<!--<minimizeJar>true</minimizeJar>-->
 							<artifactSet>
 								<includes>
+									<include>commons-codec:commons-codec</include>
+									<include>commons-io:commons-io</include>
 									<include>ca.uhn.hapi.fhir:hapi-fhir-base</include>
 									<include>ca.uhn.hapi.fhir:hapi-fhir-structures-dstu</include>
 									<include>ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2</include>
@@ -96,6 +142,7 @@
 									<include>org.slf4j:slf4j*</include>
 									<include>org.apache.commons:*</include>
 									<include>org.apache.httpcomponents:*</include>
+									<include>org.glassfish:javax.json</include>
 								</includes>
 							</artifactSet>
 							<relocations>
@@ -109,20 +156,20 @@
 								</relocation>
 							</relocations>
 							<filters>
-								<!-- 
 								<filter>
 									<artifact>ca.uhn.hapi.fhir:hapi-fhir-base</artifact>
+									<!--
+									<includes>
+										<include>**/*.class</include>
+										<include>**/*.properties</include>
+										<include>**/*.html</include>
+									</includes>
+									-->
 									<excludes>
 										<exclude>ca/uhn/fhir/model/dstu/valueset/**</exclude>
+										<exclude>**/*.java</exclude>
 									</excludes>
 								</filter>
-								<filter>
-									<artifact>ca.uhn.hapi.fhir:hapi-fhir-base</artifact>
-									<includes>
-										<include>ca/uhn/fhir/model/dstu/valueset/NarrativeStatusEnum.class</include>
-									</includes>
-								</filter>
-								-->
 							</filters>
 						</configuration>
 					</execution>

hapi-fhir-android/src/main/resources/META-INF/services/ca.uhn.fhir.repackage.javax.xml.stream.XMLInputFactory

@@ -0,0 +1 @@
+com.ctc.wstx.stax.WstxInputFactory

hapi-fhir-android/src/main/resources/META-INF/services/ca.uhn.fhir.repackage.javax.xml.stream.XMLOutputFactory

@@ -0,0 +1 @@
+com.ctc.wstx.stax.WstxOutputFactory

hapi-fhir-android/src/test/java/android/util/Log.java

@@ -0,0 +1,25 @@
+package android.util;
+
+public class Log {
+
+	public static final int VERBOSE = 2;
+	public static final int DEBUG = 3;
+	public static final int INFO = 4;
+	public static final int WARN = 5;
+	public static final int ERROR = 6;
+	public static final int ASSERT = 7;
+
+	public static boolean isLoggable(String theName, int thePriority) {
+		return true;
+	}
+
+	public static boolean isLoggable(int thePriority) {
+		return true;
+	}
+	
+	public static int println(int thePriority, String theName, String theMessage) {
+		System.out.println("[" + theName + "] " + theMessage);
+		return 0;
+	}
+	
+}

hapi-fhir-android/src/test/java/ca/uhn/fhir/android/BuiltJarIT.java

@@ -0,0 +1,87 @@
+package ca.uhn.fhir.android;
+
+import static org.junit.Assert.*;
+
+import java.io.File;
+import java.util.Collection;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.filefilter.WildcardFileFilter;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.dstu2.resource.Patient;
+import ca.uhn.fhir.rest.client.IGenericClient;
+import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
+
+public class BuiltJarIT {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BuiltJarIT.class);
+
+	@Test
+	public void testParser() {
+		FhirContext ctx = FhirContext.forDstu2();
+		
+		Patient p = new Patient();
+		p.addIdentifier().setSystem("system");
+		
+		String str = ctx.newXmlParser().encodeResourceToString(p);
+		Patient p2 = ctx.newXmlParser().parseResource(Patient.class, str);
+		
+		assertEquals("system", p2.getIdentifierFirstRep().getSystemElement().getValueAsString());
+	}
+	
+	/**
+	 * A simple client test - We try to connect to a server that doesn't exist, but
+	 * if we at least get the right exception it means we made it up to the HTTP/network stack
+	 * 
+	 * Disabled for now - TODO: add the old version of the apache client (the one that
+	 * android uses) and see if this passes
+	 */
+	public void testClient() {
+		FhirContext ctx = FhirContext.forDstu2();
+		try {
+			IGenericClient client = ctx.newRestfulGenericClient("http://127.0.0.1:44442/SomeBase");
+			client.conformance();
+		} catch (FhirClientConnectionException e) {
+			// this is good
+		}
+	}
+	
+	/**
+	 * Android does not like duplicate entries in the JAR
+	 */
+	@Test
+	public void testJarForDuplicates() throws Exception {
+		Collection<File> files = FileUtils.listFiles(new File("target"), new WildcardFileFilter("*-shaded.jar"), null);
+		if (files.isEmpty()) {
+			throw new Exception("No files matching target/*-shaded.jar");
+		}
+
+		for (File file : files) {
+			ourLog.info("Testing file: {}", file);
+
+			ZipFile zip = new ZipFile(file);
+			try {
+				Set<String> names = new HashSet<String>();
+				for (Enumeration<? extends ZipEntry> iter = zip.entries(); iter.hasMoreElements();) {
+					ZipEntry next = iter.nextElement();
+					String nextName = next.getName();
+					if (!names.add(nextName)) {
+						throw new Exception("File " + file + " contains duplicate contents: " + nextName);
+					}
+				}
+				
+				ourLog.info("File {} contains {} entries", file, names.size());
+				
+			} finally {
+				zip.close();
+			}
+		}
+	}
+
+}

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

@@ -57,18 +57,18 @@ import com.ctc.wstx.stax.WstxOutputFactory;
  * This class contains code adapted from the Apache Axiom project.
  */
 public class XmlUtil {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlUtil.class);
-	private static volatile XMLOutputFactory ourOutputFactory;
-	private static volatile XMLInputFactory ourInputFactory;
-	private static volatile boolean ourHaveLoggedStaxImplementation;
-	private static final Map<String, Integer> VALID_ENTITY_NAMES;
-	private static final ExtendedEntityReplacingXmlResolver XML_RESOLVER = new ExtendedEntityReplacingXmlResolver();
-	private static final Attributes.Name IMPLEMENTATION_TITLE = new Attributes.Name("Implementation-Title");
-	private static final Attributes.Name IMPLEMENTATION_VENDOR = new Attributes.Name("Implementation-Vendor");
-	private static final Attributes.Name IMPLEMENTATION_VERSION = new Attributes.Name("Implementation-Version");
 	private static final Attributes.Name BUNDLE_SYMBOLIC_NAME = new Attributes.Name("Bundle-SymbolicName");
 	private static final Attributes.Name BUNDLE_VENDOR = new Attributes.Name("Bundle-Vendor");
 	private static final Attributes.Name BUNDLE_VERSION = new Attributes.Name("Bundle-Version");
+	private static final Attributes.Name IMPLEMENTATION_TITLE = new Attributes.Name("Implementation-Title");
+	private static final Attributes.Name IMPLEMENTATION_VENDOR = new Attributes.Name("Implementation-Vendor");
+	private static final Attributes.Name IMPLEMENTATION_VERSION = new Attributes.Name("Implementation-Version");
+	private static volatile boolean ourHaveLoggedStaxImplementation;
+	private static volatile XMLInputFactory ourInputFactory;
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlUtil.class);
+	private static volatile XMLOutputFactory ourOutputFactory;
+	private static final Map<String, Integer> VALID_ENTITY_NAMES;
+	private static final ExtendedEntityReplacingXmlResolver XML_RESOLVER = new ExtendedEntityReplacingXmlResolver();
 
 	static {
 		HashMap<String, Integer> validEntityNames = new HashMap<String, Integer>();
@@ -189,6 +189,18 @@ public class XmlUtil {
 		return er;
 	}
 
+	public static XMLStreamWriter createXmlStreamWriter(Writer theWriter) throws FactoryConfigurationError, XMLStreamException {
+		XMLOutputFactory outputFactory = getOrCreateOutputFactory();
+		XMLStreamWriter retVal = outputFactory.createXMLStreamWriter(theWriter);
+		return retVal;
+	}
+
+	public static XMLEventWriter createXmlWriter(Writer theWriter) throws FactoryConfigurationError, XMLStreamException {
+		XMLOutputFactory outputFactory = getOrCreateOutputFactory();
+		XMLEventWriter retVal = outputFactory.createXMLEventWriter(theWriter);
+		return retVal;
+	}
+
 	private static XMLInputFactory getOrCreateInputFactory() throws FactoryConfigurationError {
 		if (ourInputFactory == null) {
 			XMLInputFactory inputFactory = XMLInputFactory.newInstance();
@@ -218,6 +230,56 @@ public class XmlUtil {
 		return ourInputFactory;
 	}
 
+	private static XMLOutputFactory getOrCreateOutputFactory() throws FactoryConfigurationError {
+		if (ourOutputFactory == null) {
+			XMLOutputFactory outputFactory = XMLOutputFactory.newInstance();
+
+			if (!ourHaveLoggedStaxImplementation) {
+				logStaxImplementation(outputFactory.getClass());
+			}
+
+			/*
+			 * Note that these properties are Woodstox specific and they cause a crash in environments where SJSXP is
+			 * being used (e.g. glassfish) so we don't set them there.
+			 */
+			try {
+				Class.forName("com.ctc.wstx.stax.WstxOutputFactory");
+				if (outputFactory instanceof WstxOutputFactory) {
+					outputFactory.setProperty(XMLOutputFactory2.P_TEXT_ESCAPER, new MyEscaper());
+				}
+			} catch (ClassNotFoundException e) {
+				ourLog.debug("WstxOutputFactory (Woodstox) not found on classpath");
+			}
+			ourOutputFactory = outputFactory;
+		}
+		return ourOutputFactory;
+	}
+
+	private static URL getRootUrlForClass(Class<?> cls) {
+		ClassLoader classLoader = cls.getClassLoader();
+		String resource = cls.getName().replace('.', '/') + ".class";
+		if (classLoader == null) {
+			// A null class loader means the bootstrap class loader. In this case we use the
+			// system class loader. This is safe since we can assume that the system class
+			// loader uses parent first as delegation policy.
+			classLoader = ClassLoader.getSystemClassLoader();
+		}
+		URL url = classLoader.getResource(resource);
+		if (url == null) {
+			return null;
+		}
+		String file = url.getFile();
+		if (file.endsWith(resource)) {
+			try {
+				return new URL(url.getProtocol(), url.getHost(), url.getPort(), file.substring(0, file.length() - resource.length()));
+			} catch (MalformedURLException ex) {
+				return null;
+			}
+		} else {
+			return null;
+		}
+	}
+
 	private static void logStaxImplementation(Class<?> theClass) {
 		try {
 			URL rootUrl = getRootUrlForClass(theClass);
@@ -262,70 +324,21 @@ public class XmlUtil {
 		}
 	}
 
-	private static URL getRootUrlForClass(Class<?> cls) {
-		ClassLoader classLoader = cls.getClassLoader();
-		String resource = cls.getName().replace('.', '/') + ".class";
-		if (classLoader == null) {
-			// A null class loader means the bootstrap class loader. In this case we use the
-			// system class loader. This is safe since we can assume that the system class
-			// loader uses parent first as delegation policy.
-			classLoader = ClassLoader.getSystemClassLoader();
-		}
-		URL url = classLoader.getResource(resource);
-		if (url == null) {
-			return null;
-		}
-		String file = url.getFile();
-		if (file.endsWith(resource)) {
-			try {
-				return new URL(url.getProtocol(), url.getHost(), url.getPort(), file.substring(0, file.length() - resource.length()));
-			} catch (MalformedURLException ex) {
-				return null;
-			}
-		} else {
-			return null;
-		}
-	}
-
-	public static XMLStreamWriter createXmlStreamWriter(Writer theWriter) throws FactoryConfigurationError, XMLStreamException {
-		XMLOutputFactory outputFactory = getOrCreateOutputFactory();
-		XMLStreamWriter retVal = outputFactory.createXMLStreamWriter(theWriter);
-		return retVal;
-	}
-
-	public static XMLEventWriter createXmlWriter(Writer theWriter) throws FactoryConfigurationError, XMLStreamException {
-		XMLOutputFactory outputFactory = getOrCreateOutputFactory();
-		XMLEventWriter retVal = outputFactory.createXMLEventWriter(theWriter);
-		return retVal;
-	}
-
 	public static void main(String[] args) {
 		System.out.println(Character.toString((char) 167));
 	}
 
-	private static XMLOutputFactory getOrCreateOutputFactory() throws FactoryConfigurationError {
+	private static final class ExtendedEntityReplacingXmlResolver implements XMLResolver {
-		if (ourOutputFactory == null) {
+		@Override
-			XMLOutputFactory outputFactory = XMLOutputFactory.newInstance();
+		public Object resolveEntity(String thePublicID, String theSystemID, String theBaseURI, String theNamespace) throws XMLStreamException {
-
+			if (thePublicID == null && theSystemID == null) {
-			if (!ourHaveLoggedStaxImplementation) {
+				if (theNamespace != null && VALID_ENTITY_NAMES.containsKey(theNamespace)) {
-				logStaxImplementation(outputFactory.getClass());
+					return new String(Character.toChars(VALID_ENTITY_NAMES.get(theNamespace)));
-			}
-
-			/*
-			 * Note that these properties are Woodstox specific and they cause a crash in environments where SJSXP is
-			 * being used (e.g. glassfish) so we don't set them there.
-			 */
-			try {
-				Class.forName("com.ctc.wstx.stax.WstxOutputFactory");
-				if (outputFactory instanceof WstxOutputFactory) {
-					outputFactory.setProperty(XMLOutputFactory2.P_TEXT_ESCAPER, new MyEscaper());
 				}
-			} catch (ClassNotFoundException e) {
-				ourLog.debug("WstxOutputFactory (Woodstox) not found on classpath");
 			}
-			ourOutputFactory = outputFactory;
+
+			return null;
 		}
-		return ourOutputFactory;
 	}
 
 	public static class MyEscaper implements EscapingWriterFactory {
@@ -379,17 +392,4 @@ public class XmlUtil {
 
 	}
 
-	private static final class ExtendedEntityReplacingXmlResolver implements XMLResolver {
-		@Override
-		public Object resolveEntity(String thePublicID, String theSystemID, String theBaseURI, String theNamespace) throws XMLStreamException {
-			if (thePublicID == null && theSystemID == null) {
-				if (theNamespace != null && VALID_ENTITY_NAMES.containsKey(theNamespace)) {
-					return new String(Character.toChars(VALID_ENTITY_NAMES.get(theNamespace)));
-				}
-			}
-
-			return null;
-		}
-	}
-
 }

hapi-fhir-structures-dstu/pom.xml

@@ -307,9 +307,6 @@
 			<resource>
 				<directory>${basedir}/src/main/resources</directory>
 			</resource>
-			<resource>
-				<directory>${basedir}/target/generated-sources/tinder</directory>
-			</resource>
 			<resource>
 				<directory>${basedir}/target/generated-resources/tinder</directory>
 			</resource>

hapi-fhir-structures-dstu2/pom.xml

@@ -372,9 +372,6 @@
 			<resource>
 				<directory>${basedir}/src/main/resources</directory>
 			</resource>
-			<resource>
-				<directory>${basedir}/target/generated-sources/tinder</directory>
-			</resource>
 			<resource>
 				<directory>${basedir}/target/generated-resources/tinder</directory>
 			</resource>

pom.xml

@@ -172,6 +172,7 @@
 		<junit_version>4.12</junit_version>
 		<logback_version>1.1.2</logback_version>
 		<maven_assembly_plugin_version>2.4.1</maven_assembly_plugin_version>
+		<maven_failsafe_plugin_version>2.18.1</maven_failsafe_plugin_version>
 		<maven_javadoc_plugin_version>2.10.1</maven_javadoc_plugin_version>
 		<maven_jxr_plugin_version>2.5</maven_jxr_plugin_version>
 		<maven_license_plugin_version>1.7</maven_license_plugin_version>
@@ -190,6 +191,8 @@
 		<thymeleaf-version>2.1.4.RELEASE</thymeleaf-version>
 		<ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>
 		<woodstox_version>4.4.0</woodstox_version>
+
+		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 	</properties>
 
 	<build>
@@ -715,7 +718,8 @@
 				<module>restful-server-example-test</module>
 				<module>hapi-fhir-testpage-overlay</module>
 				<module>hapi-fhir-jpaserver-uhnfhirtest</module>
-			<!--	<module>hapi-fhir-dist</module> -->
+				<module>hapi-fhir-android</module>
+				<module>hapi-fhir-dist</module>
 			</modules>
 		</profile>
 	</profiles>