Doc updates

hapi-fhir-base/pom.xml

@@ -264,8 +264,10 @@
 		var pres = elements[i].getElementsByTagName("pre");
 		for (var j = 0; j < pres.length; j++) {
 			var pre = pres[j];
-			if (pre.innerHTML.match(/\\\*/)) {
+			if (pre.innerHTML.match(/\/\*/)) {
 				pre.className = 'brush: java';
+			} else if (pre.innerHTML.match(/^\#/)) {
+				pre.className = 'brush: bash';
 			} else if (pre.innerHTML.match(/\&lt\;\//)) {
 				pre.className = 'brush: xml';
 			} else {

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative/BaseThymeleafNarrativeGenerator.java

@@ -51,9 +51,14 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 	private HashMap<String, String> myProfileToNarrativeName;
 	private HashMap<Class<?>, String> myClassToNarrativeName;
 	private HashMap<String, String> myNameToNarrativeTemplate;
-
+	private boolean myApplyDefaultDatatypeTemplates=true;
 	private volatile boolean myInitialized;
 
+	@Override
+	public NarrativeDt generateNarrative(IResource theResource) {
+		return generateNarrative(null, theResource);
+	}
+
 	@Override
 	public NarrativeDt generateNarrative(String theProfile, IResource theResource) {
 		if (!myInitialized) {
@@ -115,6 +120,9 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 		}
 
 		try {
+			if (myApplyDefaultDatatypeTemplates) {
+				loadProperties(DefaultThymeleafNarrativeGenerator.NARRATIVES_PROPERTIES);
+			}
 			loadProperties(propFileName);
 		} catch (IOException e) {
 			throw new ConfigurationException("Can not load property file " + propFileName, e);
@@ -139,9 +147,12 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 	protected abstract String getPropertyFile();
 
 	/**
-	 * If set to <code>true</code> (which is the default), most whitespace will be trimmed from the generated narrative before it is returned.
+	 * If set to <code>true</code> (which is the default), most whitespace will
+	 * be trimmed from the generated narrative before it is returned.
 	 * <p>
-	 * Note that in order to preserve formatting, not all whitespace is trimmed. Repeated whitespace characters (e.g. "\n       \n       ") will be trimmed to a single space.
+	 * Note that in order to preserve formatting, not all whitespace is trimmed.
+	 * Repeated whitespace characters (e.g. "\n       \n       ") will be
+	 * trimmed to a single space.
 	 * </p>
 	 */
 	public boolean isCleanWhitespace() {
@@ -149,24 +160,30 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 	}
 
 	/**
-	 * If set to <code>true</code>, which is the default, if any failure occurs during narrative generation the generator will suppress any generated exceptions, and simply return a default narrative
+	 * If set to <code>true</code>, which is the default, if any failure occurs
-	 * indicating that no narrative is available.
+	 * during narrative generation the generator will suppress any generated
+	 * exceptions, and simply return a default narrative indicating that no
+	 * narrative is available.
 	 */
 	public boolean isIgnoreFailures() {
 		return myIgnoreFailures;
 	}
 
 	/**
-	 * If set to true, will return an empty narrative block for any profiles where no template is available
+	 * If set to true, will return an empty narrative block for any profiles
+	 * where no template is available
 	 */
 	public boolean isIgnoreMissingTemplates() {
 		return myIgnoreMissingTemplates;
 	}
 
 	/**
-	 * If set to <code>true</code> (which is the default), most whitespace will be trimmed from the generated narrative before it is returned.
+	 * If set to <code>true</code> (which is the default), most whitespace will
+	 * be trimmed from the generated narrative before it is returned.
 	 * <p>
-	 * Note that in order to preserve formatting, not all whitespace is trimmed. Repeated whitespace characters (e.g. "\n       \n       ") will be trimmed to a single space.
+	 * Note that in order to preserve formatting, not all whitespace is trimmed.
+	 * Repeated whitespace characters (e.g. "\n       \n       ") will be
+	 * trimmed to a single space.
 	 * </p>
 	 */
 	public void setCleanWhitespace(boolean theCleanWhitespace) {
@@ -174,15 +191,18 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 	}
 
 	/**
-	 * If set to <code>true</code>, which is the default, if any failure occurs during narrative generation the generator will suppress any generated exceptions, and simply return a default narrative
+	 * If set to <code>true</code>, which is the default, if any failure occurs
-	 * indicating that no narrative is available.
+	 * during narrative generation the generator will suppress any generated
+	 * exceptions, and simply return a default narrative indicating that no
+	 * narrative is available.
 	 */
 	public void setIgnoreFailures(boolean theIgnoreFailures) {
 		myIgnoreFailures = theIgnoreFailures;
 	}
 
 	/**
-	 * If set to true, will return an empty narrative block for any profiles where no template is available
+	 * If set to true, will return an empty narrative block for any profiles
+	 * where no template is available
 	 */
 	public void setIgnoreMissingTemplates(boolean theIgnoreMissingTemplates) {
 		myIgnoreMissingTemplates = theIgnoreMissingTemplates;
@@ -261,11 +281,11 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 		} else if (name.startsWith("file:")) {
 			File file = new File(name.substring("file:".length()));
 			if (file.exists() == false) {
-				throw new IOException("Can not read file: " + file.getAbsolutePath());
+				throw new IOException("File not found: " + file.getAbsolutePath());
 			}
 			return new FileInputStream(file);
 		} else {
-			throw new IOException("Invalid resource name: '" + name + "'");
+			throw new IOException("Invalid resource name: '" + name + "' (must start with classpath: or file: )");
 		}
 	}
 
@@ -337,11 +357,14 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 			final IStandardExpression expression = expressionParser.parseExpression(configuration, theArguments, attributeValue);
 			final Object value = expression.execute(configuration, theArguments);
 
+
+			theElement.removeAttribute(theAttributeName);
+			theElement.clearChildren();
+
 			Context context = new Context();
 			context.setVariable("resource", value);
 			
 			String name = myClassToNarrativeName.get(value.getClass());
-
 			if (name == null) {
 				if (myIgnoreMissingTemplates) {
 					ourLog.debug("No narrative template available for type: {}", value.getClass());
@@ -354,9 +377,6 @@ public abstract class BaseThymeleafNarrativeGenerator implements INarrativeGener
 			String result = myProfileTemplateEngine.process(name, context);
 			Document dom = DOMUtils.getXhtmlDOMFor(new StringReader(result));
 
-			theElement.removeAttribute(theAttributeName);
-			theElement.clearChildren();
-
 			Element firstChild = (Element) dom.getFirstChild();
 			for (Node next : firstChild.getChildren()) {
 				theElement.addChild(next);

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative/DefaultThymeleafNarrativeGenerator.java

@@ -1,16 +1,13 @@
 package ca.uhn.fhir.narrative;
 
-import java.io.IOException;
 
 public class DefaultThymeleafNarrativeGenerator extends BaseThymeleafNarrativeGenerator implements INarrativeGenerator {
 
-	public DefaultThymeleafNarrativeGenerator() throws IOException {
+	static final String NARRATIVES_PROPERTIES = "classpath:ca/uhn/fhir/narrative/narratives.properties";
-		super();
-	}
 
 	@Override
 	protected String getPropertyFile() {
-		return "classpath:ca/uhn/fhir/narrative/narratives.properties";
+		return NARRATIVES_PROPERTIES;
 	}
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/narrative/INarrativeGenerator.java

@@ -6,6 +6,8 @@ import ca.uhn.fhir.parser.DataFormatException;
 
 public interface INarrativeGenerator {
 
-	public NarrativeDt generateNarrative(String theProfile, IResource theResource) throws DataFormatException;
+	NarrativeDt generateNarrative(String theProfile, IResource theResource) throws DataFormatException;
+
+	NarrativeDt generateNarrative(IResource theResource);
 
 }

hapi-fhir-base/src/site/example/java/example/NarrativeGenerator.java

@@ -0,0 +1,25 @@
+package example;
+
+import java.io.IOException;
+
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.narrative.CustomThymeleafNarrativeGenerator;
+
+public class NarrativeGenerator {
+
+	@Test
+	public void testGenerator() throws IOException {
+
+//START SNIPPET: gen
+String propFile = "classpath:/com/foo/customnarrative.properties";
+CustomThymeleafNarrativeGenerator gen = new CustomThymeleafNarrativeGenerator(propFile);
+
+FhirContext ctx = new FhirContext();
+ctx.setNarrativeGenerator(gen);
+//END SNIPPET: gen
+
+	
+	}
+}

hapi-fhir-base/src/site/site.xml

@@ -56,6 +56,7 @@
 			<script type="text/javascript" src="syntaxhighlighter/shCore.js"></script>
 			<script type="text/javascript" src="syntaxhighlighter/shBrushJScript.js"></script>
 			<script type="text/javascript" src="syntaxhighlighter/shBrushJava.js"></script>
+			<script type="text/javascript" src="syntaxhighlighter/shBrushBash.js"></script>
 			<script type="text/javascript" src="syntaxhighlighter/shBrushXml.js"></script>
 			<link href="syntaxhighlighter/shCore.css" rel="stylesheet" type="text/css" />
 			<link href="syntaxhighlighter/shThemeDefault.css" rel="stylesheet" type="text/css" />

hapi-fhir-base/src/site/xdoc/doc_download.xml.vm

@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document xmlns="http://maven.apache.org/XDOC/2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/XDOC/2.0 http://maven.apache.org/xsd/xdoc-2.0.xsd">
+
+	<properties>
+		<title>Download - HAPI FHIR</title>
+		<author email="jamesagnew@users.sourceforge.net">James Agnew</author>
+	</properties>
+
+	<body>
+
+		<section name="Downloading HAPI FHIR">
+
+			<p>
+				The easiest way to get started with HAPI-FHIR is to either download the
+				source code from our
+				<a href="https://sourceforge.net/p/hl7api/fhircode/ci/master/tree/">Git Repository</a>
+				, or to use Maven:
+			</p>
+			<source><![CDATA[<dependency>
+   <groupId>ca.uhn.hapi.fhir</groupId>
+   <artifactId>hapi-fhir-base</artifactId>
+   <version>${project.version}</version>
+</dependency>]]></source>
+			
+			<subsection name="Non-Maven Users">
+				
+				<p>
+					Non-maven users can grab the files from the
+					<a href="https://sourceforge.net/projects/hl7api/files/hapi-fhir/">Sourceforge File Release System</a>.
+				</p>
+			
+			</subsection>
+
+		</section>
+
+	</body>
+
+</document>

hapi-fhir-base/src/site/xdoc/doc_intro.xml

@@ -9,7 +9,7 @@
 	<body>
 
 		<!-- The body of the document contains a number of sections -->
-		<section name="Developing using FHIR-HAPI">
+		<section name="Developing using HAPI FHIR">
 			
 			<macro name="toc">
 			</macro>
@@ -45,23 +45,9 @@
 		<section name="Getting Started">
 			
 			<p>
-				The easiest way to get started with HAPI-FHIR is to either download the
+				To get started with HAPI FHIR, first download a copy and add it
-				source code from our
+				to your project. See the <a href="doc_download.html">Download Page</a>
-				<a href="https://sourceforge.net/p/hl7api/fhircode/ci/master/tree/">Git Repository</a>
+				for instructions.
-				, or to use Maven:
-			</p>
-			<source><![CDATA[<dependency>
-   <groupId>ca.uhn.hapi.fhir</groupId>
-   <artifactId>hapi-fhir-base</artifactId>
-   <version>1.0-SNAPSHOT</version>
-</dependency>]]></source>
-			
-			<p>
-				If you are not using Maven, you can download the latest version
-				of the snapshot JAR (and optionally the Javadoc and Sources JAR) from the Maven
-				repo here: <a href="http://oss.sonatype.org/content/repositories/snapshots/ca/uhn/hapi/fhir/hapi-fhir-base/1.0-SNAPSHOT/">download</a>.
-				Once a formal release has been created, it will be uploaded through the Sourceforge
-				file release system (as the HAPI v2 libraries are).
 			</p>			
 			
 			<subsection name="Introcuding the FHIR Context">

hapi-fhir-base/src/site/xdoc/doc_narrative.xml

@@ -111,6 +111,63 @@
 			
 		</section>
 		
+		<section name="Creating your own Templates">
+		
+			<p>
+				To use your own templates for narrative generation,
+				simply create one or more templates, using the Thymeleaf
+				HTML based syntax. 
+			</p>
+		
+			<macro name="snippet">
+				<param name="file" value="src/test/resources/narrative/Practitioner.html" />
+			</macro>
+
+			<p>
+				Then create a properties file which describes your
+				templates. In this properties file, each resource to 
+				be defined has a pair or properties. 
+			</p>
+						
+			<p>
+				The first (name.class) defines the class name of the resource to define a 
+				template for. The second (name.narrative) defines the path/classpath to the
+				template file. The format of this path is <code>file:/path/foo.html</code> or  <code>classpath:/com/classpath/foo.html</code>
+			</p>
+			
+			<source><![CDATA[# Two property lines in the file per template
+practitioner.class=ca.uhn.fhir.model.dstu.resource.Practitioner
+practitioner.narrative=file:src/test/resources/narrative/Practitioner.html
+
+observation.class=ca.uhn.fhir.model.dstu.resource.Observation
+observation.narrative=file:src/test/resources/narrative/Observation.html
+
+# etc...]]></source>
+
+			<p>
+				You may also override/define behaviour for datatypes. These datatype narrative
+				definitions will be used as content within <code>th:narrative</code> blocks
+				in resource templates. See the example resource template above for an example.
+			</p>
+			  
+			<source><![CDATA[# datatypes use the same format as resources
+humanname.class=ca.uhn.fhir.model.dstu.composite.HumanNameDt
+humanname.narrative=classpath:ca/uhn/fhir/narrative/HumanNameDt.html]]></source>
+		
+			<p>
+				Finally, use the 
+				<a href="./apidocs/ca/uhn/fhir/narrative/CustomThymeleafNarrativeGenerator.html">CustomThymeleafNarrativeGenerator</a> 
+				and provide it
+				to the FhirContext.
+			</p>
+
+			<macro name="snippet">
+				<param name="id" value="gen" />
+				<param name="file" value="src/site/example/java/example/NarrativeGenerator.java" />
+			</macro>
+		
+		</section>
+		
 	</body>
 
 </document>

hapi-fhir-base/src/test/java/ca/uhn/fhir/narrative/CustomThymeleafNarrativeGeneratorTest.java

@@ -1,18 +1,36 @@
 package ca.uhn.fhir.narrative;
 
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
+
 import java.io.IOException;
 
 import org.junit.Test;
 
+import ca.uhn.fhir.model.dstu.composite.NarrativeDt;
+import ca.uhn.fhir.model.dstu.resource.Practitioner;
+
 public class CustomThymeleafNarrativeGeneratorTest {
 
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CustomThymeleafNarrativeGeneratorTest.class);
+
 	@Test
 	public void testGenerator() throws IOException {
 
-		CustomThymeleafNarrativeGenerator gen = new CustomThymeleafNarrativeGenerator("src/test/resources/narrative/customnarrative.properties");
+		CustomThymeleafNarrativeGenerator gen = new CustomThymeleafNarrativeGenerator("file:src/test/resources/narrative/customnarrative.properties");
 
+		Practitioner p = new Practitioner();
+		p.addIdentifier("sys", "val1");
+		p.addIdentifier("sys", "val2");
+		p.getAddress().addLine("line1").addLine("line2");
+		p.getName().addFamily("fam1").addGiven("given");
 
+		NarrativeDt narrative = gen.generateNarrative(p);
+
+		String actual = narrative.getDiv().getValueAsString();
+		ourLog.info(actual);
+
+		assertThat(actual, containsString("<h1>Name</h1><div> given <b>FAM1 </b></div><h1>Address</h1><div><span>line1 </span><br/><span>line2 </span><br/></div></div>"));
 		
 	}
-	
 }

hapi-fhir-base/src/test/java/ca/uhn/fhir/narrative/DefaultThymeleafNarrativeGeneratorTest.java

@@ -27,7 +27,7 @@ public class DefaultThymeleafNarrativeGeneratorTest {
 	private DefaultThymeleafNarrativeGenerator gen;
 
 	@Before
-	public void before() throws IOException {
+	public void before() {
 		gen = new DefaultThymeleafNarrativeGenerator();
 		gen.setIgnoreFailures(false);
 		gen.setIgnoreMissingTemplates(false);

hapi-fhir-base/src/test/resources/narrative/Practitioner.html

@@ -10,12 +10,10 @@
 	HAPI also defines a custom tag, th:narrative="value", which is
 	used to render a datatype.
 	 -->
-	<div th:narrative="${resource.addressFirstRep}"></div>
+	<h1>Name</h1>
+	<div th:narrative="${resource.name}"></div>
+	<h1>Address</h1>
+	<div th:narrative="${resource.address}"></div>
 
-	<!-- 
-	HAPI also defines a custom tag, th:narrative="value", which is
-	used to render a datatype.
-	 -->
-	<div th:narrative="${resource.nameFirstRep}"></div>
 
 </div>

hapi-fhir-base/src/test/resources/narrative/customnarrative.properties

@@ -9,7 +9,7 @@
 # Format is file:/path/foo.html  or  classpath:/com/classpath/foo.html
 #
 practitioner.class=ca.uhn.fhir.model.dstu.resource.Practitioner
-practitioner.narrative=file:src/test/resource/narrative/Practitioner.html
+practitioner.narrative=file:src/test/resources/narrative/Practitioner.html
 
 # You may also override/define behaviour for datatypes  
 humanname.class=ca.uhn.fhir.model.dstu.composite.HumanNameDt