improved abstract service and unit tests

i2b2-server/pom.xml

@@ -160,5 +160,42 @@
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 		</dependency>
+<!-- https://mvnrepository.com/artifact/org.jboss.resteasy/resteasy-undertow -->
+<dependency>
+    <groupId>org.jboss.resteasy</groupId>
+    <artifactId>resteasy-undertow</artifactId>
+    <version>3.0.18.Final</version>
+    <scope>test</scope>
+</dependency>
+<!-- https://mvnrepository.com/artifact/org.jboss.resteasy/resteasy-cdi -->
+<dependency>
+    <groupId>org.jboss.resteasy</groupId>
+    <artifactId>resteasy-cdi</artifactId>
+    <version>3.0.18.Final</version>
+    <scope>test</scope>
+</dependency>
+<!-- https://mvnrepository.com/artifact/javax.enterprise/cdi-api -->
+<dependency>
+    <groupId>javax.enterprise</groupId>
+    <artifactId>cdi-api</artifactId>
+    <version>1.2</version>
+    <scope>test</scope>
+</dependency>
+<!-- https://mvnrepository.com/artifact/org.jboss.weld.servlet/weld-servlet -->
+<dependency>
+    <groupId>org.jboss.weld.servlet</groupId>
+    <artifactId>weld-servlet</artifactId>
+    <version>2.3.5.Final</version>
+    <scope>test</scope>
+</dependency>
+<!-- https://mvnrepository.com/artifact/io.undertow/undertow-servlet -->
+<dependency>
+    <groupId>io.undertow</groupId>
+    <artifactId>undertow-servlet</artifactId>
+    <version>1.3.23.Final</version>
+    <scope>test</scope>
+</dependency>
+
+
 	</dependencies>
 </project>
\ No newline at end of file

i2b2-server/src/main/java/de/sekmi/histream/i2b2/api/pm/SessionManager.java

@@ -23,6 +23,15 @@ public interface SessionManager {
 	public Session accessSession(String sessionId);
 	
 	public Session createSession(String userId);
+	public void deleteSession(String sessionId);
+	
+
+	/**
+	 * Get the timeout duration in milliseconds. Sessions
+	 * last accessed longer than this will be discarded.
+	 * @return timeout in milliseconds
+	 */
+	public long getTimeoutMillis();
 	/**
 	 * Iterate over all sessions. The remove() operation should
 	 * be supported by the iterators.

i2b2-server/src/main/java/de/sekmi/histream/i2b2/api/pm/User.java

@@ -9,4 +9,5 @@ public interface User extends Principal{
 	Iterable<Project> getProjects();
 	// check password
 	boolean hasPassword(char[] password);
+	void setPassword(char[] newPassword);
 }

i2b2-server/src/main/java/de/sekmi/histream/i2b2/services/AbstractService.java

@@ -9,7 +9,6 @@ import java.util.logging.Logger;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.stream.XMLOutputFactory;
 import javax.xml.xpath.XPathConstants;
 import javax.xml.xpath.XPathExpression;
 import javax.xml.xpath.XPathExpressionException;
@@ -26,15 +25,26 @@ public abstract class AbstractService {
 	public static final String HIVE_NS="http://www.i2b2.org/xsd/hive/msg/1.1/";
 	
 	/**
-	 * Service name (for communication to client)
+	 * Service name (for communication to client).
+	 * <p>
+	 *  The default implementation returns {@link Class#getSimpleName()}.
+	 * </p>
 	 * @return service name, e.g. Workplace Cell
 	 */
-	public abstract String getName();
+	public String getName(){
+		return getClass().getSimpleName();
+	}
 	/**
 	 * Service version (for communication to client)
+	 * <p>
+	 * The default implementation returns {@link Package#getImplementationVersion()}
+	 * for the implementing class.
+	 * </p>
 	 * @return service version, e.g. 1.700
 	 */
-	public abstract String getVersion();
+	public String getVersion(){
+		return getClass().getPackage().getImplementationVersion();
+	}
 	
 	DocumentBuilder newDocumentBuilder() throws ParserConfigurationException{
 		DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
@@ -54,6 +64,9 @@ public abstract class AbstractService {
 		}
 		return dom;
 	}
+	HiveRequest parseRequest(Document request){
+		return HiveRequest.parse(request.getDocumentElement());
+	}
 	private void stripWhitespace(Element node) throws XPathExpressionException{
 		XPathFactory xf = XPathFactory.newInstance();
 		// XPath to find empty text nodes.
@@ -67,24 +80,32 @@ public abstract class AbstractService {
 		}
 	}
 	
-	private void appendTextNode(Element el, String name, String value){
-		Element sub = (Element)el.appendChild(el.getOwnerDocument().createElement(name));
-		if( value != null ){
-			sub.appendChild(el.getOwnerDocument().createTextNode(value));
-		}
-	}
+//	private void appendTextNode(Element el, String name, String value){
+//		Element sub = (Element)el.appendChild(el.getOwnerDocument().createElement(name));
+//		if( value != null ){
+//			sub.appendChild(el.getOwnerDocument().createTextNode(value));
+//		}
+//	}
 	Document createResponse(DocumentBuilder builder, Element request_header){
 		Document dom = builder.newDocument();
 		Element re = (Element)dom.appendChild(dom.createElementNS(HIVE_NS, "response"));
-		appendTextNode(re, "i2b2_version_compatible", "1.1");
-		appendTextNode(re, "hl7_version_compatible", "2.4");
-		// find sending application from request
-		NodeList nl = request_header.getElementsByTagName("sending_application");
-		Element el = (Element)re.appendChild(dom.createElement("receiving_application"));
-		appendTextNode(el, "application_name", nl.item(0).getFirstChild().getTextContent());
-		appendTextNode(el, "application_version", nl.item(0).getLastChild().getTextContent());
-
-		// TODO read response_header.xml template, fill and parse
+		NodeList nl;
+		try {
+			Document rh = builder.parse(getClass().getResourceAsStream("/templates/response_header.xml"));
+			stripWhitespace(rh.getDocumentElement());
+			// sending application
+			nl = rh.getElementsByTagName("sending_application").item(0).getChildNodes();
+			nl.item(0).setTextContent(getName());
+			nl.item(1).setTextContent(getVersion());
+			// timestamp
+			rh.getElementsByTagName("datetime_of_message").item(0).setTextContent(Instant.now().toString());
+			// security
+			nl = rh.getElementsByTagName("security").item(0).getChildNodes();
+			// TODO message_id, project, session
+			re.appendChild(dom.adoptNode(rh.getDocumentElement()));
+		} catch (SAXException | IOException | XPathExpressionException e) {
+			log.log(Level.WARNING, "unable to process response header template", e);
+		}
 		
 		return dom;
 	}

i2b2-server/src/main/java/de/sekmi/histream/i2b2/services/HiveRequest.java

+package de.sekmi.histream.i2b2.services;
+
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+public class HiveRequest {
+	// message header
+	String clientName;
+	String clientVersion;
+	String secDomain;
+	String secUser;
+	String secPassword;
+	boolean secToken;
+	String messageId;
+	String projectId;
+	// request header
+	// message body
+	Element messageBody;
+
+	public static HiveRequest parse(Element request){
+		HiveRequest me = new HiveRequest();
+		Node n = request.getFirstChild();
+		if( n.getNodeType() != Node.ELEMENT_NODE || !n.getNodeName().equals("message_header") ){
+			throw new RuntimeException("request should have message_header as first node instead of "+n.getNodeName());
+		}
+		Element mh = (Element)n;
+		NodeList nl = mh.getElementsByTagName("sending_application").item(0).getChildNodes();
+		me.clientName = nl.item(0).getTextContent();
+		me.clientVersion = nl.item(1).getTextContent();
+		nl = mh.getElementsByTagName("security").item(0).getChildNodes();
+		me.secDomain = nl.item(0).getTextContent();
+		me.secUser = nl.item(1).getTextContent();
+		me.secPassword = nl.item(2).getTextContent();
+		me.secToken = ((Element)nl.item(2)).getAttribute("is_token").equals("true");
+		me.messageId = mh.getElementsByTagName("message_control_id").item(0).getFirstChild().getTextContent();
+		n = request.getLastChild();
+		if( n.getNodeType() == Node.ELEMENT_NODE && n.getNodeName().equals("message_body") ){
+			me.messageBody = (Element)n;
+		}
+		return me;
+	}
+}

i2b2-server/src/main/java/de/sekmi/histream/i2b2/services/PMService.java

@@ -20,7 +20,7 @@ import freemarker.template.TemplateException;
 
 @Singleton
 @Path("/i2b2/services/PMService")
-public class PMService {
+public class PMService extends AbstractService{
 	private static final Logger log = Logger.getLogger(PMService.class.getName());
 
 	@Inject
@@ -56,4 +56,9 @@ public class PMService {
 		
 		return Response.ok(w.toString()).build();
 	}
+	@Override
+	public String getVersion() {
+		// TODO Auto-generated method stub
+		return null;
+	}
 }

i2b2-server/src/main/resources/templates/response_header.xml

-    <message_header>
+    <message_header xmlns="http://www.i2b2.org/xsd/hive/msg/1.1/">
         <i2b2_version_compatible>1.1</i2b2_version_compatible>
         <hl7_version_compatible>2.4</hl7_version_compatible>
         <sending_application>
-            <application_name>Workplace Cell</application_name>
-            <application_version>1.700</application_version>
+            <application_name>${service_name}</application_name>
+            <application_version>${service_version}</application_version>
         </sending_application>
         <sending_facility>
             <facility_name>i2b2 Hive</facility_name>
         </sending_facility>
         <receiving_application>
-            <application_name>i2b2 Ontology</application_name>
-            <application_version>1.6</application_version>
+            <application_name>${client_name}</application_name>
+            <application_version>${client_version}</application_version>
         </receiving_application>
         <receiving_facility>
             <facility_name>i2b2 Hive</facility_name>

i2b2-server/src/test/java/de/sekmi/histream/i2b2/services/TestAbstractService.java

@@ -4,7 +4,6 @@ import java.io.IOException;
 
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.TransformerException;
 
 import org.junit.Test;
 import org.w3c.dom.Document;
@@ -31,6 +30,16 @@ public class TestAbstractService extends AbstractService{
 		Document resp = createResponse(b, el);
 		XMLUtils.printDOM(resp, System.out);
 	}
+	
+	@Test
+	public void parse_PM_request() throws Exception{
+		DocumentBuilder b = newDocumentBuilder();
+		Document dom = parseRequest(b, getClass().getResourceAsStream("/pm_request_test.xml"));
+		HiveRequest hr = parseRequest(dom);
+		assertEquals("i2b2 Project Management", hr.clientName);
+		assertEquals("1.6", hr.clientVersion);
+		assertEquals("8b5M3z5lb2nU1g6Zq2QSm", hr.messageId);
+	}
 
 	@Override
 	public String getName() {

i2b2-server/src/test/java/de/sekmi/histream/i2b2/services/TestPMService.java

 package de.sekmi.histream.i2b2.services;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import org.jboss.resteasy.cdi.CdiInjectorFactory;
+import org.jboss.resteasy.plugins.server.undertow.UndertowJaxrsServer;
+import org.jboss.resteasy.spi.ResteasyDeployment;
+import org.jboss.resteasy.test.TestPortProvider;
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
 import org.junit.Test;
 
-public class TestPMService {
+import io.undertow.servlet.Servlets;
+import io.undertow.servlet.api.DeploymentInfo;
+
+public class TestPMService{
+
+	private UndertowJaxrsServer server;
 
+	@Before
+	public void startServer() throws Exception {
+		server = new UndertowJaxrsServer().start();
+		ResteasyDeployment rd = new ResteasyDeployment();
+//		rd.getActualResourceClasses().add(WorkplaceService.class);
+		rd.getActualResourceClasses().add(PMService.class);
+		rd.setInjectorFactoryClass(CdiInjectorFactory.class.getName());
+		DeploymentInfo di = server.undertowDeployment(rd);
+		di.setClassLoader(getClass().getClassLoader());
+		di.setDeploymentName("TestPM");
+		di.setContextPath("/");
+		di.addListeners(Servlets.listener(org.jboss.weld.environment.servlet.Listener.class));
+		server.deploy(di);
+	}
+	
+	public URL createURL(String name) throws MalformedURLException{
+		return TestPortProvider.createURL("/i2b2/services/PMService"+name);
+	}
+	
 	@Test
-	public void dummy(){
+	public void testPost() throws MalformedURLException, IOException{
+		URL url = createURL("/getServices");
+		System.out.println(url);
+		HttpURLConnection c = (HttpURLConnection)url.openConnection();
+		c.setRequestMethod("POST");
+		c.connect();
+		Assert.assertEquals(200, c.getResponseCode());
+		InputStream in = c.getInputStream();
+		in.close();
+	}
+	
+	@Test
+	public void invalidLoginCredentialsShouldFail(){
 		
 	}
+
+	@After
+	public void stopServer() {
+		server.stop();
+	}
+
+
 }

i2b2-server/src/test/java/de/sekmi/histream/i2b2/services/TestTemplates.java

+package de.sekmi.histream.i2b2.services;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+
+import org.junit.Test;
+
+import freemarker.core.ParseException;
+import freemarker.template.MalformedTemplateNameException;
+import freemarker.template.Template;
+import freemarker.template.TemplateException;
+import freemarker.template.TemplateHashModel;
+import freemarker.template.TemplateModel;
+import freemarker.template.TemplateModelException;
+import freemarker.template.TemplateNotFoundException;
+import freemarker.template.TemplateScalarModel;
+
+public class TestTemplates {
+
+	@Test
+	public void test() throws TemplateNotFoundException, MalformedTemplateNameException, ParseException, IOException, TemplateException{
+		Settings s = new Settings();
+		Template t = s.getFreemarkerConfiguration().getTemplate("templates/response_header.xml");
+		t.process(new TemplateHashModel() {
+			@Override
+			public boolean isEmpty() throws TemplateModelException {
+				return false;
+			}
+			
+			@Override
+			public TemplateModel get(String key) throws TemplateModelException {
+				return new TemplateScalarModel() {
+					@Override
+					public String getAsString() throws TemplateModelException {
+						return "dummy";
+					}
+				};
+			}
+		}, new PrintWriter(System.out));
+	}
+}