exchange API example XML documents completed, partial JAXB implementation

pom.xml

@@ -70,6 +70,13 @@
 		
 	</build> 
 	<dependencies>
+		<!-- TODO export project as dynamic dependency 
+		<dependency>
+			<groupId>de.sekmi.histream</groupId>
+			<artifactId>histream-export</artifactId>
+			<version>0.8-SNAPSHOT</version>
+		</dependency>
+		  -->
 		<!-- unit tests -->
 		<dependency>
 			<groupId>junit</groupId>

src/main/java/org/aktin/exchange/NodeStatus.java

 package org.aktin.exchange;
 
+import java.time.Duration;
+import java.time.Instant;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+
 /**
  * Status for a data warehouse node
  * 
  * @author R.W.Majeed
  *
  */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlRootElement(name="node-status")
 public class NodeStatus {
 	
 	public NodeStatus(){
-		apiVersion = getClass().getPackage().getImplementationVersion();
 	}
 	/**
 	 * Version of the dwh-api component
 	 */
-	String apiVersion;
+	Instant timestamp;
+	Duration uptime;
+	@XmlElement(name="module")
+	List<SoftwareModule> modules;
 }

src/main/java/org/aktin/exchange/Query.java

@@ -6,11 +6,11 @@ import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAnyElement;
 import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlElementWrapper;
 import javax.xml.bind.annotation.XmlRootElement;
 
 import org.w3c.dom.Element;
 
+
 /**
  * Query which can be executed in an i2b2
  * data warehouse by the AKTIN remote query 
@@ -53,10 +53,7 @@ public class Query {
 	@XmlElement(required=true)
 	public QuerySchedule schedule;
 	
-	@XmlElementWrapper(name="concepts",required=true)
-	@XmlElement(name="concept",required=true)
-	public List<AbstractConcept> concepts;
-
 	@XmlAnyElement
-	public Element definition;
+	public List<Element> extensions;
+
 }

src/main/java/org/aktin/exchange/RawConcept.java

-package org.aktin.exchange;
-
-import javax.xml.bind.annotation.XmlType;
-
-@XmlType(name="raw")
-public class RawConcept extends AbstractConcept{
-	
-}

src/main/java/org/aktin/exchange/AbstractConcept.java → src/main/java/org/aktin/exchange/SoftwareModule.java

 package org.aktin.exchange;
 
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlSeeAlso;
 
-@XmlSeeAlso({RawConcept.class})
-public abstract class AbstractConcept {
-
-	/**
-	 * Unique identifier of the concept.
-	 */
+@XmlAccessorType(XmlAccessType.FIELD)
+public class SoftwareModule {
 	@XmlAttribute
-	public String id;
+	String id;
+	String version;
+	String url;
 }

src/test/java/org/aktin/exchange/TestUnmarshallDocuments.java

@@ -3,6 +3,7 @@ package org.aktin.exchange;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URL;
+import java.time.Duration;
 
 import javax.xml.bind.JAXB;
 import javax.xml.parsers.ParserConfigurationException;
@@ -19,6 +20,7 @@ import javax.xml.validation.Validator;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
+import org.w3c.dom.Element;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 import org.xml.sax.XMLReader;
@@ -79,14 +81,9 @@ public class TestUnmarshallDocuments {
 		//System.out.println("Duration:"+se.duration);
 		//System.out.println("Reference:"+se.reference);
 		
-		
-		// print XML output
-		//se.duration = Period.ofMonths(1);
-		//se.reference = Instant.now();
-		//JAXB.marshal(query, System.out);
-		System.out.println("Query definition ns: "+query.definition.getNamespaceURI());
-		System.out.println("Query definition elem: "+query.definition.getLocalName());
-		
+		for( Element el : query.extensions ){
+			System.out.println("Extension name="+el.getLocalName()+", ns="+el.getNamespaceURI());
+		}		
 	}
 	@Test
 	public void validateQueryRequest() throws IOException, SAXException, TransformerException{
@@ -101,4 +98,12 @@ public class TestUnmarshallDocuments {
 		Assert.assertNotNull(r.deadline);
 	}
 
+	@Test
+	public void unmarshall_node_status(){
+		NodeStatus n = JAXB.unmarshal(getResource("/node-status.xml"), NodeStatus.class);
+		Assert.assertNotNull(n.timestamp);
+		Assert.assertNotNull(n.uptime);
+		
+	}
+
 }

src/test/resources/broker-status.xml

+<broker-status>
+	<timestamp></timestamp>
+	<uptime></uptime>
+	<!-- latest software for nodes -->
+	<node-software>
+		<module id="dwh">
+			<version></version>
+			<url></url>
+		</module>
+		<module id="aktin.art-decor.runtime">
+			<version></version>
+			<url></url>
+		</module>
+	</node-software>
+</broker-status>
\ No newline at end of file

src/test/resources/node-status.xml

-<node-status>
+<node-status xmlns="http://aktin.org/ns/exchange">
 	<!-- when the status was collected -->
-	<timestamp>now</timestamp>
+	<timestamp>2016-07-08T00:00:00Z</timestamp>
 	<!-- duration the (application)server is running -->
-	<uptime></uptime>
+	<uptime>PT15S</uptime>
 	<!-- timestamp when the latest data/CDA was imported -->
 	<latest-import></latest-import>
 	<!-- version number of the running EAR, all other versions 
 	can be deduced from the release POM -->
 	<!-- get this info via new InitialContext().lookup("java:app/AppName") -->
-	<software>dwh-ear-0.2-SNAPSHOT</software>
+	<module id="dwh">
+		<version>dwh-ear-0.2-SNAPSHOT</version>
+	</module>
+	<module id="aktin.art-decor.runtime">
+		<version></version>
+	</module>
 </node-status>
\ No newline at end of file

src/test/resources/query.xml

-<query xmlns="http://aktin.org/ns/exchange"
-	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xmlns:dwh="http://aktin.org/ns/dwh"
-	xmlns:psm="http://www.i2b2.org/xsd/cell/crc/psm/1.1/">
+<query xmlns="http://aktin.org/ns/exchange" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xmlns:dwh="http://aktin.org/ns/dwh" xmlns:psm="http://www.i2b2.org/xsd/cell/crc/psm/1.1/">
 	<id>123</id>
 	<description>Lala</description>
 	<principal>
@@ -9,21 +7,38 @@
 		<organisation>AKTIN</organisation>
 		<email>it-support@aktin.org</email>
 		<phone>+49 (441) 798 - 2772</phone>
-		<!-- optional cryptographic signature at a later release
-		<signature></signature>
-		-->
+		<!-- optional cryptographic signature at a later release <signature></signature> -->
 	</principal>
 	<schedule xsi:type="singleExecution">
 		<duration>-P1M</duration>
 		<reference>2016-04-01T00:00:00Z</reference>
 	</schedule>
+	<!-- export descriptor -->
+	<export xmlns="http://sekmi.de/ns/histream/export-v1" xmlns:eav="http://sekmi.de/histream/ns/eav-data">
 		<concepts>
-		<concept id="birthdate" xsi:type="raw"/>
+			<group class="diag">
+				<concept wildcard-notation="ICD10:*" />
+			</group>
+			<concept notation="T:full" />
+			<concept wildcard-notation="CEDIS:*" />
 		</concepts>
+		<patient-table>
+			<column header="pid" xpath="@id" />
+			<column header="dob" xpath="eav:birthdate" />
+			<column header="sex" xpath="eav:gender" />
+			<column header="modified" xpath="eav:source/@timestamp" />
+		</patient-table>
+		<visit-table>
+			<column header="vid" xpath="@id" />
+			<column header="start" xpath="eav:start" />
+			<column header="f_start" xpath="eav:fact[@concept='T:full']/@start" />
+			<column header="f_end" xpath="eav:fact[@concept='T:full']/@end" />
+			<column header="f_loc" xpath="eav:fact[@concept='T:full']/@location" />
+			<column header="f_val" xpath="eav:fact[@concept='T:full']/eav:value" />
+		</visit-table>
+	</export>
 	<!-- also possible: xsi:type="psm:query_definition" -->
-	<!-- also possible: xsi:type="dwh:eclectic_query", 
-	see http://methods.schattauer.de/en/contents/archivestandard/issue/2168/manuscript/21349/show.html
-		-->
+	<!-- also possible: xsi:type="dwh:eclectic_query", see http://methods.schattauer.de/en/contents/archivestandard/issue/2168/manuscript/21349/show.html -->
 	<dwh:sql xsi:type="dwh:sqlt">
 		SELECT a, b;
 	</dwh:sql>