JAXB marshalling/unmarshalling of export descriptor

histream-export/src/main/java/de/sekmi/histream/export/FactClassAnnotator.java

@@ -66,4 +66,15 @@ public class FactClassAnnotator {
 			((Element)fact).setAttribute("class", clazz);
 		}
 	}
+	
+	public void annotateFactSiblings(Node first){
+		annotateFact(first);
+		Node next = first.getNextSibling();
+		while( next != null ){
+			if( next.getNodeType() == Node.ELEMENT_NODE && next.getLocalName().equals("fact") ){
+				annotateFact(next);
+			}
+			next = next.getNextSibling();
+		}
+	}
 }

histream-export/src/main/java/de/sekmi/histream/export/config/AbstractTable.java

@@ -2,13 +2,23 @@ package de.sekmi.histream.export.config;
 
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlTransient;
 
 @XmlTransient
 @XmlAccessorType(XmlAccessType.NONE)
 public abstract class AbstractTable {
 
-	public abstract String[] getHeaders();
-	public abstract AbstractColumn getColumn(int index);
-	public abstract AbstractColumn getColumnByHeader(String header);
+	@XmlElement(name="column")
+	Column[] columns;
+	public String[] getHeaders(){
+		String[] headers = new String[columns.length];
+		for( int i=0; i<columns.length; i++ ){
+			headers[i] = columns[i].header;
+		}
+		return headers;
+	}
+	public Column getColumn(int index){
+		return columns[index];
+	}
 }

histream-export/src/main/java/de/sekmi/histream/export/config/AbstractColumn.java → histream-export/src/main/java/de/sekmi/histream/export/config/Column.java

@@ -3,13 +3,9 @@ package de.sekmi.histream.export.config;
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlSeeAlso;
-import javax.xml.bind.annotation.XmlTransient;
 
-@XmlTransient
 @XmlAccessorType(XmlAccessType.NONE)
-@XmlSeeAlso({SequenceColumn.class, IdColumn.class})
-public abstract class AbstractColumn {
+public class Column {
 
 	/**
 	 * Column header name
@@ -28,25 +24,16 @@ public abstract class AbstractColumn {
 	String na;
 	
 	/**
-	 * Prepare the column for the next row. This
-	 * method is called once for every row. 
-	 * <p> The default implementation does nothing.</p>
+	 * XPath expression to select the column's value
 	 */
-	protected void prepareRow(){
-		
-	}
+	@XmlAttribute(required=true)
+	String xpath;
 	
-	/**
-	 * Initializes the column. This method will be called
-	 * only once and before any other method.
-	 */
-	protected void initialize(){
-		
+	public Column(String header, String xpath){
+		this.header = header;
+		this.xpath = xpath;
+	}
+	// constructor for JAXB
+	protected Column(){
 	}
-	
-	/**
-	 * Get the column value for the current row.
-	 * @return String value or {@code null} for NA.
-	 */
-	public abstract Object getValueString();
 }

histream-export/src/main/java/de/sekmi/histream/export/config/Concept.java

+package de.sekmi.histream.export.config;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+
+@XmlAccessorType(XmlAccessType.NONE)
+public class Concept {
+	@XmlAttribute
+	String iri;
+	@XmlAttribute
+	String notation;
+	@XmlAttribute(name="wildcard-notation")
+	String wildcardNotation;
+	
+	public static Concept newWildcard(String wildcardNotation){
+		Concept c = new Concept();
+		c.wildcardNotation = wildcardNotation;
+		return c;
+	}
+	public static Concept newIRI(String iri){
+		Concept c = new Concept();
+		c.iri = iri;
+		return c;	
+	}
+	public static Concept newNotation(String notation){
+		Concept c = new Concept();
+		c.notation = notation;
+		return c;	
+	}
+}

histream-export/src/main/java/de/sekmi/histream/export/config/ConceptGroup.java

+package de.sekmi.histream.export.config;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlID;
+
+public class ConceptGroup {
+	public ConceptGroup(String clazz){
+		this.clazz = clazz;
+		this.concepts = new ArrayList<>();
+	}
+	// constructor for JAXB
+	protected ConceptGroup(){
+	}
+	
+	@XmlID
+	@XmlAttribute(name="class")
+	String clazz;
+	@XmlElement(name="concept")
+	List<Concept> concepts;
+}
\ No newline at end of file

histream-export/src/main/java/de/sekmi/histream/export/config/Concepts.java

+package de.sekmi.histream.export.config;
+
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+
+@XmlAccessorType(XmlAccessType.NONE)
+public class Concepts {
+
+	@XmlElement(name="group")
+	List<ConceptGroup> groups;
+	
+	@XmlElement(name="concept")
+	List<Concept> concepts;
+	
+	Iterable<Concept> allConcepts(){
+		return new IterableIterable<Concept,ConceptGroup>(groups, group -> group.concepts.iterator(), concepts);
+	}
+}

histream-export/src/main/java/de/sekmi/histream/export/config/EavTable.java

+package de.sekmi.histream.export.config;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlID;
+import javax.xml.bind.annotation.XmlIDREF;
+
+public class EavTable extends AbstractTable{
+
+	@XmlID
+	@XmlAttribute
+	String id;
+	
+	@XmlIDREF
+	@XmlAttribute(name="class")
+	ConceptGroup clazz;
+}

histream-export/src/main/java/de/sekmi/histream/export/config/ExportDescriptor.java

@@ -7,11 +7,14 @@ import javax.xml.bind.annotation.XmlRootElement;
 public class ExportDescriptor {
 
 	@XmlElement
+	Concepts concepts;
+	
+	@XmlElement(name="patient-table")
 	PatientTable patient;
 	
-	@XmlElement
+	@XmlElement(name="visit-table")
 	VisitTable visit;
 	
-	@XmlElement(name="table")
-	FactTable[] tables;
+	@XmlElement(name="eav-table")
+	EavTable[] tables;
 }

histream-export/src/main/java/de/sekmi/histream/export/config/FactTable.java

-package de.sekmi.histream.export.config;
-
-public class FactTable {
-
-}

histream-export/src/main/java/de/sekmi/histream/export/config/IdColumn.java

-package de.sekmi.histream.export.config;
-
-/**
- * Column which outputs intrinsic ID values. This
- * column can only be used in {@link PatientTable} and
- * {@link VisitTable}.
- * 
- * @author R.W.Majeed
- *
- */
-public class IdColumn extends AbstractColumn{
-
-	@Override
-	public Object getValueString() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-}

histream-export/src/main/java/de/sekmi/histream/export/config/IterableIterable.java

+package de.sekmi.histream.export.config;
+
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+import java.util.function.Function;
+
+class IterableIterable<T,U> implements Iterable<T>{
+
+	Function<U, Iterator<T>> extractor;
+	Iterable<T> direct;
+	Iterable<U> indirect;
+	
+	public IterableIterable(Iterable<U> indirect, Function<U,Iterator<T>> extractor, Iterable<T> direct){
+		this.indirect = indirect;
+		this.direct = direct;
+		this.extractor = extractor;
+	}
+	@Override
+	public Iterator<T> iterator() {
+		return new Iterator<T>() {
+			Iterator<U> outer = indirect.iterator();
+			Iterator<T> current = null;
+			boolean last = false;
+
+			@Override
+			public boolean hasNext() {
+				while( current == null || !current.hasNext() ){
+					if( outer.hasNext() ){
+						current = extractor.apply(outer.next());
+					}else if( !last ){
+						current = direct.iterator();
+						last = true;
+					}else{
+						return false;
+					}					
+				}
+				return true;
+			}
+
+			@Override
+			public T next() {
+				if( hasNext() ){
+					return current.next();
+				}else{
+					throw new NoSuchElementException();
+				}
+			}
+		};
+	}
+}
\ No newline at end of file

histream-export/src/main/java/de/sekmi/histream/export/config/PatientTable.java

 package de.sekmi.histream.export.config;
 
-import javax.xml.bind.annotation.XmlElement;
 
-public class PatientTable {
+public class PatientTable extends AbstractTable{
 
-	@XmlElement(name="column")
-	AbstractColumn[] columns;
 }

histream-export/src/main/java/de/sekmi/histream/export/config/SequenceColumn.java

-package de.sekmi.histream.export.config;
-
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-
-@XmlRootElement(name="sequence")
-public class SequenceColumn extends AbstractColumn{
-	@XmlElement(required=true)
-	String id;
-	
-	@XmlElement
-	Long start;
-	
-	long value;
-	
-	protected SequenceColumn(){
-	}
-	public SequenceColumn(String id){
-		this.id = id;
-	}
-	
-	@Override
-	protected void initialize(){
-		if( start != null ){
-			value = start;
-		}else{
-			value = 1;
-		}
-	}
-	@Override
-	public Object getValueString() {
-		return value;
-		// TODO increment value somewhere else
-	}
-}

histream-export/src/main/java/de/sekmi/histream/export/config/VisitTable.java

 package de.sekmi.histream.export.config;
 
-public class VisitTable {
+public class VisitTable extends AbstractTable{
 
 }

histream-export/src/main/java/de/sekmi/histream/export/config/package-info.java

@@ -3,6 +3,13 @@
  * 
  */
 @javax.xml.bind.annotation.XmlSchema(
-		namespace="http://sekmi.de/ns/histream/export"
-)
+		namespace="http://sekmi.de/ns/histream/export-v1",
+		elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED, 
+		xmlns = { 
+				@javax.xml.bind.annotation.XmlNs(
+						namespaceURI = "http://sekmi.de/ns/histream/export-v1", 
+						prefix = "") 
+				}
+		)
+
 package de.sekmi.histream.export.config;
\ No newline at end of file

histream-export/src/test/java/de/sekmi/histream/export/config/TestMarshal.java

 package de.sekmi.histream.export.config;
 
+import java.util.ArrayList;
+import java.util.stream.StreamSupport;
+
+import javax.xml.bind.JAXB;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Marshaller;
 
+import org.junit.Assert;
 import org.junit.Test;
 
 public class TestMarshal {
 
-	@Test
-	public void verifyMarshal() throws JAXBException{
+	private ExportDescriptor createDescriptor(){
 		ExportDescriptor e = new ExportDescriptor();
+		e.concepts = new Concepts();
+		e.concepts.concepts = new ArrayList<>();
+		e.concepts.concepts.add(Concept.newNotation("ABC"));
+		e.concepts.concepts.add(Concept.newWildcard("CEDIS:*"));
+
+		e.concepts.groups = new ArrayList<>();
+		ConceptGroup d = new ConceptGroup("diag");
+		d.concepts.add(Concept.newWildcard("ICD10:*"));
+		e.concepts.groups.add(d);
 		e.patient = new PatientTable();
-		e.patient.columns = new AbstractColumn[2];
-		e.patient.columns[0] = new IdColumn();
-		e.patient.columns[0].header = "pid";
-		e.patient.columns[1] = new SequenceColumn("seq1");
-		e.patient.columns[1].header = "seq";
-		
+		e.patient.columns = new Column[2];
+		e.patient.columns[0] = new Column("pid","@id");
+		e.patient.columns[1] = new Column("dob","birthdate");
+
+		return e;
+	}
+	@Test
+	public void verifyMarshal() throws JAXBException{
+		ExportDescriptor e = createDescriptor();
 		JAXBContext j = JAXBContext.newInstance(ExportDescriptor.class);
 		Marshaller m = j.createMarshaller();
 		m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
 		m.marshal(e, System.out);
-		
+	}
+	
+	@Test
+	public void verifyIterableIterable(){
+		ExportDescriptor e = createDescriptor();
+		long count = StreamSupport.stream(e.concepts.allConcepts().spliterator(), false).count();
+		Assert.assertEquals(3, count);
+	}
+	
+	@Test
+	public void verifyUnmarshall(){
+		ExportDescriptor e;
+		// first example
+		e = JAXB.unmarshal(getClass().getResourceAsStream("/export1.xml"), ExportDescriptor.class);
+		Assert.assertEquals(3, StreamSupport.stream(e.concepts.allConcepts().spliterator(), false).count());
+		// second example
+		e = JAXB.unmarshal(getClass().getResourceAsStream("/export2.xml"), ExportDescriptor.class);
+		Assert.assertEquals(5, StreamSupport.stream(e.concepts.allConcepts().spliterator(), false).count());
 	}
 }

histream-export/src/test/resources/export1.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<export xmlns="http://sekmi.de/ns/histream/export">
-	<patient>
-		<column header="pid" type="id"/>
-		<column header="seq" type="sequence">
-			<id>seq1</id>
-		</column>
-	</patient>
-	<visit>
-		<column header="pid" type="patient-ref"/>
-		<column header="visit" type="id"/>
-		<!-- concepts for the visit table must occur only once
-		per visit and may not repeat -->
-		<column header="start" type="attribute">
-			<property>start</property>
-		</column>
-		<!-- What is better? -->
-		<!-- (a) First column, then concepts with value -->
-		<column header="diagnostik_labort_ts" na="NULL" type="fact">
-			<concept code="LOINC:26436-6"/>
-			<concept code="LOINC:26436-6:NEG"/>
-			<value type="script">
-					<eval>fact.conceptId.substring(6)</eval>
-			</value>
-		</column>
-		<!-- (b) first concepts then columns with value -->
-		<group>
-			<concept code="LOINC:26436-6"/>
-			<concept code="LOINC:26436-6:NEG"/>
-			<column header="lab_ts" type="attribute">
-				<attribute>start</attribute>
-			</column>
-			<!-- We want this: 
-					6:NEG -> not tested
-					6/mod=OPB -> tested non pathological
-					6/mod=PB -> tested pathological 
-			-->
-			<column header="lab_ergebnis" type="attribute">
-				<modifier>PB</modifier>
-				<attribute>start</attribute>
-			</column>
-		</group>
-	</visit>
-	<table id="diagnosen">
-		<!-- makes more sense for fact tables to specify
-			the list of concepts first. -->
-		<concept wildcard="ICD10:*"/>
-		<concept code="ICD9:123"/>
-		<column header="pid" type="patient-ref"/>
-		<column header="visit" type="visit-ref"/>
-		<column header="start" type="attribute">
-			<attribute>start</attribute>
-		</column>
-		<column header="primary" type="attribute" na="nein">
-			<modifier>fuehrend</modifier>
-			<!-- if a modifier element is provided, the property
-			 will use the context of that modifier -->
-			<constant-value>ja</constant-value>
-		</column>
-		<column header="text" type="attribute">
-			<modifier>originalText</modifier>
-			<property>value</property>
-		</column>
-		<!-- reference sequence from patient -->
-		<column header="seq1" type="sequence">
-			<sequence ref="seq1"/>
-		</column>
-	</table>
-</export>
\ No newline at end of file
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<ns2:export xmlns:ns2="http://sekmi.de/ns/histream/export-v1">
+    <concepts>
+        <group class="diag">
+            <concept wildcard-notation="ICD10:*"/>
+        </group>
+        <concept notation="ABC"/>
+        <concept wildcard-notation="CEDIS:*"/>
+    </concepts>
+    <patient-table>
+        <column header="pid" xpath="@id"/>
+        <column header="dob" xpath="birthdate"/>
+    </patient-table>
+</ns2:export>

histream-export/src/test/resources/export2.xml

@@ -18,14 +18,17 @@ to construct table data.
 -->
 	<concepts>
 		<group class="d_lab">
-			<concept id="LOINC:26436-6" />
-			<concept id="LOINC:26436-6:NEG" />
+			<concept notation="LOINC:26436-6" />
+			<concept notation="LOINC:26436-6:NEG" />
 		</group>
 		<group class="diag">
-			<concept wildcard="ICD10:*" />
+			<concept wildcard-notation="ICD10:*" />
+			<concept iri="http://data.dzl.de/ns/ont/xxx"/>
 		</group>
+		<concept notation="XYZ" />
 	</concepts>
-	
+
+
 	<patient-table>
 		<column header="pid" xpath="@id"/>
 		<column header="birthdate" xpath="birthdate"/>
@@ -53,12 +56,12 @@ to construct table data.
 			-->
 	</visit-table>
 	<!-- export separate table for repeating elements -->
-	<repeating-table id="diag" class="diag">
+	<eav-table id="diag" class="diag">
 		<!-- context for XPath expressions is each fact node -->
 		<column header="pid" xpath="patient-ref"/>
 		<column header="visit" xpath="visit-ref"/>
 		<column header="start" type="@start"/>
 		<column header="code" type="@concept"/>
 		<column header="primary" xpath="modifier[@code='fuehrend']/@code"/>
-	</repeating-table>
+	</eav-table>
 </export>
\ No newline at end of file