fact class annotator integrated, test case adde

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

@@ -7,6 +7,7 @@ import java.util.Map;
 
 import org.w3c.dom.Element;
 import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
 
 /**
  * Annotates DOM fact objects with a {@code @class} attribute.
@@ -67,6 +68,20 @@ class FactClassAnnotator {
 		}
 	}
 	
+	/**
+	 * Annotates all elements with local name 'fact' contained
+	 * in the provided node list. Other nodes are ignored.
+	 * @param facts node list containing 'fact' elements (among other nodes)
+	 */
+	public void annotateFacts(NodeList facts){
+		for( int i=0; i<facts.getLength(); i++ ){
+			Node next = facts.item(i);
+			if( next.getNodeType() == Node.ELEMENT_NODE && next.getLocalName().equals("fact") ){
+				annotateFact(next);
+			}
+		}
+	}
+
 	public void annotateFactSiblings(Node first){
 		annotateFact(first);
 		Node next = first.getNextSibling();

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

@@ -7,8 +7,11 @@ import javax.xml.stream.XMLStreamException;
 import javax.xml.xpath.XPath;
 
 import org.w3c.dom.Element;
+import org.w3c.dom.NodeList;
 
 import de.sekmi.histream.ObservationException;
+import de.sekmi.histream.export.config.Concept;
+import de.sekmi.histream.export.config.ConceptGroup;
 import de.sekmi.histream.export.config.ExportDescriptor;
 import de.sekmi.histream.export.config.ExportException;
 
@@ -27,6 +30,7 @@ class FragmentExporter extends VisitFragmentParser {
 	TableParser patientParser;
 	TableParser visitParser;
 	private Element currentPatient;
+	private FactClassAnnotator factAnnotator;
 	
 	protected FragmentExporter(XPath xpath, ExportDescriptor desc, ExportWriter writer) throws ExportException, XMLStreamException, ParserConfigurationException {
 		super();
@@ -37,6 +41,28 @@ class FragmentExporter extends VisitFragmentParser {
 		} catch (IOException e) {
 			throw new ExportException("Unable to open table for writing", e);
 		}
+		// initialise annotator
+		factAnnotator = new FactClassAnnotator();
+		for( ConceptGroup group : desc.getConcepts().getGroups() ){
+			String clazz = group.getClazz();
+			for( Concept concept : group.getConcepts() ){
+				String s = concept.getNotation();
+				if( s != null ){
+					factAnnotator.addMapRule(s, clazz);
+					continue;
+				}
+				s = concept.getWildcardNotation();
+				if( s != null ){
+					if( s.indexOf('*') < s.length()-1 ){
+						throw new ExportException("Wildcard notation '"+s+"' must contain exactly one * at the end");
+					}
+					factAnnotator.addWildcardRule(s.substring(0, s.length()-1), clazz);
+					continue;
+				}
+				
+				throw new ExportException("Group concepts must have one of 'notation' or 'wildcard-notation' defined. Concept IRI not supported yet");
+			}
+		}
 	}
 
 	@Override
@@ -51,6 +77,8 @@ class FragmentExporter extends VisitFragmentParser {
 
 	@Override
 	protected void visitFragment(Element visit) throws ObservationException {
+		// annotate facts with class attribute
+		factAnnotator.annotateFacts(visit.getChildNodes());
 		// move visit to patient
 		// this allows XPath expressions to access the patient via
 		// the parent element. E.g. '../@id' to get the patient id

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

@@ -7,6 +7,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlID;
 
+/**
+ * Group containing concepts. Useful for grouping
+ * concepts under a common 'class' name, which can
+ * be used to identify facts later without
+ * the need to refer to their (different) concept
+ * codes.
+ * @author R.W.Majeed
+ *
+ */
 public class ConceptGroup {
 	public ConceptGroup(String clazz){
 		this.clazz = clazz;
@@ -17,8 +26,23 @@ public class ConceptGroup {
 	}
 	
 	@XmlID
-	@XmlAttribute(name="class")
+	@XmlAttribute(name="class", required=true)
 	String clazz;
 	@XmlElement(name="concept")
 	List<Concept> concepts;
+	
+	/**
+	 * Get the class (id) attribute for this group.
+	 * @return group class
+	 */
+	public String getClazz(){
+		return clazz;
+	}
+	/**
+	 * Get the concepts in this group
+	 * @return concepts
+	 */
+	public Iterable<Concept> getConcepts(){
+		return concepts;
+	}
 }
\ No newline at end of file

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

@@ -17,4 +17,11 @@ public class Concepts {
 	Iterable<Concept> allConcepts(){
 		return new IterableIterable<Concept,ConceptGroup>(groups, group -> group.concepts.iterator(), concepts);
 	}
+	
+	public List<ConceptGroup> getGroups(){
+		return groups;
+	}
+	public List<Concept> ungroupedConcepts(){
+		return concepts;
+	}
 }

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

@@ -70,12 +70,24 @@ public class ExportDescriptor {
 	/**
 	 * Get all concepts used for the export. This
 	 * may contain duplicate concepts.
+	 * <p>
+	 * The returned iterator will iterate through all concepts
+	 * contained in groups followed by all ungrouped concepts.
+	 * </p>
 	 * 
 	 * @return all concepts
 	 */
 	public Iterable<Concept> allConcepts(){
 		return concepts.allConcepts();
 	}
+	/**
+	 * Get the {@link Concepts} object which contains concept groups and
+	 * ungrouped concepts.
+	 * @return concepts
+	 */
+	public Concepts getConcepts(){
+		return concepts;
+	}
 
 	public TableExport newExport(){
 		return new TableExport(this);

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

@@ -11,4 +11,7 @@ public class ExportException extends Exception{
 	public ExportException(String message, Throwable cause){
 		super(message, cause);
 	}
+	public ExportException(String message){
+		super(message);
+	}
 }