eav table export implemented

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

+package de.sekmi.histream.export;
+
+import java.io.IOException;
+
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathExpression;
+import javax.xml.xpath.XPathExpressionException;
+
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import de.sekmi.histream.export.config.EavTable;
+import de.sekmi.histream.export.config.ExportException;
+
+public class EavTableParser extends TableParser {
+	private XPathExpression factSelector;
+	
+	public EavTableParser(EavTable table, TableWriter writer, XPath xpath) throws ExportException, IOException {
+		super(table, writer, xpath);
+		try {
+			factSelector = xpath.compile(table.getXPath());
+		} catch (XPathExpressionException e) {
+			throw new ExportException("Unable to compile xpath attribute '"+table.getXPath()+"' for table "+table.getId());
+		}
+	}
+	
+	@Override
+	public void processNode(Node visit) throws ExportException, IOException {
+		// select facts with xpath expression on visit element
+		NodeList nl;
+		try {
+			nl = (NodeList)factSelector.evaluate(visit, XPathConstants.NODESET);
+		} catch (XPathExpressionException e) {
+			throw new ExportException("XPath evaluation failed for eav-table[@id='"+getTable().getId()+"']/@xpath", e);
+		}
+		for( int i=0; i< nl.getLength(); i++ ){
+			Node n = nl.item(i);
+			// make sure only fact elements are selected
+			if( n.getNodeType() != Node.ELEMENT_NODE || !n.getLocalName().equals("fact") ){
+				throw new ExportException("xpath for eav table '"+getTable().getId()+" must select only 'fact' elements. instead found "+n.toString());
+			}
+			// write table row for each selected fact
+			super.processNode(n);
+		}
+	}
+
+
+}

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

 package de.sekmi.histream.export;
 
 import java.io.IOException;
+import java.util.function.Consumer;
 
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.stream.XMLStreamException;
@@ -11,6 +12,7 @@ import org.w3c.dom.Element;
 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.EavTable;
 import de.sekmi.histream.export.config.ExportDescriptor;
 import de.sekmi.histream.export.config.ExportException;
 
@@ -26,19 +28,34 @@ import de.sekmi.histream.export.config.ExportException;
  */
 class FragmentExporter extends VisitFragmentParser {
 
-	TableParser patientParser;
-	TableParser visitParser;
+	private TableParser patientParser;
+	private TableParser visitParser;
+	private EavTableParser[] eavParsers;
+
 	private Element currentPatient;
 	private FactClassAnnotator factAnnotator;
 	
+	private void openEavTables(EavTable[] tables, ExportWriter writer, XPath xpath) throws ExportException, IOException{
+		eavParsers = new EavTableParser[tables.length];
+		for( int i=0; i<eavParsers.length; i++ ){
+			eavParsers[i] = tables[i].createParser(writer.openEAVTable(tables[i].getId()), xpath);
+		}
+	}
 	protected FragmentExporter(XPath xpath, ExportDescriptor desc, ExportWriter writer) throws ExportException, XMLStreamException, ParserConfigurationException {
 		super();
 		
 		try {
 			patientParser = desc.getPatientTable().createParser(writer.openPatientTable(), xpath);
 			visitParser = desc.getVisitTable().createParser(writer.openVisitTable(), xpath);
+			// open eav parsers
+			openEavTables(desc.getEAVTables(), writer, xpath);
+			
 		} catch (IOException e) {
+			close( e::addSuppressed );
 			throw new ExportException("Unable to open table for writing", e);
+		} catch( ExportException e ){
+			close( e::addSuppressed );
+			throw e;
 		}
 		// initialise annotator
 		factAnnotator = new FactClassAnnotator();
@@ -68,12 +85,17 @@ class FragmentExporter extends VisitFragmentParser {
 	protected void patientFragment(Element patient) throws ObservationException {
 		currentPatient = patient;
 		try {
-			patientParser.writeRow(patient);
+			patientParser.processNode(patient);
 		} catch (ExportException | IOException e) {
 			throw new ObservationException(e);
 		}
 	}
 
+	private void writeEavFacts(Element visit) throws ExportException, IOException{
+		for( int i=0; i<eavParsers.length; i++ ){
+			eavParsers[i].processNode(visit);
+		}
+	}
 	@Override
 	protected void visitFragment(Element visit) throws ObservationException {
 		// annotate facts with class attribute
@@ -83,7 +105,8 @@ class FragmentExporter extends VisitFragmentParser {
 		// the parent element. E.g. '../@id' to get the patient id
 		currentPatient.appendChild(visit);
 		try {
-			visitParser.writeRow(visit);
+			visitParser.processNode(visit);
+			writeEavFacts(visit);
 		} catch (ExportException | IOException e) {
 			throw new ObservationException(e);
 		} finally {
@@ -91,20 +114,40 @@ class FragmentExporter extends VisitFragmentParser {
 			currentPatient.removeChild(visit);
 		}
 		// TODO check for repeating concepts and write to separate parsers
+		// iterate through facts and 
 	}
 
 	@Override
 	public void close(){
 		super.close();
-		try{
-			patientParser.close();
-		}catch( IOException e ){
-			reportError(new ObservationException(e));
+		close( e -> reportError(new ObservationException(e)) );
+	}
+	private void close(Consumer<IOException> errorAction){
+		if( patientParser != null ){
+			try{
+				patientParser.close();
+			}catch( IOException e ){
+				errorAction.accept(e);
+			}
 		}
-		try{
-			visitParser.close();
-		}catch( IOException e ){
-			reportError(new ObservationException(e));
+		if( visitParser != null ){
+			try{
+				visitParser.close();
+			}catch( IOException e ){
+				errorAction.accept(e);
+			}
+		}
+		if( eavParsers != null ){
+			for( int i=0; i<eavParsers.length; i++ ){
+				if( eavParsers[i] == null ){
+					continue;
+				}
+				try{
+					eavParsers[i].close();
+				}catch( IOException e ){
+					errorAction.accept(e);
+				}
+			}
 		}
 	}
 }

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

@@ -35,6 +35,9 @@ public class TableParser implements AutoCloseable{
 		writeHeaders();
 	}
 
+	protected AbstractTable getTable(){
+		return table;
+	}
 	private void compileXPaths() throws ExportException{
 		Column[] columns = table.getColumns();
 		xpaths = new XPathExpression[columns.length];
@@ -51,9 +54,10 @@ public class TableParser implements AutoCloseable{
 		writer.header(table.getHeaders());
 	}
 	
-	public void writeRow(Node node) throws ExportException, IOException{
+	public void processNode(Node node) throws ExportException, IOException{
 		writer.row(valuesForFragment(node));
 	}
+
 	private String[] valuesForFragment(Node node) throws ExportException{
 		Column[] columns = table.getColumns();
 		String[] values = new String[columns.length];

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

 package de.sekmi.histream.export.config;
 
+import java.io.IOException;
+
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlID;
-import javax.xml.bind.annotation.XmlIDREF;
+import javax.xml.xpath.XPath;
+
+import de.sekmi.histream.export.EavTableParser;
+import de.sekmi.histream.export.TableWriter;
 
 public class EavTable extends AbstractTable{
 
@@ -10,12 +15,20 @@ public class EavTable extends AbstractTable{
 	@XmlAttribute
 	String id;
 	
-	@XmlIDREF
-	@XmlAttribute(name="class")
-	ConceptGroup clazz;
+	@XmlAttribute
+	String xpath;
 
 	@Override
 	public String getId() {
 		return id;
 	}
+	
+	public String getXPath(){
+		return xpath;
+	}
+
+	@Override
+	public EavTableParser createParser(TableWriter writer, XPath xpath) throws ExportException, IOException {
+		return new EavTableParser(this, writer, xpath);
+	}
 }

histream-export/src/test/java/de/sekmi/histream/export/MemoryExportWriter.java

@@ -118,6 +118,13 @@ public class MemoryExportWriter implements ExportWriter{
 		}
 		return t.rows.get(row)[index];
 	}
+	public int rowCount(String table) throws IndexOutOfBoundsException{
+		MemoryTable t = tables.get(table);
+		if( t == null ){
+			throw new IndexOutOfBoundsException("Non-existing table "+table);
+		}
+		return t.rows.size();
+	}
 	@Override
 	public void close(){
 	}

histream-export/src/test/java/de/sekmi/histream/export/TestExport.java

@@ -35,8 +35,12 @@ public class TestExport {
 			export.export(s, m);
 		}
 		// verify class lookup
-		Assert.assertEquals("T:date:year", m.get(MemoryExportWriter.VISIT_TABLE, "byclass", 0));
+		Assert.assertEquals("T:type:str", m.get(MemoryExportWriter.VISIT_TABLE, "byclass", 0));
 		m.dump();
+		// verify eav table
+		Assert.assertEquals(6, m.rowCount("eavtabletest"));
+		Assert.assertEquals("T:date:month", m.get("eavtabletest", "code", 4));
+		
 		// TODO something wrong with namespaces in xpath/dom
 	}
 

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

@@ -52,7 +52,7 @@ public class TestMarshal {
 		ExportDescriptor e;
 		// first example
 		e = JAXB.unmarshal(getClass().getResourceAsStream("/export1.xml"), ExportDescriptor.class);
-		Assert.assertEquals(3, StreamSupport.stream(e.concepts.allConcepts().spliterator(), false).count());
+		Assert.assertEquals(4, 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

@@ -3,7 +3,11 @@
 			xmlns:eav="http://sekmi.de/histream/ns/eav-data">
     <concepts>
         <group class="testclass">
-            <concept wildcard-notation="T:date:yea*"/>
+            <concept wildcard-notation="T:type:st*"/>
+        </group>
+        <group class="testeav">
+        	<!-- will cause problems if wildcards are overlapping -->
+        	<concept wildcard-notation="T:date:*"/>
         </group>
         <concept notation="T:full"/>
         <concept wildcard-notation="CEDIS:*"/>
@@ -24,4 +28,12 @@
 		<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>
+	<eav-table id="eavtabletest" xpath="eav:fact[@class='testeav']">
+		<!-- context for XPath expressions is each fact node -->
+		<column header="pid" xpath="../../@id"/>
+		<column header="visit" xpath="../@id"/>
+		<column header="code" xpath="@concept"/>
+		<column header="start" xpath="@start"/>
+	</eav-table>
+
 </export>