simplified exceptions, visit table parsing successful

histream-import/src/main/java/de/sekmi/histream/etl/ColumnMap.java

@@ -2,6 +2,7 @@ package de.sekmi.histream.etl;
 
 import java.util.HashMap;
 import java.util.Map;
+import java.util.Objects;
 
 import de.sekmi.histream.etl.config.Column;
 
@@ -24,19 +25,26 @@ public class ColumnMap{
 		this.map = new HashMap<>();
 	}
 	
-	public boolean registerColumn(Column column){
+	/**
+	 * Register a column and lookup it's index in the header list.
+	 * @param column
+	 * @throws ParseException if the column cannot be found in the headers
+	 * @throws NullPointerException if column is null
+	 */
+	public void registerColumn(Column column)throws ParseException{
+		Objects.requireNonNull(column);
 		if( map.containsKey(column.getName()) ){
 			// column name already registered
-			return true;
+			return;
 		}
 		// find name and map to index
 		for( int i=0; i<headers.length; i++ ){
 			if( headers[i].equals(column.getName()) ){
 				map.put(column.getName(), Integer.valueOf(i) );
-				return true;
+				return;
 			}
 		}
-		return false;
+		throw new ParseException("Column name '"+column.getName()+"' not found in header");
 	}
 	public Integer indexOf(Column column){
 		return map.get(column.getName());

histream-import/src/main/java/de/sekmi/histream/etl/FileRowSupplier.java

@@ -27,7 +27,7 @@ public class FileRowSupplier extends RowSupplier {
 	}
 	
 	@Override
-	public String[] getHeaders() throws IOException {
+	public String[] getHeaders() {
 		return headers;
 	}
 

histream-import/src/main/java/de/sekmi/histream/etl/ParseException.java

@@ -9,4 +9,8 @@ public class ParseException extends Exception {
 	public ParseException(String message){
 		super(message);
 	}
+	
+	public ParseException(String message, Throwable cause){
+		super(message, cause);
+	}
 }

histream-import/src/main/java/de/sekmi/histream/etl/RecordSupplier.java

@@ -10,7 +10,7 @@ public class RecordSupplier<R> implements Supplier<R>, AutoCloseable{
 	Table<R> table;
 	ColumnMap map;
 	
-	public RecordSupplier(RowSupplier rows, Table<R> table) throws IOException{
+	public RecordSupplier(RowSupplier rows, Table<R> table)throws ParseException{
 		this.rows = rows;
 		this.table = table;
 		this.map = table.getColumnMap(rows.getHeaders());

histream-import/src/main/java/de/sekmi/histream/etl/RowSupplier.java

@@ -8,7 +8,7 @@ public abstract class RowSupplier implements Supplier<Object[]>, AutoCloseable{
 	public RowSupplier(){
 		
 	}
-	public abstract String[] getHeaders()throws IOException;
+	public abstract String[] getHeaders();
 	
 	@Override
 	public abstract Object[] get();

histream-import/src/main/java/de/sekmi/histream/etl/VisitRow.java

 package de.sekmi.histream.etl;
 
-public class VisitRow {
+import de.sekmi.histream.impl.VisitImpl;
+
+public class VisitRow extends VisitImpl{
+
 
 }

histream-import/src/main/java/de/sekmi/histream/etl/config/PatientTable.java

@@ -36,26 +36,16 @@ public class PatientTable extends Table<PatientRow> implements WideInterface{
 	}
 
 	@Override
-	public ColumnMap getColumnMap(String[] headers) {
+	public ColumnMap getColumnMap(String[] headers) throws ParseException {
 		ColumnMap map = new ColumnMap(headers);
-		if( !map.registerColumn(idat.patientId) ){
-			throw new IllegalArgumentException("patientId column name '"+idat.patientId.name+"' not found in patient table headers");
-		}
-		if( idat.firstname != null && !map.registerColumn(idat.firstname) ){
-			throw new IllegalArgumentException("firstname column not found in patient header");
-		}
-		if( idat.surname != null && !map.registerColumn(idat.surname) ){
-			throw new IllegalArgumentException("surname column not found in patient header");
-		}
-		if( idat.birthdate != null && !map.registerColumn(idat.birthdate) ){
-			throw new IllegalArgumentException("birthdate column not found in patient header");
-		}
-		if( idat.deathdate != null && !map.registerColumn(idat.deathdate) ){
-			throw new IllegalArgumentException("deathdate column not found in patient header");
-		}
-		if( idat.gender != null && !map.registerColumn(idat.gender) ){
-			throw new IllegalArgumentException("gender column not found in patient header");
-		}
+		
+		map.registerColumn(idat.patientId);
+		map.registerColumn(idat.firstname);
+		map.registerColumn(idat.surname);
+		map.registerColumn(idat.birthdate);
+		map.registerColumn(idat.deathdate);
+		map.registerColumn(idat.gender);
+		
 		return map;
 	}
 	

histream-import/src/main/java/de/sekmi/histream/etl/config/Table.java

@@ -19,28 +19,40 @@ public abstract class Table<T> {
 	 * Retrieve a column map for this table
 	 * @param headers row headers
 	 * @return column map
+	 * @throws ParseException if the map cannot be constructed
 	 */
-	public abstract ColumnMap getColumnMap(String[] headers);
+	public abstract ColumnMap getColumnMap(String[] headers) throws ParseException;
 	
 	/**
 	 * Register all columns for the given concept to the column map
 	 * @param map column map
 	 * @param c concept to register
+	 * @throws ParseException if headers could not be found/mapped
 	 */
-	protected void mapRegisterConcept(ColumnMap map, Concept c){
+	protected void mapRegisterConcept(ColumnMap map, Concept c) throws ParseException{
 		map.registerColumn(c.start);
-		map.registerColumn(c.end);
-		map.registerColumn(c.value);
-		map.registerColumn(c.unit);
-		for( Concept.Modifier m : c.modifiers ){
-			map.registerColumn(m.value);
-			map.registerColumn(m.unit);
+		if( c.end != null ){
+			map.registerColumn(c.end);
+		}
+		if( c.value != null ){
+			map.registerColumn(c.value);
+		}
+		if( c.unit != null ){
+			map.registerColumn(c.unit);
+		}
+		if( c.modifiers != null ){
+			for( Concept.Modifier m : c.modifiers ){
+				map.registerColumn(m.value);
+				if( m.unit != null ){
+					map.registerColumn(m.unit);
+				}
+			}
 		}
 	}
 	
 	public abstract T fillRecord(ColumnMap map, Object[] row) throws ParseException;
 	
-	public RecordSupplier<T> open() throws IOException{
+	public RecordSupplier<T> open() throws IOException, ParseException{
 		return new RecordSupplier<>(source.rows(), this);
 	}
 

histream-import/src/main/java/de/sekmi/histream/etl/config/VisitTable.java

@@ -6,6 +6,7 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlElementWrapper;
 import javax.xml.bind.annotation.XmlType;
 
+import de.sekmi.histream.DateTimeAccuracy;
 import de.sekmi.histream.etl.ColumnMap;
 import de.sekmi.histream.etl.ParseException;
 import de.sekmi.histream.etl.VisitRow;
@@ -29,8 +30,9 @@ public class VisitTable extends Table<VisitRow> implements WideInterface{
 		Column[] ignore;
 	}
 	@Override
-	public ColumnMap getColumnMap(String[] headers) {
+	public ColumnMap getColumnMap(String[] headers) throws ParseException {
 		ColumnMap map = new ColumnMap(headers);
+		
 		map.registerColumn(idat.patientId);
 		map.registerColumn(idat.visitId);
 		map.registerColumn(idat.start);
@@ -38,11 +40,18 @@ public class VisitTable extends Table<VisitRow> implements WideInterface{
 		for( Concept c : concepts ){
 			mapRegisterConcept(map, c);
 		}
+		
 		return map;
 	}
+
 	@Override
 	public VisitRow fillRecord(ColumnMap map, Object[] row) throws ParseException {
-		// TODO Auto-generated method stub
-		return null;
-	}
-}
+		VisitRow visit = new VisitRow();
+		visit.setId(idat.visitId.valueOf(map, row).toString());
+		visit.setPatientId(idat.patientId.valueOf(map, row).toString());
+		visit.setStartTime((DateTimeAccuracy)idat.start.valueOf(map, row));
+		visit.setEndTime((DateTimeAccuracy)idat.end.valueOf(map, row));
+		// TODO other 
+		// TODO concepts
+		return visit;
+	}}

histream-import/src/main/java/de/sekmi/histream/etl/config/WideTable.java

@@ -17,7 +17,7 @@ public class WideTable extends Table<WideRow> {
 	Concept[] concepts;
 
 	@Override
-	public ColumnMap getColumnMap(String[] headers) {
+	public ColumnMap getColumnMap(String[] headers) throws ParseException {
 		ColumnMap map = new ColumnMap(headers);
 		map.registerColumn(idat.patientId);
 		map.registerColumn(idat.visitId);

histream-import/src/test/java/de/sekmi/histream/etl/config/TestReadTables.java

@@ -2,19 +2,23 @@ package de.sekmi.histream.etl.config;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.time.temporal.ChronoField;
 
 import javax.xml.bind.JAXB;
 
 import org.junit.Test;
 
+import de.sekmi.histream.etl.ParseException;
 import de.sekmi.histream.etl.PatientRow;
 import de.sekmi.histream.etl.RecordSupplier;
+import de.sekmi.histream.etl.VisitRow;
+
 import org.junit.Assert;
 
 public class TestReadTables {
 
 	@Test
-	public void testReadPatients() throws IOException{
+	public void testReadPatients() throws IOException, ParseException{
 		DataSource ds;
 		try( InputStream in = getClass().getResourceAsStream("/test-1-datasource.xml") ){
 			ds = JAXB.unmarshal(in, DataSource.class);
@@ -22,7 +26,20 @@ public class TestReadTables {
 		try( RecordSupplier<PatientRow> s = ds.patientTable.open() ){
 			PatientRow r = s.get();
 			Assert.assertEquals("1", r.getId());
-			System.out.println(r.getBirthDate());
+			Assert.assertEquals(2003, r.getBirthDate().get(ChronoField.YEAR));
+			
+		}
+	}
+	@Test
+	public void testReadVisits() throws IOException, ParseException{
+		DataSource ds;
+		try( InputStream in = getClass().getResourceAsStream("/test-1-datasource.xml") ){
+			ds = JAXB.unmarshal(in, DataSource.class);
+		}
+		try( RecordSupplier<VisitRow> s = ds.visitTable.open() ){
+			VisitRow r = s.get();
+			Assert.assertEquals("1", r.getId());
+			Assert.assertEquals(2013, r.getStartTime().get(ChronoField.YEAR));
 			
 		}
 	}

histream-import/src/test/resources/test-1-datasource.xml

@@ -40,15 +40,15 @@
 	<!-- optional -->
 	<visit-table>
         <source xsi:type="fileSource">
-            <url>file:test-1-visits.txt</url>
+            <url>file:src/test/resources/test-1-visits.txt</url>
             <type>text/csv</type>
 			<separator>\t</separator>
         </source>
 		<idat>
 			<patient-id>patid</patient-id>
 			<visit-id>fallnr</visit-id>
-			<start format="ISO" na="@" truncate-to="year">start</start>
-			<end>end</end>
+			<start format="d.M.u[ H[:m[:s]]]" na="@" truncate-to="year">start</start>
+			<end format="d.M.u[ H[:m[:s]]]">end</end>
 		</idat>
 		<mdat>
 			<!-- in/out code -->