base type for Column

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

@@ -31,7 +31,7 @@ public class ColumnMap{
 	 * @throws ParseException if the column cannot be found in the headers
 	 * @throws NullPointerException if column is null
 	 */
-	public void registerColumn(Column column)throws ParseException{
+	public void registerColumn(Column<?> column)throws ParseException{
 		Objects.requireNonNull(column);
 		column.validate(); // TODO: maybe call after unmarshal of column
 		
@@ -54,7 +54,7 @@ public class ColumnMap{
 		}
 		throw new ParseException("Column name '"+column.getName()+"' not found in header");
 	}
-	public Integer indexOf(Column column){
+	public Integer indexOf(Column<?> column){
 		return map.get(column.getName());
 	}
 }
\ No newline at end of file

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

 package de.sekmi.histream.etl.config;
 
-import java.text.DecimalFormat;
 import java.util.Objects;
 
 import javax.xml.bind.annotation.XmlAttribute;
@@ -20,7 +19,7 @@ import de.sekmi.histream.etl.ParseException;
  */
 @XmlTransient
 @XmlSeeAlso({StringColumn.class})
-public abstract class Column {
+public abstract class Column<T> {
 	protected Column(){
 	}
 	public Column(String name){
@@ -75,6 +74,8 @@ public abstract class Column {
 	
 	public String getName(){return name;}
 	
+	public abstract T valueOf(Object input) throws ParseException;
+	
 	/**
 	 * Convert a string input value to the output data type. The resulting type depends
 	 * on the type attribute and can be one of Long, BigDecimal, String, DateTime
@@ -85,7 +86,7 @@ public abstract class Column {
 	 * @param value input value. e.g. from text table column
 	 * @return output type representing the input value
 	 */
-	public Object valueOf(Object value)throws ParseException{
+	public Object preprocessValue(Object value)throws ParseException{
 		if( constantValue != null ){
 			value = constantValue;
 		}
@@ -105,7 +106,7 @@ public abstract class Column {
 		return value;
 	}
 	
-	public Object valueOf(ColumnMap map, Object[] row) throws ParseException{
+	public T valueOf(ColumnMap map, Object[] row) throws ParseException{
 		if( name.isEmpty() ){
 			// use constant value if available
 			return valueOf(null);
@@ -121,18 +122,6 @@ public abstract class Column {
 		// TODO: apply
 		return input;
 	}
-
-	public static class DecimalColumn extends Column{
-		@XmlTransient
-		DecimalFormat decimalFormat;
-		
-		/**
-		 * Decimal format string for parsing via {@link DecimalFormat}
-		 * @see DecimalFormat#DecimalFormat(String)
-		 */
-		@XmlAttribute
-		String format;
-	}
 	
 	public void validate()throws ParseException{
 		if( name.isEmpty() && constantValue == null ){

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

@@ -25,7 +25,7 @@ public class Concept{
 	@XmlAttribute(required=true)
 	String id;
 	// TODO: value should contain also type (string,decimal,integer,...)
-	Column value;
+	Column<?> value;
 	StringColumn unit;
 	@XmlElement(required=true)
 	DateTimeColumn start;
@@ -39,7 +39,7 @@ public class Concept{
 		@XmlAttribute(required=true)
 		String id;
 		// TODO: value with type
-		Column value;
+		Column<?> value;
 		StringColumn unit;
 		
 		private Modifier(){
@@ -60,7 +60,7 @@ public class Concept{
 	}
 	
 	protected Observation createObservation(String patid, String visit, ObservationFactory factory, ColumnMap map, Object[] row) throws ParseException{
-		DateTimeAccuracy start = (DateTimeAccuracy)this.start.valueOf(map,row);
+		DateTimeAccuracy start = this.start.valueOf(map,row);
 		Observation o = factory.createObservation(patid, this.id, start);
 		if( visit != null ){
 			o.setEncounterId(visit);
@@ -68,8 +68,9 @@ public class Concept{
 		Object value = this.value.valueOf(map, row);
 		String unit = null;
 		if( this.unit != null ){
-			unit = (String)this.unit.valueOf(map, row);
+			unit = this.unit.valueOf(map, row);
 		}
+		// TODO: use type of column this.value to infer value type
 		if( value == null ){
 			// no value
 			o.setValue(null);

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

@@ -16,7 +16,7 @@ import de.sekmi.histream.etl.ParseException;
  * @author Raphael
  *
  */
-public class DateTimeColumn extends Column{
+public class DateTimeColumn extends Column<DateTimeAccuracy>{
 	@XmlTransient
 	DateTimeFormatter formatter;
 	/**
@@ -37,8 +37,8 @@ public class DateTimeColumn extends Column{
 	}
 	
 	@Override
-	public Object valueOf(Object value) throws ParseException{
-		value = super.valueOf(value);
+	public DateTimeAccuracy valueOf(Object value) throws ParseException{
+		value = super.preprocessValue(value);
 		if( value instanceof String ){
 			// parse date according to format
 			if( formatter == null && format != null ){

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

@@ -6,7 +6,6 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlElementWrapper;
 
-import de.sekmi.histream.DateTimeAccuracy;
 import de.sekmi.histream.ObservationFactory;
 import de.sekmi.histream.etl.ColumnMap;
 import de.sekmi.histream.etl.ParseException;
@@ -33,7 +32,7 @@ public class PatientTable extends Table<PatientRow> implements WideInterface{
 		DateTimeColumn birthdate;
 		DateTimeColumn deathdate;
 		StringColumn gender;
-		Column[] ignore;
+		Column<?>[] ignore;
 	}
 
 	@Override
@@ -54,10 +53,10 @@ public class PatientTable extends Table<PatientRow> implements WideInterface{
 	@Override
 	public PatientRow fillRecord(ColumnMap map, Object[] row, ObservationFactory factory) throws ParseException {
 		PatientRow patient = new PatientRow();
-		patient.setId(idat.patientId.valueOf(map, row).toString());
-		patient.setNames((String)idat.firstname.valueOf(map, row), (String)idat.surname.valueOf(map, row));
-		patient.setBirthDate((DateTimeAccuracy)idat.birthdate.valueOf(map, row));
-		patient.setDeathDate((DateTimeAccuracy)idat.deathdate.valueOf(map, row));
+		patient.setId(idat.patientId.valueOf(map, row));
+		patient.setNames(idat.firstname.valueOf(map, row), idat.surname.valueOf(map, row));
+		patient.setBirthDate(idat.birthdate.valueOf(map, row));
+		patient.setDeathDate(idat.deathdate.valueOf(map, row));
 		// TODO concepts
 		return patient;
 	}

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

 package de.sekmi.histream.etl.config;
 
-public class StringColumn extends Column{
+import de.sekmi.histream.etl.ParseException;
+
+public class StringColumn extends Column<String>{
 
 	public StringColumn(String name) {
 		super(name);
@@ -8,5 +10,11 @@ public class StringColumn extends Column{
 	protected StringColumn(){
 		super();
 	}
+	@Override
+	public String valueOf(Object input) throws ParseException {
+		Object value = preprocessValue(input);
+		if( value != null )return value.toString();
+		else return null;
+	}
 	
 }
\ No newline at end of file

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

@@ -6,7 +6,6 @@ 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.ObservationFactory;
 import de.sekmi.histream.etl.ColumnMap;
 import de.sekmi.histream.etl.ParseException;
@@ -28,7 +27,7 @@ public class VisitTable extends Table<VisitRow> implements WideInterface{
 		DateTimeColumn start;
 		DateTimeColumn end;
 		// TODO inpatient/outpatient state
-		Column[] ignore;
+		Column<?>[] ignore;
 	}
 	@Override
 	public ColumnMap getColumnMap(String[] headers) throws ParseException {
@@ -48,10 +47,10 @@ public class VisitTable extends Table<VisitRow> implements WideInterface{
 	@Override
 	public VisitRow fillRecord(ColumnMap map, Object[] row, ObservationFactory factory) throws ParseException {
 		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));
+		visit.setId(idat.visitId.valueOf(map, row));
+		visit.setPatientId(idat.patientId.valueOf(map, row));
+		visit.setStartTime(idat.start.valueOf(map, row));
+		visit.setEndTime(idat.end.valueOf(map, row));
 		// TODO other 
 		// TODO concepts
 		return visit;

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

@@ -31,8 +31,8 @@ public class WideTable extends Table<WideRow> {
 
 	@Override
 	public WideRow fillRecord(ColumnMap map, Object[] row, ObservationFactory factory) throws ParseException {
-		String patid = (String)idat.patientId.valueOf(map, row);
-		String visit = (String)idat.visitId.valueOf(map, row);
+		String patid = idat.patientId.valueOf(map, row);
+		String visit = idat.visitId.valueOf(map, row);
 		WideRow rec = new WideRow(patid,visit);
 		for( Concept c : concepts ){
 			Observation o = c.createObservation(patid, visit, factory, map, row);