Commit a950d496 authored by rwm's avatar rwm
Browse files

changed column name from xml value to xml attribute

parent ad8b58bc

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

+1 −1
Original line number Diff line number Diff line
@@ -42,7 +42,7 @@ public class ColumnMap{ 
		Objects.requireNonNull(column);

		column.validate(); // TODO: maybe call after unmarshal of column

		

		if( column.getName().isEmpty() ){

		if( column.getName() == null || column.getName().isEmpty() ){

			// no reference to column, probably constant value

			// no need to register

			return;

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

+8 −7
Original line number Diff line number Diff line
@@ -5,7 +5,6 @@ import java.util.Objects; 
import javax.xml.bind.annotation.XmlAttribute;

import javax.xml.bind.annotation.XmlSeeAlso;

import javax.xml.bind.annotation.XmlTransient;

import javax.xml.bind.annotation.XmlValue;



import de.sekmi.histream.etl.ColumnMap;

import de.sekmi.histream.etl.ParseException;
@@ -25,7 +24,7 @@ public abstract class Column<T> { 
	}

	public Column(String name){

		this();

		this.name = name;

		this.column = name;

	}

	/**

	 * If this string is found in the column data, the resulting value will be null.
@@ -70,14 +69,14 @@ public abstract class Column<T> { 
	/**

	 * Column name to use for reading input values.

	 */

	@XmlValue

	String name;

	@XmlAttribute

	String column;

	

	/**

	 * Column name to use for reading input values

	 * @return column name

	 */

	public String getName(){return name;}

	public String getName(){return column;}

	

	public abstract T valueOf(Object input) throws ParseException;
@@ -113,7 +112,7 @@ public abstract class Column<T> { 
	}

	

	public T valueOf(ColumnMap map, Object[] row) throws ParseException{

		if( name.isEmpty() ){

		if( column == null || column.isEmpty() ){

			// use constant value if available

			return valueOf(null);

		}
@@ -130,8 +129,10 @@ public abstract class Column<T> { 
	}

	

	public void validate()throws ParseException{

		if( name.isEmpty() && constantValue == null ){

		if( column == null && constantValue == null ){

			throw new ParseException("Empty column name only allowed if constant-value is specified");

		}else if( column != null && column.isEmpty() ){

			throw new ParseException("No empty column attribute allowed. Remove attribute for constant values");

		}

	}

}

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

+4 −0
Original line number Diff line number Diff line
@@ -82,6 +82,10 @@ public class Concept{ 
			// numeric

			NumericValue v = new NumericValue((BigDecimal)value,unit);

			o.setValue(v);

		}else if( value instanceof Long ){

			// numeric

			NumericValue v = new NumericValue((Long)value,unit);

			o.setValue(v);

		}else{

			throw new ParseException("Unsupported value type for concept id "+this.id+": "+value.getClass());

		}

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

+10 −10
Original line number Diff line number Diff line
@@ -27,33 +27,33 @@ public class TestMarshall { 
			Assert.assertNotNull(ds.patientTable.source);

			Assert.assertEquals("\\t", ((FileSource)ds.patientTable.source).separator);

			Assert.assertNotNull(ds.patientTable.idat);

			Assert.assertEquals("patid",ds.patientTable.idat.patientId.name);

			Assert.assertEquals("geburtsdatum",ds.patientTable.idat.birthdate.name);

			Assert.assertEquals("geschlecht",ds.patientTable.idat.gender.name);

			Assert.assertEquals("vorname",ds.patientTable.idat.givenName.name);

			Assert.assertEquals("nachname",ds.patientTable.idat.surname.name);

			Assert.assertEquals("patid",ds.patientTable.idat.patientId.column);

			Assert.assertEquals("geburtsdatum",ds.patientTable.idat.birthdate.column);

			Assert.assertEquals("geschlecht",ds.patientTable.idat.gender.column);

			Assert.assertEquals("vorname",ds.patientTable.idat.givenName.column);

			Assert.assertEquals("nachname",ds.patientTable.idat.surname.column);

			

			// visit table

			Assert.assertNotNull(ds.visitTable);

			Assert.assertNotNull(ds.visitTable.source);

			Assert.assertNotNull(ds.visitTable.idat);

			Assert.assertEquals("patid",ds.visitTable.idat.patientId.name);

			Assert.assertEquals("fallnr",ds.visitTable.idat.visitId.name);

			Assert.assertEquals("patid",ds.visitTable.idat.patientId.column);

			Assert.assertEquals("fallnr",ds.visitTable.idat.visitId.column);

			// wide table

			Assert.assertNotNull(ds.wideTables);

			Assert.assertEquals(1, ds.wideTables.length);

			WideTable t = ds.wideTables[0];

			Assert.assertNotNull(t);

			Assert.assertNotNull(t.idat);

			Assert.assertEquals("patid",t.idat.patientId.name);

			Assert.assertEquals("fallnr",t.idat.visitId.name);

			Assert.assertEquals("patid",t.idat.patientId.column);

			Assert.assertEquals("fallnr",t.idat.visitId.column);

			// concepts

			Assert.assertNotNull(t.concepts);

			Assert.assertTrue(t.concepts.length > 0);

			Concept c = t.concepts[0];

			Assert.assertNotNull(c);

			Assert.assertEquals("natrium", c.id);

			Assert.assertEquals("na", c.value.name);

			Assert.assertEquals("na", c.value.column);

			Assert.assertEquals("mmol/l", c.unit.constantValue);

		}

	}

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

+36 −30
Original line number Diff line number Diff line
@@ -11,14 +11,20 @@ 
			<separator>\t</separator>

		</source>

		<idat>

			<patient-id>patid</patient-id>

			<given-name>vorname</given-name>

			<surname>nachname</surname>

			<birthdate format="d.M.u" na="">geburtsdatum</birthdate>

			<deathdate format="d.M.u" na="">verstorben</deathdate>

			<gender>geschlecht</gender>

			<ignore xsi:type="string">ignoriert1</ignore>

			<ignore xsi:type="string">patfakt1</ignore>

			<patient-id column="patid"/>

			<given-name column="vorname"/>

			<surname column="nachname"/>

			<birthdate format="d.M.u" na="" column="geburtsdatum"/>

			<deathdate format="d.M.u" na="" column="verstorben"/>

			<gender column="geschlecht">

				<map>

					<map if-value="W" set-value="F"/>

					<map if-value="M" set-value="M"/>

					<otherwise set-value=""/>

				</map>

			</gender>

			<ignore xsi:type="string" column="ignoriert1"/>

			<ignore xsi:type="string" column="patfakt1"/>

		</idat>

		<!-- for MDAT in patient table, use the same patient-table also as

		a visit table (visit date needed). the patient id can be re-used
@@ -32,17 +38,17 @@ 
			<separator>\t</separator>

		</source>

		<idat>

			<patient-id>patid</patient-id>

			<visit-id>fallnr</visit-id>

			<start format="d.M.u[ H[:m[:s]]]" na="" truncate-to="year">start</start>

			<end format="d.M.u[ H[:m[:s]]]" na="">end</end>

			<patient-id column="patid"/>

			<visit-id column="fallnr"/>

			<start column="start" format="d.M.u[ H[:m[:s]]]" na="" truncate-to="year"/>

			<end column="end" format="d.M.u[ H[:m[:s]]]" na=""/>

		</idat>

		<mdat>

			<!-- in/out code -->

			<concept id="weight">

				<value xsi:type="string">gewicht</value>

				<value column="gewicht" xsi:type="string"/>

				<!-- TODO: verify that na values are no allowed for concept start timestamps -->

				<start format="d.M.u[ H[:m[:s]]]" na="">start</start>

				<start column="start" format="d.M.u[ H[:m[:s]]]" na=""/>

			</concept>

		</mdat>

	</visit-table>
@@ -52,21 +58,21 @@ 
			<separator>\t</separator>

		</source>

		<idat>

			<patient-id>patid</patient-id>

			<visit-id>fallnr</visit-id>

			<patient-id column="patid"/>

			<visit-id column="fallnr"/>

		</idat>

		<mdat>

			<concept id="natrium">

				<value xsi:type="decimal">na</value>

				<start format="d.M.u[ H[:m[:s]]]">zeitpunkt</start>

				<value column="na" xsi:type="decimal"/>

				<start column="zeitpunkt" format="d.M.u[ H[:m[:s]]]"/>

				<unit constant-value="mmol/l" />

				<modifier id="other">

					<value xsi:type="string" constant-value=""/>

				</modifier>

			</concept>

			<concept id="kalium">

				<value xsi:type="decimal">k</value>

				<start format="d.M.u[ H[:m[:s]]]">zeitpunkt</start>

				<value column="k" xsi:type="decimal"/>

				<start column="zeitpunkt" format="d.M.u[ H[:m[:s]]]"/>

			</concept>

		</mdat>
@@ -77,19 +83,19 @@ 
			<separator>\t</separator>

		</source>

		<idat>

			<patient-id>patid</patient-id>

			<visit-id>event</visit-id>

			<ignore xsi:type="string">locat</ignore>

			<ignore xsi:type="string">user</ignore>

			<patient-id column="patid"/>

			<visit-id column="event"/>

			<ignore column="locat" xsi:type="string"/>

			<ignore column="user" xsi:type="string"/>

		</idat>

		<mdat>

			<concept>param</concept>

			<start format="u-M-d">start_ts</start>

			<end format="u-M-d" na="@">end</end>

			<concept column="param"/>

			<start column="start_ts" format="u-M-d"/>

			<end column="end" format="u-M-d" na="@"/>

			<!-- location -->

			<type>type</type>

			<value na="@">value</value>

			<unit na="@">unit</unit>

			<type column="type"/>

			<value column="value" na="@"/>

			<unit column="unit" na="@"/>

		</mdat>

	</eav-table>