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Commit a950d496 authored by rwm's avatar rwm
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changed column name from xml value to xml attribute

parent ad8b58bc
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Showing with 59 additions and 48 deletions
histream-import/src/main/java/de/sekmi/histream/etl/ColumnMap.java
View file @ a950d496
......@@ -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
View file @ a950d496
......@@ -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
View file @ a950d496
......@@ -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
View file @ a950d496
......@@ -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
View file @ a950d496
......@@ -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>
......
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