test case for concept class annotator

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

@@ -2,14 +2,29 @@ package de.sekmi.histream.export;
 
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.LinkedList;
+import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
+/**
+ * Keeps the table data in memory. Mainly useful for
+ * tests.
+ * <p>
+ * The patient and visit tables can be accessed with the
+ * constants {@link #PATIENT_TABLE} and {@link #VISIT_TABLE}.
+ * </p>
+ * @author R.W.Majeed
+ *
+ */
 public class MemoryExportWriter implements ExportWriter{
-	List<MemoryTable> tables;
+	public static final String PATIENT_TABLE = "patients";
+	public static final String VISIT_TABLE = "visits";
+	
+	Map<String, MemoryTable> tables;
 	
 	public MemoryExportWriter(){
-		tables = new LinkedList<>();
+		tables = new HashMap<>();
 	}
 	public static class MemoryTable implements TableWriter{
 		List<String[]> rows;
@@ -52,32 +67,57 @@ public class MemoryExportWriter implements ExportWriter{
 	
 	@Override
 	public TableWriter openPatientTable() {
-		MemoryTable t = new MemoryTable("patients");
-		tables.add(t);
+		MemoryTable t = new MemoryTable(PATIENT_TABLE);
+		tables.put(t.id, t);
 		return t;
 	}
 
 	@Override
 	public TableWriter openVisitTable() {
-		MemoryTable t = new MemoryTable("visits");
-		tables.add(t);
+		MemoryTable t = new MemoryTable(VISIT_TABLE);
+		tables.put(t.id, t);
 		return t;
 	}
 
 	@Override
 	public TableWriter openEAVTable(String id) {
+		if( tables.containsKey(id) ){
+			throw new IllegalArgumentException("Duplicate table id: "+id);
+		}
 		MemoryTable t = new MemoryTable(id);
-		tables.add(t);
+		tables.put(t.id, t);
 		return t;
 	}
 
 	public void dump(){
-		for( MemoryTable t : tables ){
+		for( MemoryTable t : tables.values() ){
 			t.dump();
 			System.out.println();
 		}
 	}
 
+	/**
+	 * Access table data
+	 * @param table table id
+	 * @param column column name
+	 * @param row row number
+	 * @return data
+	 * @throws IndexOutOfBoundsException if any of table, column, row does not exist
+	 */
+	public String get(String table, String column, int row) throws IndexOutOfBoundsException{
+		MemoryTable t = tables.get(table);
+		if( t == null ){
+			throw new IndexOutOfBoundsException("Non-existing table "+table);
+		}
+		int index = Arrays.asList(t.headers).indexOf(column);
+		if( index == -1 ){
+			throw new IndexOutOfBoundsException("Table "+table+" does not contain column "+column);
+		}
+		if( row < 0 || row >= t.rows.size() ){
+			throw new IndexOutOfBoundsException("Unable to access row "+row+" in table "+table+" (has only "+t.rows.size()+" rows)");
+		}
+		return t.rows.get(row)[index];
+	}
 	@Override
 	public void close(){
 	}

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

@@ -34,6 +34,8 @@ public class TestExport {
 		try( ObservationSupplier s = t.getExampleSupplier() ){
 			export.export(s, m);
 		}
+		// verify class lookup
+		Assert.assertEquals("T:date:year", m.get(MemoryExportWriter.VISIT_TABLE, "byclass", 0));
 		m.dump();
 		// TODO something wrong with namespaces in xpath/dom
 	}

histream-export/src/test/resources/export1.xml

@@ -2,8 +2,8 @@
 <export xmlns="http://sekmi.de/ns/histream/export-v1"
 			xmlns:eav="http://sekmi.de/histream/ns/eav-data">
     <concepts>
-        <group class="diag">
-            <concept wildcard-notation="ICD10:*"/>
+        <group class="testclass">
+            <concept wildcard-notation="T:date:yea*"/>
         </group>
         <concept notation="T:full"/>
         <concept wildcard-notation="CEDIS:*"/>
@@ -18,6 +18,7 @@
         <column header="pid" xpath="../@id"/>
 		<column header="vid" xpath="@id"/>
 		<column header="start" xpath="eav:start"/>
+		<column header="byclass" xpath="eav:fact[@class='testclass']/@concept"/>
 		<column header="f_start" xpath="eav:fact[@concept='T:full']/@start"/>
 		<column header="f_end" xpath="eav:fact[@concept='T:full']/@end"/>
 		<column header="f_loc" xpath="eav:fact[@concept='T:full']/@location"/>