LMS-1883 unit test for ignoring column property

SVN: 18948

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessorConfiguration.java

@@ -21,12 +21,17 @@ import java.util.HashSet;
 import java.util.Properties;
 import java.util.Set;
 
+import ch.rinn.restrictions.Private;
 import ch.systemsx.cisd.common.utilities.PropertyUtils;
 import ch.systemsx.cisd.utils.CsvFileReaderHelper.ICsvFileReaderConfiguration;
 
 class FeatureVectorStorageProcessorConfiguration implements
         ICsvFileReaderConfiguration
 {
+    private static final String DEFAULT_COLUMNS_TO_BE_IGNORED = "barcode";
+
+    @Private static final String COLUMNS_TO_BE_IGNORED_KEY = "columns-to-be-ignored";
+
     private static final String SEPARATOR_PROPERTY_KEY = "separator";
 
     private static final String IGNORE_COMMENTS_PROPERTY_KEY = "ignore-comments";
@@ -67,8 +72,8 @@ class FeatureVectorStorageProcessorConfiguration implements
         this.wellColumn = properties.getProperty(WELL_NAME_COL_PROPERTY_KEY, DEFAULT_WELL_COL);
         
         columnsToBeIgnored =
-                new HashSet<String>(Arrays.asList(properties.getProperty("columns-to-be-ignored",
-                        "barcode").split(", *")));
+                new HashSet<String>(Arrays.asList(properties.getProperty(COLUMNS_TO_BE_IGNORED_KEY,
+                        DEFAULT_COLUMNS_TO_BE_IGNORED).split(", *")));
     }
 
     public char getColumnDelimiter()

screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVectorTest.java

@@ -16,18 +16,22 @@
 
 package ch.systemsx.cisd.openbis.dss.etl.featurevector;
 
+import static ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessorConfiguration.COLUMNS_TO_BE_IGNORED_KEY;
+
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Properties;
 
 import org.testng.AssertJUnit;
 import org.testng.annotations.Test;
 
 import com.csvreader.CsvReader;
 
+import ch.rinn.restrictions.Friend;
 import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvToCanonicalFeatureVector.CsvToCanonicalFeatureVectorConfiguration;
 import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
@@ -39,6 +43,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFe
 /**
  * @author Chandrasekhar Ramakrishnan
  */
+@Friend(toClasses=FeatureVectorStorageProcessorConfiguration.class)
 public class CsvToCanonicalFeatureVectorTest extends AssertJUnit
 {
     @Test
@@ -77,6 +82,44 @@ public class CsvToCanonicalFeatureVectorTest extends AssertJUnit
         assertEquals(0.001052f, darr.getForWellLocation(2, 1));
     }
 
+    @Test
+    public void testIgnoringColumns() throws IOException
+    {
+        Properties properties = new Properties();
+        properties.setProperty(COLUMNS_TO_BE_IGNORED_KEY, "RelativeInfectionIndex, Log2RelativeInfectionIndex,ZScore");
+        CsvToCanonicalFeatureVectorConfiguration config =
+            new CsvToCanonicalFeatureVectorConfiguration(new FeatureVectorStorageProcessorConfiguration(properties));
+        CsvToCanonicalFeatureVector converter =
+            new CsvToCanonicalFeatureVector(getDatasetFileLines(), config, 16, 24);
+        ArrayList<CanonicalFeatureVector> fvs = converter.convert();
+        // Not all the columns are not empty
+        assertEquals(15, fvs.size());
+        // Check total cells feature
+        CanonicalFeatureVector totalCells = fvs.get(0);
+        ImgFeatureDefDTO def = totalCells.getFeatureDef();
+        assertEquals("TotalCells", def.getLabel());
+        assertEquals(1, totalCells.getValues().size());
+        ImgFeatureValuesDTO values = totalCells.getValues().get(0);
+        PlateFeatureValues darr = values.getValues();
+        assertTrue("Dimensions are " + darr.getGeometry().toPlateGeometryStr(),
+                Geometry.GEOMETRY_384_16X24.equals(darr.getGeometry()));
+        assertEquals(2825.0f, darr.getForWellLocation(1, 1));
+        assertEquals(5544.0f, darr.getForWellLocation(1, 2));
+        assertEquals(5701.0f, darr.getForWellLocation(2, 1));
+        // Check InfectionIndex
+        CanonicalFeatureVector infectionIndex = fvs.get(2);
+        def = infectionIndex.getFeatureDef();
+        assertEquals("InfectionIndex", def.getLabel());
+        assertEquals(1, infectionIndex.getValues().size());
+        values = infectionIndex.getValues().get(0);
+        darr = values.getValues();
+        assertTrue("Dimensions are " + darr.getGeometry().toPlateGeometryStr(),
+                Geometry.GEOMETRY_384_16X24.equals(darr.getGeometry()));
+        assertEquals(0.009558f, darr.getForWellLocation(1, 1));
+        assertEquals(0.037157f, darr.getForWellLocation(1, 2));
+        assertEquals(0.001052f, darr.getForWellLocation(2, 1));
+    }
+    
     /**
      * Return the tabular data as a DatasetFileLines.
      */