Merge branch '1515-separate-backgrounds-and-overlays-in-admin-panel' into 'master'

Resolve "separate backgrounds and overlays in admin panel"

Closes #1515

See merge request !1311

CHANGELOG

+minerva (16.0.0~beta.1) stable; urgency=medium
+  * Backward incompatibility: layout parameter in minerva url is not supported
+    anymore
+  * Small improvement: info about background and dat aoverlays is separated in
+    edit project panel (#1515)
+  * Bug fix: there was issue with updating data overlay in admin panel "Unknown
+    parameter: defaultOverlay"
+  * Bug fix: data overlays uploaded in complex map were not processed properly
+    (#1485)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 9 Jun 2021 15:00:00 +0200
+
 minerva (16.0.0~beta.0) stable; urgency=medium
   * Backward incompatibility: debian package cannot be upgraded from version
     prior to 12.1.0 (#1464)

CellDesigner-plugin/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~beta.0</version>
+		<version>16.0.0~beta.1</version>
 	</parent>
 	<artifactId>CellDesigner-plugin</artifactId>
 	<!-- dependency from the MapViewer model -->
@@ -50,19 +50,19 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>commons</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<dependency>

annotation/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~beta.0</version>
+		<version>16.0.0~beta.1</version>
 	</parent>
 	<artifactId>annotation</artifactId>
 	<name>Annotation module</name>
@@ -18,7 +18,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer dao -->
@@ -26,7 +26,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>persist</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer cell designer parser (we need access 
@@ -34,13 +34,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<!-- Log4J2 -->

commons/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~beta.0</version>
+		<version>16.0.0~beta.1</version>
 	</parent>
 	<artifactId>commons</artifactId>
 	<name>Mapviewer commons</name>

converter-CellDesigner/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~beta.0</version>
+		<version>16.0.0~beta.1</version>
 	</parent>
 	<artifactId>converter-CellDesigner</artifactId>
 	<name>CellDesigner converter</name>
@@ -17,13 +17,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<!-- Log4J2 -->

converter-SBGNML/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~beta.0</version>
+		<version>16.0.0~beta.1</version>
 	</parent>
 	<artifactId>converter-SBGNML</artifactId>
 
@@ -20,26 +20,26 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>persist</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 			<scope>test</scope>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-graphics</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<dependency>

converter-graphics/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~beta.0</version>
+		<version>16.0.0~beta.1</version>
 	</parent>
 	<artifactId>converter-graphics</artifactId>
 	<name>MapViewer graphics converter</name>
@@ -18,13 +18,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model-command</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<!-- Log4J2-->

converter-sbml/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.0~beta.0</version>
+		<version>16.0.0~beta.1</version>
 	</parent>
 	<artifactId>converter-sbml</artifactId>
 	<name>converter-sbml</name>
@@ -40,22 +40,22 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model-command</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 		</dependency>
 
 		<!-- Log4J2 -->
@@ -154,7 +154,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-graphics</artifactId>
-			<version>16.0.0~beta.0</version>
+			<version>16.0.0~beta.1</version>
 			<scope>test</scope>
 		</dependency>
 

converter/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>lcsb.mapviewer</groupId>
     <artifactId>parent</artifactId>
-    <version>16.0.0~beta.0</version>
+    <version>16.0.0~beta.1</version>
   </parent>
   
   <artifactId>converter</artifactId>
@@ -15,7 +15,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
       <artifactId>model</artifactId>
-      <version>16.0.0~beta.0</version>
+      <version>16.0.0~beta.1</version>
     </dependency>
 		<dependency>
 			<groupId>xerces</groupId>

service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java → converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaColumn.java

-package lcsb.mapviewer.services.utils.data;
+package lcsb.mapviewer.converter;
 
 import java.util.HashSet;
 import java.util.Set;

service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java → converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaReader.java

-package lcsb.mapviewer.services.utils;
+package lcsb.mapviewer.converter;
 
 import java.awt.Color;
 import java.io.*;
-import java.lang.reflect.Field;
 import java.util.*;
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
-import lcsb.mapviewer.annotation.services.MiriamConnector;
 import lcsb.mapviewer.common.*;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.common.geometry.ColorParser;
-import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesMapping;
 import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
 import lcsb.mapviewer.model.map.*;
 import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.model.map.species.*;
 import lcsb.mapviewer.model.overlay.*;
-import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
 
 /**
  * Class that reads information about set of {@link DataOverlayEntry color
@@ -46,6 +43,22 @@ public class ColorSchemaReader {
    */
   private static final int MIN_GV_RED_VALUE = 128;
 
+  private static Map<String, Class<? extends BioEntity>> speciesMapping;
+  static {
+    speciesMapping = new HashMap<>();
+    speciesMapping.put("protein", Protein.class);
+    speciesMapping.put("gene", Gene.class);
+    speciesMapping.put("complex", Complex.class);
+    speciesMapping.put("simple_molecule", SimpleMolecule.class);
+    speciesMapping.put("ion", Ion.class);
+    speciesMapping.put("phenotype", Phenotype.class);
+    speciesMapping.put("drug", Drug.class);
+    speciesMapping.put("rna", Rna.class);
+    speciesMapping.put("antisense_rna", AntisenseRna.class);
+    speciesMapping.put("unknown", Unknown.class);
+    speciesMapping.put("degraded", Degraded.class);
+  }
+
   /**
    * Object that parses colors from string.
    */
@@ -56,11 +69,6 @@ public class ColorSchemaReader {
    */
   private Logger logger = LogManager.getLogger();
 
-  /**
-   * Objects that manipulates {@link MiriamData}.
-   */
-  private MiriamConnector mc = new MiriamConnector();
-
   /**
    * Reads information about set of {@link DataOverlayEntry color schemas} from
    * the input stream.
@@ -196,9 +204,9 @@ public class ColorSchemaReader {
           if (typeColumn != null) {
             String[] types = values[typeColumn].split(",");
             for (String string : types) {
-              SpeciesMapping mapping = SpeciesMapping.getMappingByString(string);
-              if (mapping != null) {
-                schema.addType(mapping.getModelClazz());
+              Class<? extends BioEntity> clazz = speciesMapping.get(string.toLowerCase());
+              if (clazz != null) {
+                schema.addType(clazz);
               } else {
                 throw new InvalidDataOverlayException("[Line " + lineIndex + "] Unknown class type: " + string + ".");
               }
@@ -274,10 +282,10 @@ public class ColorSchemaReader {
 
   private void processGeneralIdentifier(String string, DataOverlayEntry schema, String errorPrefix)
       throws InvalidDataOverlayException {
-    if (mc.isValidIdentifier(string)) {
+    try {
       schema.addMiriamData(MiriamType.getMiriamDataFromIdentifier(string));
-    } else {
-      throw new InvalidDataOverlayException(errorPrefix + " Invalid identifier: " + string);
+    } catch (InvalidArgumentException e) {
+      throw new InvalidDataOverlayException(errorPrefix + " Invalid identifier: " + string, e);
     }
   }
 
@@ -564,16 +572,13 @@ public class ColorSchemaReader {
     String[] types = typesString.split(",");
     for (String string : types) {
       if (!string.isEmpty()) {
-        SpeciesMapping mapping = SpeciesMapping.getMappingByString(string);
-        if (mapping != null) {
-          result.add(mapping.getModelClazz());
+        Class<? extends BioEntity> clazz = speciesMapping.get(string.toLowerCase());
+        if (clazz != null) {
+          result.add(clazz);
         } else {
-          String validStrings = "";
-          for (SpeciesMapping speciesMapping : SpeciesMapping.values()) {
-            validStrings += speciesMapping.getCellDesignerString() + ", ";
-          }
           throw new InvalidDataOverlayException(
-              errorPrefix + "Unknown class type: " + string + ". Valid values are: " + validStrings);
+              errorPrefix + "Unknown class type: " + string + ". Valid values are: "
+                  + StringUtils.join(speciesMapping.values(), ","));
         }
       }
     }

converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java

@@ -21,8 +21,7 @@ import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.map.model.*;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.*;
-import lcsb.mapviewer.model.overlay.DataOverlayType;
-import lcsb.mapviewer.model.overlay.DataOverlay;
+import lcsb.mapviewer.model.overlay.*;
 
 /**
  * This class allows to create complex {@link Model} that contains submaps. It's
@@ -304,9 +303,10 @@ public class ComplexZipConverter {
    * @return {@link DataOverlay} for a given {@link LayoutZipEntryFile}
    * @throws IOException
    *           thrown when there is a problem with accessing {@link ZipFile}
+   * @throws InvalidInputDataExecption 
    */
   public DataOverlay layoutZipEntryFileToLayout(ComplexZipConverterParams params, ZipFile zipFile, ZipEntry entry,
-      LayoutZipEntryFile layoutEntry, int order) throws IOException {
+      LayoutZipEntryFile layoutEntry, int order) throws IOException, InvalidInputDataExecption {
     DataOverlay layout = new DataOverlay();
     layout.setDescription(layoutEntry.getDescription());
     UploadedFileEntry fileEntry = new UploadedFileEntry();
@@ -329,6 +329,14 @@ public class ComplexZipConverter {
     layout.setPublic(true);
     layout.setName(layoutEntry.getName());
     layout.setOrderIndex(order);
+
+    ColorSchemaReader reader = new ColorSchemaReader();
+    ByteArrayInputStream baos = new ByteArrayInputStream(fileEntry.getFileContent());
+    try {
+      layout.addEntries(reader.readColorSchema(baos, parameters));
+    } catch (InvalidDataOverlayException e) {
+      throw new InvalidInputDataExecption(e);
+    }
     return layout;
   }
 

converter/src/test/java/lcsb/mapviewer/converter/AllTests.java

@@ -7,7 +7,9 @@ import org.junit.runners.Suite.SuiteClasses;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParserTest;
 
 @RunWith(Suite.class)
-@SuiteClasses({ ComplexZipConverterParamsTest.class,
+@SuiteClasses({
+    ColorSchemaReaderTest.class,
+    ComplexZipConverterParamsTest.class,
     ComplexZipConverterTest.class,
     OverviewParserTest.class,
     ProjectFactoryTest.class,

service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java → converter/src/test/java/lcsb/mapviewer/converter/ColorSchemaReaderTest.java

-package lcsb.mapviewer.services.utils;
+package lcsb.mapviewer.converter;
 
 import static org.junit.Assert.*;
 
@@ -12,16 +12,13 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.junit.*;
 
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.ColorModelCommand;
+import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.TextFileUtils;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.overlay.*;
-import lcsb.mapviewer.services.ServiceTestFunctions;
 
-public class ColorSchemaReaderTest extends ServiceTestFunctions {
+public class ColorSchemaReaderTest extends ConverterTestFunctions {
   Logger logger = LogManager.getLogger();
 
   ColorSchemaReader reader;
@@ -37,17 +34,17 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
 
   @Test
   public void testReadSchema() throws Exception {
-    Collection<DataOverlayEntry> schemas = reader.readColorSchema("testFiles/enricoData/ageing.txt");
+    Collection<DataOverlayEntry> schemas = reader.readColorSchema("testFiles/coloring/ageing.txt");
 
     assertNotNull(schemas);
     assertEquals(412, schemas.size());
 
-    schemas = reader.readColorSchema("testFiles/enricoData/ge001.txt");
+    schemas = reader.readColorSchema("testFiles/coloring/ge001.txt");
 
     assertNotNull(schemas);
     assertEquals(3057, schemas.size());
 
-    schemas = reader.readColorSchema("testFiles/enricoData/ge005.txt");
+    schemas = reader.readColorSchema("testFiles/coloring/ge005.txt");
 
     assertNotNull(schemas);
     assertEquals(4338, schemas.size());
@@ -174,7 +171,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
     assertEquals(1, collection.size());
     DataOverlayEntry schema = collection.iterator().next();
     assertEquals("re1", schema.getElementId());
-    assertEquals(3.0, schema.getLineWidth(), EPSILON);
+    assertEquals(3.0, schema.getLineWidth(), Configuration.EPSILON);
     assertEquals(Color.RED, schema.getColor());
   }
 
@@ -186,19 +183,6 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
     assertEquals(3, schemas.size());
   }
 
-  @Test
-  public void testColoring3() throws Exception {
-    ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
-
-    Model model = getModelForFile("testFiles/coloring/protein_to_color.xml", false);
-
-    Collection<DataOverlayEntry> schemas = reader.readColorSchema("testFiles/coloring/problematicSchema.txt");
-    ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
-    factory.execute();
-
-    assertFalse(model.getElementByElementId("sa1").getFillColor().equals(Color.WHITE));
-  }
-
   @Test
   public void testColoringWithValueOrColor() throws Exception {
     Map<String, String> params = new HashMap<>();

converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java

@@ -284,17 +284,18 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
   public void testLayoutZipEntryFileToLayoutOrder() throws Exception {
     ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
     ComplexZipConverterParams params = new ComplexZipConverterParams();
-    ZipFile file = Mockito.mock(ZipFile.class);
-    params.zipFile(file);
+    ZipFile file1 = Mockito.mock(ZipFile.class);
+    ZipFile file2 = Mockito.mock(ZipFile.class);
     LayoutZipEntryFile entry1 = new LayoutZipEntryFile("overlay1.txt", "name", "desc1");
     LayoutZipEntryFile entry2 = new LayoutZipEntryFile("overlay2.txt", "name", "desc1");
     params.entry(entry1);
     params.entry(entry2);
     ZipEntry entry = Mockito.mock(ZipEntry.class);
-    Mockito.when(file.getInputStream(entry)).thenReturn(new ByteArrayInputStream("".getBytes()));
+    Mockito.when(file1.getInputStream(entry)).thenReturn(new ByteArrayInputStream("name\tvalue\n".getBytes()));
+    Mockito.when(file2.getInputStream(entry)).thenReturn(new ByteArrayInputStream("name\tvalue\n".getBytes()));
 
-    DataOverlay overlay1 = converter.layoutZipEntryFileToLayout(params, file, entry, entry1, 1);
-    DataOverlay overlay2 = converter.layoutZipEntryFileToLayout(params, file, entry, entry2, 2);
+    DataOverlay overlay1 = converter.layoutZipEntryFileToLayout(params, file1, entry, entry1, 1);
+    DataOverlay overlay2 = converter.layoutZipEntryFileToLayout(params, file2, entry, entry2, 2);
     assertTrue(overlay1.getOrderIndex() > 0);
     assertTrue(overlay2.getOrderIndex() > overlay1.getOrderIndex());
   }

converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java

@@ -18,8 +18,10 @@ import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.*;
 import lcsb.mapviewer.model.map.layout.graphics.Layer;
 import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.*;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.overlay.DataOverlay;
 
 public class ProjectFactoryTest extends ConverterTestFunctions {
   Logger logger = LogManager.getLogger();
@@ -221,4 +223,28 @@ public class ProjectFactoryTest extends ConverterTestFunctions {
     return result;
   }
 
+  @Test
+  public void testWithOverlay() throws Exception {
+    ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+    ProjectFactory projectFactory = new ProjectFactory(converter);
+    ZipFile zipFile = new ZipFile("testFiles/complex_model_with_layouts.zip");
+    ComplexZipConverterParams params = new ComplexZipConverterParams();
+    params.zipFile(zipFile);
+
+    ZipEntryFileFactory factory = new ZipEntryFileFactory();
+    Enumeration<? extends ZipEntry> entries = zipFile.entries();
+    while (entries.hasMoreElements()) {
+      ZipEntry entry = entries.nextElement();
+      if (!entry.isDirectory()) {
+        params.entry(factory.createZipEntryFile(entry, zipFile));
+      }
+    }
+
+    Project project = projectFactory.create(params);
+    assertNotNull(project);
+    assertEquals(1, project.getDataOverlays().size());
+    DataOverlay overlay = project.getDataOverlays().get(0);
+    assertTrue(overlay.getEntries().size() > 0);
+  }
+
 }

converter/testFiles/coloring/gene_variants.txt

+#TYPE=GENETIC_VARIANT						
+#GENOME_TYPE=UCSC						
+#GENOME_VERSION=hg38						
+position	original_dna	alternative_dna	gene_name	description	color	contig
+10146	AC	A	DDX11L1	upstream	#ff0000	chr1
+10439	AC	A	DDX11L1;WASH7P	upstream;downstream	#ff0001	chr1
+10583	G	A	DDX11L1;WASH7P	upstream;downstream	#ff0002	chr1
+10611	C	G	DDX11L1;WASH7P	upstream;downstream	#ff0003	chr1
+10616	CCGCCGTTGCAAAGGCGCGCCG	C	DDX11L1;WASH7P	upstream;downstream	#ff0004	chr1
+10904	G	A	DDX11L1;WASH7P	upstream;downstream	#ff0005	chr1
+12783	G	A	DDX11L1	intronic	#ff0006	chr1
+13116	T	G	DDX11L1	intronic	#ff0007	chr1
+13118	A	G	DDX11L1	intronic	#ff0008	chr1
+13143	G	C	DDX11L1	intronic	#ff0009	chr1
+13273	G	C	DDX11L1	intronic	#ff0010	chr1
+13302	C	T	DDX11L1	intronic	#ff0011	chr1
+13417	C	CGAGA	DDX11L1	exonic	#ff0012	chr1
+13550	G	A	DDX11L1	exonic	#ff0013	chr1
+13656	CAG	C	DDX11L1	UTR3	#ff0014	chr1
+13668	G	A	DDX11L1	UTR3	#ff0015	chr1
+13813	T	G	DDX11L1	UTR3	#ff0016	chr1
+13838	C	T	DDX11L1	UTR3	#ff0017	chr1
+13868	A	G	DDX11L1	UTR3	#ff0018	chr1
+13896	C	A	DDX11L1	UTR3	#ff0019	chr1
+13957	TC	T	DDX11L1	UTR3	#ff0020	chr1
+14354	C	A	DDX11L1	UTR3	#ff0021	chr1
+14464	A	T	WASH7P	ncRNA_exonic	#ff0022	chr1
+14653	C	T	WASH7P	ncRNA_exonic	#ff0023	chr1
+14671	G	C	WASH7P	ncRNA_exonic	#ff0024	chr1
+14673	G	C	WASH7P	ncRNA_exonic	#ff0025	chr1
+14677	G	A	WASH7P	ncRNA_exonic	#ff0026	chr1
+14699	C	G	WASH7P	ncRNA_exonic	#ff0027	chr1
+14907	A	G	WASH7P	ncRNA_exonic	#ff0028	chr1
+14930	A	G	WASH7P	ncRNA_exonic	#ff0029	chr1