some columns are marked as deprecated

CHANGELOG

 minerva (12.3.1~beta.1) unstable; urgency=low
   * Small improvement: model_name renamed to map_name in data overlay columns 
     (#827)
+  * Small improvement: name, type, reference_genome_type and 
+    reference_genome_version column in genetic variant data overlay are 
+    deprecated (#827)
+  * Bug fix: deprecated columns in data overlay are not visible to the end user
+    (#827)
   * Bug fix: invalid color in data overlay provides proper feedback to the user
     (#822)
   * Bug fix: genetic variant overlay without name caused problems (#832)

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

@@ -7,6 +7,7 @@ import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.lang.reflect.Field;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -720,7 +721,15 @@ public class ColorSchemaReader {
         } else {
           String columnNames = "";
           for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
-            if (schemaColumn.getTypes().contains(type)) {
+            boolean deprecated = false;
+            try {
+              Field f = ColorSchemaColumn.class.getField(schemaColumn.name());
+              if (f.isAnnotationPresent(Deprecated.class))
+                deprecated = true;
+            } catch (NoSuchFieldException | SecurityException e) {
+            }
+
+            if (schemaColumn.getTypes().contains(type) && !deprecated) {
               columnNames += schemaColumn.getColumnName() + ", ";
             }
           }

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

@@ -19,7 +19,7 @@ public enum ColorSchemaColumn {
   /**
    * Name of the element.
    */
-  NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+  NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC}),
 
   GENE_NAME(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
 
@@ -43,7 +43,7 @@ public enum ColorSchemaColumn {
   /**
    * Class type of the element.
    */
-  TYPE(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+  TYPE(new ColorSchemaType[] { ColorSchemaType.GENERIC}),
 
   /**
    * New element/reaction color.
@@ -99,11 +99,13 @@ public enum ColorSchemaColumn {
   /**
    * What's the {@link ReferenceGenomeType}.
    */
+  @Deprecated
   REFERENCE_GENOME_TYPE(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
 
   /**
    * {@link ReferenceGenome#version Version} of the reference genome.
    */
+  @Deprecated
   REFERENCE_GENOME_VERSION(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
 
   /**