redundant references field in gene variants data overlay is now deprecated

CHANGELOG

@@ -17,6 +17,8 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
   * Small improvement: overlay name is obligatory (#698)
   * Small improvement: target gene in search panel contains also information
     about type of database that identifies the target (#66)
+  * Small improvement: redundant 'references' field in gene variants data 
+    overlay is now deprecated (#850)
   * Bug fix: export to CellDesigner of reaction with two modifiers connected
     with boolean operator resulted was skipping some layout information
   * Bug fix: reaction in SBGNML file containing two products was improperly

model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariation.java

@@ -74,11 +74,6 @@ public class GeneVariation implements Serializable {
    */
   private String referenceGenomeVersion;
 
-  /**
-   * List of references connected to this variant.
-   */
-  private List<MiriamData> references = new ArrayList<>();
-
   /**
    * Constructor that creates copy of the {@link GeneVariation}.
    * 
@@ -91,7 +86,6 @@ public class GeneVariation implements Serializable {
     this.setModifiedDna(original.getModifiedDna());
     this.setReferenceGenomeType(original.getReferenceGenomeType());
     this.setReferenceGenomeVersion(original.getReferenceGenomeVersion());
-    this.addReferences(original.getReferences());
     this.setContig(original.getContig());
     this.setAllelFrequency(original.getAllelFrequency());
     this.setVariantIdentifier(original.getVariantIdentifier());
@@ -104,19 +98,6 @@ public class GeneVariation implements Serializable {
   public GeneVariation() {
   }
 
-  /**
-   * Adds references.
-   * 
-   * @param references
-   *          references to add
-   * @see #references
-   */
-  private void addReferences(Collection<MiriamData> references) {
-    for (MiriamData reference : references) {
-      addReference(reference);
-    }
-  }
-
   /**
    * @return the position
    * @see #position
@@ -185,14 +166,6 @@ public class GeneVariation implements Serializable {
     this.referenceGenomeType = referenceGenomeType;
   }
 
-  /**
-   * @return the references
-   * @see #references
-   */
-  public List<MiriamData> getReferences() {
-    return references;
-  }
-
   /**
    * @return the referenceGenomeVersion
    * @see #referenceGenomeVersion
@@ -210,17 +183,6 @@ public class GeneVariation implements Serializable {
     this.referenceGenomeVersion = referenceGenomeVersion;
   }
 
-  /**
-   * Adds reference.
-   * 
-   * @param reference
-   *          reference to add
-   * @see #references
-   */
-  public void addReference(MiriamData reference) {
-    this.references.add(reference);
-  }
-
   /**
    * Creates copy of the object.
    * 

model/src/test/java/lcsb/mapviewer/model/map/layout/GeneVariationTest.java

@@ -46,18 +46,6 @@ public class GeneVariationTest {
 		}
 	}
 
-	@Test
-	public void testAddReference() throws Exception {
-		try {
-			GeneVariation gv = new GeneVariation();
-			gv.addReference(new MiriamData());
-			assertEquals(1, gv.getReferences().size());
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
 	@Test
 	public void testCopy() throws Exception {
 		try {
@@ -66,12 +54,10 @@ public class GeneVariationTest {
 			GeneVariation gv = new GeneVariation();
 
 			gv.setModifiedDna(modifiedDna);
-			gv.addReference(new MiriamData());
 
 			GeneVariation copy = gv.copy();
 
 			assertEquals(gv.getModifiedDna(), copy.getModifiedDna());
-			assertEquals(1, copy.getReferences().size());
 		} catch (Exception e) {
 			e.printStackTrace();
 			throw e;

service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java

@@ -655,11 +655,6 @@ public class LayoutService implements ILayoutService {
             sb.append(schema.getGeneVariations().get(0).getReferenceGenomeVersion() + "\t");
         } else if (column.equals(ColorSchemaColumn.CONTIG)) {
             sb.append(schema.getGeneVariations().get(0).getContig() + "\t");
-        } else if (column.equals(ColorSchemaColumn.REFERENCES)) {
-            MiriamConnector mc = new MiriamConnector();
-            for (MiriamData md : schema.getGeneVariations().get(0).getReferences()) {
-                sb.append(mc.miriamDataToUri(md) + "\t");
-            }
         } else {
             throw new InvalidArgumentException("Unknown column type: " + column + " for schema type: " + schema.getClass());
         }

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

@@ -177,7 +177,6 @@ public class ColorSchemaReader {
       Integer originalDnaColumn = schemaColumns.get(ColorSchemaColumn.ORIGINAL_DNA);
       Integer alternativeDnaColumn = schemaColumns.get(ColorSchemaColumn.ALTERNATIVE_DNA);
       Integer descriptionColumn = schemaColumns.get(ColorSchemaColumn.DESCRIPTION);
-      Integer referencesColumn = schemaColumns.get(ColorSchemaColumn.REFERENCES);
       Integer referenceGenomeTypeColumn = schemaColumns.get(ColorSchemaColumn.REFERENCE_GENOME_TYPE);
       Integer referenceGenomeVersionColumn = schemaColumns.get(ColorSchemaColumn.REFERENCE_GENOME_VERSION);
       Integer aminoAcidChangeColumn = schemaColumns.get(ColorSchemaColumn.AMINO_ACID_CHANGE);
@@ -273,16 +272,6 @@ public class ColorSchemaReader {
           if (aminoAcidChangeColumn != null) {
             gv.setAminoAcidChange(values[aminoAcidChangeColumn]);
           }
-          if (referencesColumn != null) {
-            String[] references = values[referencesColumn].split(";");
-            for (String string : references) {
-              try {
-                gv.addReference(MiriamType.getMiriamByUri(string));
-              } catch (InvalidArgumentException e) {
-                throw new InvalidColorSchemaException("[Line " + lineIndex + "] Invalid reference: " + string, e);
-              }
-            }
-          }
           if (referenceGenomeTypeColumn != null) {
             gv.setReferenceGenomeType(extractReferenceGenomeType(values[referenceGenomeTypeColumn]));
           } else {

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

@@ -53,7 +53,7 @@ public enum ColorSchemaColumn {
   /**
    * Identifier of the element.
    */
-  IDENTIFIER(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+  IDENTIFIER("references",new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
 
   /**
    * Element identifier.
@@ -91,11 +91,6 @@ public enum ColorSchemaColumn {
    */
   DESCRIPTION(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }),
 
-  /**
-   * Variant references.
-   */
-  REFERENCES(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
-
   /**
    * What's the {@link ReferenceGenomeType}.
    */