colouring by column identifier_xxx did not work for genetic variants

CHANGELOG

@@ -9,6 +9,8 @@ minerva (14.0.6) stable; urgency=medium
     project removal doesn't hang (#1058)
   * Bug fix: coloring of the reaction wasn't applied to center of reaction
     (regression 14.0.0, #1057)
+  * Bug fix: genetic variant overlay improperly processed elements identified
+    by miriam identifiers, like uniprot (#1059)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 18 Dec 2019 12:00:00 +0200
 

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

@@ -81,9 +81,7 @@ public class ColorSchemaReader {
     if (Integer.valueOf(params.get(TextFileUtils.COLUMN_COUNT_PARAM)) == 1) {
       return readSimpleNameColorSchema(colorInputStream);
     } else if (params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) == null) {
-      {
-        return readGenericColorSchema(colorInputStream);
-      }
+      return readGenericColorSchema(colorInputStream);
     } else {
       ColorSchemaType type = null;
       try {
@@ -393,10 +391,10 @@ public class ColorSchemaReader {
   private Collection<ColorSchema> mergeSchemas(Collection<ColorSchema> schemas) {
     Map<String, ColorSchema> schemasByName = new HashMap<>();
     for (ColorSchema colorSchema : schemas) {
-      ColorSchema mergedSchema = schemasByName.get(colorSchema.getName());
+      ColorSchema mergedSchema = schemasByName.get(getColorSchemaIdentifiablePart(colorSchema));
       if (mergedSchema == null) {
         mergedSchema = colorSchema.copy();
-        schemasByName.put(colorSchema.getName(), mergedSchema);
+        schemasByName.put(getColorSchemaIdentifiablePart(colorSchema), mergedSchema);
       } else {
         if (mergedSchema instanceof GeneVariationColorSchema) {
           if (colorSchema instanceof GeneVariationColorSchema) {
@@ -420,6 +418,16 @@ public class ColorSchemaReader {
     return schemasByName.values();
   }
 
+  private String getColorSchemaIdentifiablePart(ColorSchema colorSchema) {
+    List<String> identifiers = new ArrayList<>();
+    for (MiriamData md : colorSchema.getMiriamData()) {
+      identifiers.add(md.toString());
+    }
+    Collections.sort(identifiers);
+
+    return StringUtils.join(identifiers, "\n") + "\n" + colorSchema.getName();
+  }
+
   /**
    * Gets color that should be assigned to {@link GeneVariationColorSchema}.
    * 
@@ -771,7 +779,7 @@ public class ColorSchemaReader {
       if (schema.getLineWidth() != null) {
         result.add(ColorSchemaColumn.LINE_WIDTH);
       }
-      if (schema.getName() != null) {
+      if (getColorSchemaIdentifiablePart(schema) != null) {
         result.add(ColorSchemaColumn.NAME);
       }
       if (schema.getModelName() != null) {

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

@@ -376,4 +376,18 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
     reader.readColorSchema(fis, TextFileUtils.getHeaderParametersFromFile(fis2));
 
   }
+
+  @Test
+  public void testGeneticVariantByUniprotIdentifier() throws Exception {
+    File f = new File("testFiles/coloring/uniprot-identifiers.txt");
+    byte[] data = fileToByteArray(f);
+
+    ByteArrayInputStream bin = new ByteArrayInputStream(data);
+
+    Collection<ColorSchema> schemas = reader.readColorSchema(bin,
+        TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
+    assertNotNull(schemas);
+    assertEquals(2, schemas.size());
+  }
+
 }

service/testFiles/coloring/uniprot-identifiers.txt

+#TYPE=GENETIC_VARIANT						
+#GENOME_VERSION=hg19						
+#GENOME_TYPE=UCSC						
+position	original_DNA	alternative_DNA	contig	allele_frequency	color	identifier_uniprot
+90648003	T	G	4	0.3750000	#e58e00	P14416
+90656320	T	C	4	0.7034621	#e58e00	P14416
+90755218	G	A	4	0.1379310	#e58ec5	P02511
+161709831	G	T	6	0.6025862	#e58ec5	P02511
+162525131	G	T	6	0.7025762	#e58ec5	P02511