Merge branch '833-reupload-overlay-issue' into 'devel_13.1.x'

Resolve "reuploading of an overlay and incorrect error thrown"

See merge request !800

CHANGELOG

@@ -9,6 +9,10 @@ minerva (12.3.1~beta.1) unstable; urgency=low
   * Bug fix: invisible layer shouldn't be shown in the on th map (#813)
   * Bug fix: list of availbale annotators is sorted alphabetically (#815)
   * Bug fix: redirect url from export panel is fixed (#819)
+  * Bug fix: allow to reupload the same file without closing add overlay dialog
+    (#833)
+  * Bug fix: gene_name column is allowed only in the genetic variant data 
+    overlay
   * Bug fix: protein types are sorted properly in "Select valid annotations"
     dialog (#815)
   * Bug fix: if there is a description of (sub)map then it is available in

frontend-js/src/main/js/gui/AddOverlayDialog.js

@@ -94,7 +94,9 @@ AddOverlayDialog.prototype.createGui = function () {
     name: "overlay-file"
   });
   fileInput.addEventListener("change", function () {
-    return self.processFile(fileInput.files[0]).then(null, GuiConnector.alert);
+    return self.processFile(fileInput.files[0]).then(function () {
+      $(fileInput).val("");
+    }).catch(GuiConnector.alert);
   }, false);
   content.appendChild(fileInput);
   content.appendChild(guiUtils.createNewLine());

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

@@ -162,6 +162,9 @@ public class ColorSchemaReader {
       Integer nameColumn = schemaColumns.get(ColorSchemaColumn.NAME);
       if (nameColumn == null) {
         nameColumn = schemaColumns.get(ColorSchemaColumn.GENE_NAME);
+      } else if (schemaColumns.get(ColorSchemaColumn.GENE_NAME) != null) {
+        throw new InvalidColorSchemaException(ColorSchemaColumn.GENE_NAME + " and " + ColorSchemaColumn.NAME
+            + " column cannot appear in the same dataset");
       }
       Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MODEL_NAME);
       Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER);
@@ -292,7 +295,7 @@ public class ColorSchemaReader {
           gv.setContig(values[contigColumn]);
 
           schema.addGeneVariation(gv);
-          if (schema.getName()!=null && schema.getName().contains(";")) {
+          if (schema.getName() != null && schema.getName().contains(";")) {
             String[] names = schema.getName().split(";");
             for (String string : names) {
               if (!string.trim().isEmpty()) {

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

@@ -21,7 +21,7 @@ public enum ColorSchemaColumn {
    */
   NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
 
-  GENE_NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+  GENE_NAME(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
 
   /**
    * Name of the element.