Merge branch '835-add-gene-mapping' into 'devel_13.1.x'

Resolve "MINERVANET - Error Report 77"

See merge request minerva/core!826

CHANGELOG

+minerva (13.1.1) stable; urgency=medium
+  * Bug fix: adding gene mapping before the genome caused an error (#835)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 28 Jun 2019 17:00:00 +0200
+
 minerva (13.1.0) stable; urgency=medium
   * Feature: annotators are more flexible - you can define set of input and
     outputs used by annotator (#617)

frontend-js/src/main/js/gui/admin/EditGenomeDialog.js

@@ -175,7 +175,8 @@ EditGenomeDialog.prototype.createGeneMappingTabContent = function () {
 
   var result = Functions.createElement({
     type: "div",
-    style: "margin-top:10px;"
+    style: "margin-top:10px;",
+    className: "minerva-gene-mapping-tab"
   });
 
   var geneMappingTable = Functions.createElement({
@@ -513,6 +514,10 @@ EditGenomeDialog.prototype.refresh = function () {
     //it should be simplified, but I couldn't make it work
     dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
 
+    if (self.isNew()) {
+      guiUtils.disableTab($(".minerva-gene-mapping-tab", self.getElement())[0], "First add a genome to be able to add mapping");
+    }
+
     return self._fillOrganismSelect(genome);
   });
 };

rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java

@@ -491,7 +491,7 @@ public abstract class BaseRestImpl {
     return result;
   }
 
-  protected Integer parseInteger(Object value) throws QueryException {
+  protected Integer parseInteger(Object value, String fieldName) throws QueryException {
     if (value instanceof Integer) {
       return (Integer) value;
     } else if (value instanceof Double) {
@@ -506,12 +506,16 @@ public abstract class BaseRestImpl {
         try {
           return Integer.parseInt((String) value);
         } catch (NumberFormatException e) {
-          throw new QueryException("Invalid integer value: " + value);
+          throw new QueryException("Invalid " + fieldName + " value: " + value);
         }
       }
     } else {
-      throw new QueryException("Invalid integer value: " + value);
+      throw new QueryException("Invalid " + fieldName + " value: " + value);
     }
   }
 
+  protected Integer parseInteger(Object value) throws QueryException {
+    return parseInteger(value, "integer");
+  }
+
 }

rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java

@@ -256,8 +256,9 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
     if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
       throw new SecurityException("Access denied");
     }
+    
 
-    int id = Integer.parseInt(genomeId);
+    int id = parseInteger(genomeId, "genomeId");
     try {
       ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(id, token);
       String name = getFirstValue(formData.get("name"));