Merge branch 'migration-script-issues' into 'master'

Migration script issues

See merge request !1289

persist/src/main/java/lcsb/mapviewer/persist/migration/V16_0_0_20200922_2__generic_article_data_migration.java

@@ -78,7 +78,11 @@ public abstract class V16_0_0_20200922_2__generic_article_data_migration extends
               insert.setString(3, article.getJournal());
               insert.setString(4, article.getLink());
               insert.setString(5, article.getTitle());
-              insert.setInt(6, article.getYear());
+              if (article.getYear() == null) {
+                insert.setNull(6, Types.INTEGER);
+              } else {
+                insert.setInt(6, article.getYear());
+              }
               if (insert.executeUpdate() == 0) {
                 logger.error("Problem with migrating cached article data: " + xmlArticle);
               } else {
@@ -104,7 +108,7 @@ public abstract class V16_0_0_20200922_2__generic_article_data_migration extends
               }
             }
           } catch (Exception e) {
-            logger.error("Problem with migrating cached article data: " + xmlArticle);
+            logger.error("Problem with migrating cached article data: " + xmlArticle, e);
           }
         }
       }
@@ -113,7 +117,7 @@ public abstract class V16_0_0_20200922_2__generic_article_data_migration extends
     }
 
     try (Statement select = context.getConnection().createStatement()) {
-      select.executeQuery("delete from cache_query_table where query like 'pubmed:%'");
+      select.executeUpdate("delete from cache_query_table where query like 'pubmed:%'");
     } catch (Exception e) {
       logger.error("Problem with purgining cached article data", e);
     }

persist/src/main/java/lcsb/mapviewer/persist/migration/V16_0_0_20200930_2__generic_data_overlay_entry_data.java

@@ -98,6 +98,10 @@ public abstract class V16_0_0_20200930_2__generic_data_overlay_entry_data extend
   private void addEntries(Integer overlayId, Set<? extends DataOverlayEntry> entries, Context context)
       throws SQLException {
     for (DataOverlayEntry dataOverlayEntry : entries) {
+      if (dataOverlayEntry.getName() != null && dataOverlayEntry.getName().length() > 255) {
+        logger.warn("Data overlay entry with too long name. Skipping: \"" + dataOverlayEntry.getName() + "\"");
+        continue;
+      }
       String distinguisher = "GENERIC_DATA_OVERLAY";
       if (dataOverlayEntry instanceof GeneVariantDataOverlayEntry) {
         distinguisher = "GENE_VARIANT_DATA_OVERLAY";
@@ -325,7 +329,7 @@ public abstract class V16_0_0_20200930_2__generic_data_overlay_entry_data extend
             result.add(extractGenericEntry(entry, columns, line.split("\t", -1)));
           } catch (Exception e) {
             logger.error("Problem with creating entry. Line:\n" + line + "\nColumns: "
-                + StringUtils.join(Arrays.asList(columns), "\t"));
+                + StringUtils.join(Arrays.asList(columns), "\t"), e);
           }
         }
         line = br.readLine();
@@ -342,7 +346,7 @@ public abstract class V16_0_0_20200930_2__generic_data_overlay_entry_data extend
     for (int i = 0; i < columns.length; i++) {
       String column = columns[i].trim().toLowerCase();
       String value = null;
-      //there might be some broken entries
+      // there might be some broken entries
       if (data.length > i) {
         value = data[i];
       }
@@ -425,7 +429,7 @@ public abstract class V16_0_0_20200930_2__generic_data_overlay_entry_data extend
           }
           break;
         case "color":
-          entry.setColor(colorParser.parse(value));
+          entry.setColor(colorParser.parse(value.trim()));
           break;
         case "references":
         case "identifier":