Changeset 4631

Timestamp:

Nov 7, 2008, 12:06:05 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1167: Base1PluginExecutor should handle reporter-id=0 as null in some cases

Test case converts all empty reporter values to 0.

Location:

trunk/src

Files:

• plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (3 diffs)
• test/Base1TestPlugin.java (modified) (1 diff)

trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -1339 +1339 @@
     // Position -> ReporterID mapping for the parent bioassay set
     Map<Integer, Integer> parentReporterPositions = new HashMap<Integer, Integer>();
+    boolean parentHasNullReporter = false;
+    boolean parentHasZeroReporter = false;
+    boolean mapZeroToNull = false;
+
     // Position -> ReporterID mapping for the child bioassay set
     Map<Integer, Integer> childReporterPositions = new HashMap<Integer, Integer>();
@@ -1466 +1470 @@
           {
             SqlResult result = positionQueryIterator.next();
-            parentReporterPositions.put(result.getInt(1), (Integer)result.getObject(2));
-          }
+            Integer reporterId = (Integer)result.getObject(2);
+            if (reporterId == null) 
+            {
+              parentHasNullReporter = true;
+            }
+            else if (reporterId.intValue() == 0)
+            {
+              parentHasZeroReporter = true;
+            }
+            parentReporterPositions.put(result.getInt(1), reporterId);
+          }
+          
+          
+          // If we have null reporter (but none with ID=0) in the export
+          // we may need to convert 0->null when importing since some
+          // BASE1 plug-ins convert null -> 0
+          mapZeroToNull = parentHasNullReporter && !parentHasZeroReporter;
         }
 
@@ -1528 +1547 @@
                 ffp.getParsedLines() + " in file '" + stdout.getName() + "'");
           }
-          
+          // Convert 0 -> null since some BASE1 plug-ins convert null -> 0
+          if (mapZeroToNull && newReporterId != null && newReporterId.intValue() == 0)
+          {
+            newReporterId = null;
+          }
+
           // Is the new reporter the same as the existing?
           // A 'null' reporter is considered the same as another 'null' reporter

trunk/src/test/Base1TestPlugin.java

@@ -131 +131 @@
           {
             FlatFileParser.Data data = ffp.nextData();
-            System.out.println(offset + data.line());
+            System.out.println(offset + data.line().replaceFirst("\\t\\t", "\t0\t"));
           }
           System.out.println();