Changeset 5201

Timestamp:

Dec 16, 2009, 10:33:25 AM (13 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1447: Annotation importer should have "crop" option for the "Too many values" error handling option

Location:

branches/2.14-stable/src

Files:

• plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java (modified) (6 diffs)
• test/TestAnnotationFlatFileImporter.java (modified) (2 diffs)
• test/data/test.annotation.import.txt (modified) (1 diff)

branches/2.14-stable/src/plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java

@@ -312 +312 @@
     "If no value is specified the default error handling is used.\n\n"+
     "skip = Skip the current annotation and continue\n"+
+    "crop = Use as many values as the annotation type allows and discard the rest\n" + 
     "fail = Stop with an error message",
-    new StringParameterType(255, null, false, 1, 0, 0, 
-        Arrays.asList( new String[] { "skip", "fail"} ))
+    new StringParameterType(255, "crop", false, 1, 0, 0, 
+        Arrays.asList( new String[] { "skip", "crop", "fail"} ))
     );  
 
@@ -617 +618 @@
   private boolean failIfMultipleFoundItems;
   private boolean failIfTooManyValues;
+  private boolean cropTooManyValues;
   
   // Messaging
@@ -680 +682 @@
     this.cropStrings = "crop".equals(job.getValue("stringTooLongError"));
     this.failIfTooManyValues = "fail".equals(getErrorOption("tooManyValuesError"));
+    this.cropTooManyValues = "crop".equals(job.getValue("tooManyValuesError"));
     
     ErrorHandler defaultErrorHandler = new SimpleErrorHandler("skip".equals(job.getValue("defaultError")));
@@ -855 +858 @@
           {
             // Add annotation value to the cache
-            item.addValue(at, annotationValue, unit);
+            item.addValue(at, annotationValue, unit, cropTooManyValues);
           }
         }
@@ -1270 +1273 @@
       error before calling this method.
     */
-    void addValue(AnnotationType at, Object value, Unit unit)
+    void addValue(AnnotationType at, Object value, Unit unit, boolean limitToMultiplicty)
     {
       List<AnnotationValue> listOfValues = values.get(at);
@@ -1277 +1280 @@
         listOfValues = new LinkedList<AnnotationValue>();
         values.put(at, listOfValues);
+      }
+      // If "Too many values"=crop we check how many is allowed by the annotation type
+      // and don't allow the list to grow larger
+      if (limitToMultiplicty)
+      {
+        int multiplicity = at.getMultiplicity();
+        if (multiplicity > 0 && listOfValues.size() >= multiplicity) value = null;
       }
       if (value != null) 

branches/2.14-stable/src/test/TestAnnotationFlatFileImporter.java

@@ -89 +89 @@
     // Test: list the result
     TestAnnotation.test_list_annotations(Item.SAMPLE, sample1, 4);
-    TestAnnotation.test_list_annotations(Item.SAMPLE, sample2, 2);
+    TestAnnotation.test_list_annotations(Item.SAMPLE, sample2, 3);
     TestAnnotation.test_list_annotations(Item.SAMPLE, sample3, 2);
     TestAnnotation.test_list_annotations(Item.SAMPLE, sample4, 2);
     TestAnnotation.test_list_annotations(Item.SAMPLE, sampleDup1, 4);
     TestAnnotation.test_list_annotations(Item.SAMPLE, sampleDup2, 4);
+    ok &= TestAnnotation.ok;
     
     if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
@@ -168 +169 @@
       request.setParameterValue("numberOutOfRangeError", "skip");
       request.setParameterValue("invalidEnumError", "skip");
-      request.setParameterValue("tooManyValuesError", "skip");
+      request.setParameterValue("tooManyValuesError", "crop");
       request.setParameterValue("multipleItemsFoundError", "all");
       response = request.invoke();

branches/2.14-stable/src/test/data/test.annotation.import.txt

@@ -5 +5 @@
 Sample #2 24  xx  BETA  Bad Not so bad
 # Test: multiple annotations on separate lines; long string that should be cropped
+#       'Too many values = crop' option should keep the 24 from previous line
 Sample #2 18      Yet another comment And one more which is too long and will be cropped
 # Test: number out of range: -12; float conversion to int; invalid enum: Gamm