Changeset 2638

Timestamp:

02/12/10 13:25:24 (2 years ago)

Author:

jvelde

Message:

Fixed a bug that caused copies of values in empty slots because of a split that returns a smaller array in case of empty values, causing values to be left behind that should be overwritten with nulls.

File:

• molgenis/3.3/src/org/molgenis/util/CsvBufferedReader.java (modified) (7 diffs)

molgenis/3.3/src/org/molgenis/util/CsvBufferedReader.java

@@ -191 +191 @@
         }
 
-        public List<Object> getForHeader(String header){
-                //TODO: very simple function, just return a single column in the form of a list by a header name
+        public List<Object> getForHeader(String header)
+        {
+                // TODO: very simple function, just return a single column in the form
+                // of a list by a header name
                 return null;
         }
-        
-        public int parse(int noElements,  CsvReaderListener... listeners) throws Exception
+
+        public int parse(int noElements, CsvReaderListener... listeners) throws Exception
         {
                 return this.parse(noElements, null, listeners);
         }
-        
+
         // @Override
         public int parse(int noElements, List<Integer> rows, CsvReaderListener... listeners) throws Exception
-        {               
+        {
                 List<String> headers = null;
                 if (hasHeader) headers = colnames();
@@ -234 +236 @@
                 int lineCount = 0;
                 // int index;
-                
+
                 // template of the tuple
                 Tuple t;
-                if (hasHeader) t = new SimpleTuple(headers); 
-                else t = new SimpleTuple();
-                
+                if (hasHeader) t = new SimpleTuple(headers);
+                else
+                        t = new SimpleTuple();
+
                 while (lineCount < noElements && (line = reader.readLine()) != null && !isBlockEnd(line))
                 {
@@ -249 +252 @@
                                 logger.warn("found empty line: " + lineCount);
                         }
-                        else if(rows == null || rows.contains(lineCount))
+                        else if (rows == null || rows.contains(lineCount))
                         {
 
@@ -276 +279 @@
                                 }
 
+                                // FIX:
+                                // if the last character is empty; split does not return the
+                                // last character, values[] is one character too short; then
+                                // missing character is not overwritten with null, causing wrong
+                                // values in subsequent last columns: previous values are
+                                // copied into empty next ones until a new non-empty one
+                                if (values.length == headers.size() - 1)
+                                {
+                                        String[] valuesNew = new String[values.length + 1];
+                                        for (int i = 0; i < values.length; i++)
+                                        {
+                                                valuesNew[i] = values[i];
+                                        }
+                                        valuesNew[values.length] = null;
+                                        values = valuesNew;
+                                }
+
                                 t.set(values);
-                                // logger.debug("found: " + t.toString());
+                                // logger.info("found: " + t.toString());
 
                                 // handle the tuple by all handlers
@@ -294 +314 @@
                                                 catch (Exception e)
                                                 {
-                                                        //e.printStackTrace();
+                                                        // e.printStackTrace();
                                                         logger.error("parsing of row " + lineCount + " failed: " + e);
                                                         throw new Exception("parse error on line " + lineCount + ": " + e.getMessage());
@@ -311 +331 @@
                 return this.parse(Integer.MAX_VALUE, listeners);
         }
-        
+
         @Override
         public int parse(List<Integer> rows, CsvReaderListener... listeners) throws Exception
@@ -333 +353 @@
          */
         private String[] split(String string, char separator)
-        {       
+        {
                 // FIXME: need to trim esp if there are spaces leading up to a \"
                 char escape = '"';