Changeset 2640

Timestamp:

02/14/10 20:07:12 (2 years ago)

Author:

jvelde

Message:

Hopefully resolved the bug where values of previous line are copied unintentionally to next line's null values.

File:

• molgenis/3.3/src/org/molgenis/util/CsvBufferedReader.java (modified) (16 diffs)

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

@@ -19 +19 @@
 {
         /** default separators */
-        public static char[] separators =
-        { ',', '\t', ';', ' ' };
+        public static char[] separators = {',', '\t', ';', ' '};
 
         /** Wrapper around the resource that is read */
@@ -60 +59 @@
          * @param reader
          */
-        public CsvBufferedReader(BufferedReader reader)
-        {
+        public CsvBufferedReader(BufferedReader reader) {
                 this.reader = reader;
         }
@@ -160 +158 @@
                 {
                         // colnames[0] = ROWNAME_COLUMN;
-                }
-                else if (dataline.length > colnames.length + 1)
-                {
-                        throw new Exception(
-                                        "Data has more columns than there are headers ("
-                                                        + dataline.length
-                                                        + ">"
-                                                        + colnames.length
-                                                        + "). Only the first column may be empty. Check whether you have data separators in your data values");
+                } else if (dataline.length > colnames.length + 1)
+                {
+                        throw new Exception("Data has more columns than there are headers (" + dataline.length + ">" + colnames.length
+                                        + "). Only the first column may be empty. Check whether you have data separators in your data values");
                 }
 
@@ -179 +172 @@
                 for (String header : result)
                 {
-                        if (header.length() == 0 && result.indexOf(header) != 0) throw new IOException(
-                                        "nameless header found at index " + result.indexOf(header) + ": " + result);
+                        if (header.length() == 0 && result.indexOf(header) != 0)
+                                throw new IOException("nameless header found at index " + result.indexOf(header) + ": " + result);
                 }
 
@@ -207 +200 @@
         {
                 List<String> headers = null;
-                if (hasHeader) headers = colnames();
+                if (hasHeader)
+                        headers = colnames();
                 String line;
                 if (this.separator == 0)
@@ -223 +217 @@
                         // skip to start
                         goToBlockStart(reader);
-                        if (hasHeader) line = reader.readLine(); // skip header line
+                        if (hasHeader)
+                                line = reader.readLine(); // skip header line
                         this.isParsing = true;
 
                         logger.debug("parsing with separator = '" + separator + "' and headers =" + headers);
-                }
-                else
+                } else
                 {
                         logger.debug("restarted parsing with limit " + noElements);
@@ -239 +233 @@
                 // template of the tuple
                 Tuple t;
-                if (hasHeader) t = new SimpleTuple(headers);
+                if (hasHeader)
+                        t = new SimpleTuple(headers);
                 else
                         t = new SimpleTuple();
@@ -251 +246 @@
                         {
                                 logger.warn("found empty line: " + lineCount);
-                        }
-                        else if (rows == null || rows.contains(lineCount))
+                        } else if (rows == null || rows.contains(lineCount))
                         {
 
@@ -265 +259 @@
                                 if (hasHeader && values.length > headers.size())
                                 {
-                                        throw new Exception("Row " + lineCount + " has more columns than there are headers ("
-                                                        + values.length + ">" + headers.size() + "). Put double \" around columns that have '"
+                                        throw new Exception("Row " + lineCount + " has more columns than there are headers (" + values.length + ">" + headers.size() + "). Put double \" around columns that have '"
                                                         + separator + "' in their value. \nRow is: " + line);
                                 }
@@ -285 +278 @@
                                 // 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];
+                                // FIX 2: in fact, this applies to any character shorter than
+                                // header length.. ie. whole null lines are copied over with
+                                // values from the previous line! hopefully fixed now.
+                                if (values.length < headers.size())
+                                {
+                                        String[] valuesNew = new String[values.length + headers.size()];
                                         for (int i = 0; i < values.length; i++)
                                         {
                                                 valuesNew[i] = values[i];
                                         }
-                                        valuesNew[values.length] = null;
+                                        
+                                        for(int i = values.length; i < values.length+headers.size(); i++){
+                                                valuesNew[i] = null;
+                                        }
+                                        
+                                //      valuesNew[values.length] = null;
+                                        
                                         values = valuesNew;
                                 }
@@ -305 +307 @@
                                         {
                                                 logger.warn("EMPTY LINE on " + lineCount + ", skipped.");
-                                        }
-                                        else
+                                        } else
                                         {
                                                 try
                                                 {
                                                         listener.handleLine(lineCount, t);
-                                                }
-                                                catch (Exception e)
+                                                } catch (Exception e)
                                                 {
                                                         // e.printStackTrace();
@@ -439 +439 @@
                 // if(separator != 0) return separator;
 
-                if (aLine == null || aLine.length() == 0) throw new IOException("could not guess separator from line '" + aLine
-                                + "'");
+                if (aLine == null || aLine.length() == 0)
+                        throw new IOException("could not guess separator from line '" + aLine + "'");
 
                 char result = '\t';
@@ -459 +459 @@
                                         sep_count++;
                                         startIndex = index + 1;
-                                }
-                                else
+                                } else
                                 {
                                         break; // no more separators found
@@ -499 +498 @@
                         while ((line = in.readLine()) != null)
                         {
-                                if (line.startsWith(blockStart)) return;
+                                if (line.startsWith(blockStart))
+                                        return;
                                 // FIXME: make regexp?
                         }
@@ -516 +516 @@
         private boolean isBlockEnd(String line)
         {
-                if (line.equals(blockEnd)) return true;
+                if (line.equals(blockEnd))
+                        return true;
                 return false;
         }
@@ -555 +556 @@
         {
                 List<String> colnames = this.colnames();
-                if (colnames.contains(from)) colnames.set(colnames.indexOf(from), to);
+                if (colnames.contains(from))
+                        colnames.set(colnames.indexOf(from), to);
                 else
                 {