[Obo-svn-commit] SF.net SVN: obo: [1517] phenote/trunk/src/java/phenote/dataadapter/ delimited

[<mg...@us...>]

Revision: 1517
          http://obo.svn.sourceforge.net/obo/?rev=1517&view=rev
Author:   mgibson
Date:     2008-02-15 11:24:45 -0800 (Fri, 15 Feb 2008)

Log Message:
-----------
fixed bug where if tabs deleted in a line delim would choke
now just skips - 
todo - give better error message and read in partial line
but at least now it will read rest of file and not collapse

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/dataadapter/delimited/DelimFieldParser.java
    phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java

Modified: phenote/trunk/src/java/phenote/dataadapter/delimited/DelimFieldParser.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/delimited/DelimFieldParser.java	2008-02-15 00:21:38 UTC (rev 1516)
+++ phenote/trunk/src/java/phenote/dataadapter/delimited/DelimFieldParser.java	2008-02-15 19:24:45 UTC (rev 1517)
@@ -64,11 +64,20 @@
 
   private boolean isTerm() { return charField.isTerm(); }
 
-  void parseField(String items[],CharacterI chr) {
+  void parseField(String items[],CharacterI chr) throws DelimitedEx {
+    if (columnIndex >= items.length)
+      throw new DelimitedEx("No more fields in line to parse "+items+" "+chr);
     // if term, first id then name
     String value = items[columnIndex];
     try {
-      String danglerName = charField.isTerm() ? items[columnIndex+1] : null;
+      String danglerName = null;
+      // if it is a term then grab next item for dangler name, but 
+      if (charField.isTerm()) {
+        //look out for mangled data that lacks a term name (user mutzed)
+        if (columnIndex+1 >= items.length)
+          throw new DelimitedEx("No more fields in line to parse "+items+" "+chr);
+        danglerName = items[columnIndex+1];
+      }
       CharFieldValue cfv = chr.setValue(charField,value,danglerName);
       // if term, and id not found, dangler -> set name of dangler
       //if (cfv.isDangler()) // throw error if not term?

Modified: phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java	2008-02-15 00:21:38 UTC (rev 1516)
+++ phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java	2008-02-15 19:24:45 UTC (rev 1517)
@@ -173,6 +173,8 @@
     String[] items = splitLine(line);
     if (items.length==0) throw new DelimitedEx(line); // BlankEx?
     for (DelimFieldParser p : fieldParsers) {
+      // throws DelEx if array not long enough for Parser (missing tabs)
+      // should ex be caught and go on?
       p.parseField(items,character); // add cfv to char or ret cfv?
     }
   }


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