Changeset 3911

Timestamp:

Nov 6, 2007, 9:42:09 AM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #811: Wildcard or regular expressions in raw data column mappings

To be consistent with exact name matching the first column found is always returned

Location:

trunk

Files:

• doc/src/docbook/admindoc/plugin_installation.xml (modified) (1 diff)
• src/core/net/sf/basedb/util/parser/ColFunction.java (modified) (4 diffs)
• src/core/net/sf/basedb/util/parser/FlatFileParser.java (modified) (5 diffs)

trunk/doc/src/docbook/admindoc/plugin_installation.xml

@@ -1372 +1372 @@
               mapping has better performance and we recommend that you use
               it unless you have to recalculate any of the numerical values.
+              In both cases, if no column matching the placeholder exactly is found 
+              the placeholder is interpreted as a regular expression that
+              is matched against each column. The first one found is used.
               Here are a few mapping examples:
             </para>
             
 <informalexample>
-<literallayout>\Name\
-\1\
-[\row\, \column\]
-=2 * col('radius')
+<literallayout>\Name\ --&gt; exact match is required
+\1\ --&gt; column with index 1 (the second column)
+[\row\, \column\] --&gt; combining row and column to a single coordinate
+=2 * col('radius') --&gt; calculate the diameter dynamically
+\F63(3|5) Median\ --&gt; use regular expression to match either F633 or F635
 </literallayout>
 </informalexample>

trunk/src/core/net/sf/basedb/util/parser/ColFunction.java

@@ -26 +26 @@
 import java.text.NumberFormat;
 import java.text.ParsePosition;
-import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Stack;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
 
 import org.nfunk.jep.ParseException;
@@ -76 +78 @@
     this.numberFormat = numberFormat;
     this.pos = new ParsePosition(0);
-    this.columnHeaders = new HashMap<String, Integer>(columnHeaders.size());
+    this.columnHeaders = new LinkedHashMap<String, Integer>(columnHeaders.size());
     int index = 0;
     for (String header : columnHeaders)
@@ -133 +135 @@
       String colName = (String)argument;
       Integer column = columnHeaders.get(colName);
-      if (column != null)
-      {
-        value = data.get(column);
-      }
-      else
+      if (column == null) column = findColumn(colName);
+      if (column == null)
       {
         throw new BaseException("Column '" + colName + "' not found in column headers.");
       }
+      value = data.get(column);
     }
     else
@@ -180 +180 @@
     this.data = data;
   }
+  
+  /**
+    Find column index by checking each column header against a
+    regular expression. The first match found is returned. The
+    map is updated with a new regex -> index entry.
+    @return The column index or null if no column is found or if the 
+      string is not a valid regular expression
+  */
+  private Integer findColumn(String regex)
+  {
+    try
+    {
+      Pattern p = Pattern.compile(regex);
+      Integer index = null;
+      for (Map.Entry<String, Integer> entry : columnHeaders.entrySet())
+      {
+        String column = entry.getKey();
+        if (p.matcher(column).matches())
+        {
+          index = entry.getValue();
+          break;
+        }
+      }
+      if (index != null) columnHeaders.put(regex, index);
+      return index;
+    }
+    catch (PatternSyntaxException ex)
+    {
+      return null;
+    }
+  }
 
 }

trunk/src/core/net/sf/basedb/util/parser/FlatFileParser.java

@@ -35 +35 @@
 import java.util.regex.Pattern;
 import java.util.regex.Matcher;
+import java.util.regex.PatternSyntaxException;
 import java.util.Arrays;
 import java.util.LinkedList;
@@ -765 +766 @@
     @param name The name of the column header
     @return The index, or null if no header with that name exists
+    @see #findColumnHeaderIndex(String)
   */
   public Integer getColumnHeaderIndex(String name)
@@ -770 +772 @@
     int index = columnHeaders.indexOf(name);
     return index >= 0 ? index : null;
+  }
+  
+  /**
+    Find the index of a column header using a regular expression for pattern
+    matching. This method should only be called after {@link #parseHeaders()} 
+    has been called. If more than one header matches the regular expression
+    only the first one found is returned.
+    
+    @param regex The regular expression used to match the header names
+    @return The index, or null if no header is matching the regular expression
+      or if the string is not a valid regular expression
+    @see #getColumnHeaderIndex(String)
+    @since 2.5
+  */
+  public Integer findColumnHeaderIndex(String regex)
+  {
+    try
+    {
+      Pattern p = Pattern.compile(regex);
+      int index = 0;
+      for (String column : columnHeaders)
+      {
+        if (p.matcher(column).matches()) return index;
+        ++index;
+      }
+    }
+    catch (PatternSyntaxException ex)
+    {}
+    return null;
   }
   
@@ -852 +883 @@
 =2 * col('Radius')
 </pre>
-
+    If no column that is matching the exact name is found the placeholder
+    is interpreted as a regular expression which is checked against each of
+    the column headers. In all cases, the first column header found is used
+    if there are multiple matches.
+    <p>
     If the expression is null, a mapper returning en empty string is returned, 
-    unless the {@link #setUseNullIfEmpty(boolean)} has been activeted. In that
+    unless the {@link #setUseNullIfEmpty(boolean)} has been activated. In that
     case the mapper returns null.
 
@@ -899 +934 @@
           {
             String name = m.group(1);
-            int column = columnHeaders.indexOf(name);
-            if (column >= 0) 
-            {
-              mappers.add(new ColumnMapper(column, name, numberFormat, nullIfException));
-            }
-            else
+            Integer column = getColumnHeaderIndex(name);
+            if (column == null) column = findColumnHeaderIndex(name);
+            if (column == null)
             {
               throw new BaseException("Column '" + name + "' not found in column headers.");
             }
+            mappers.add(new ColumnMapper(column, name, numberFormat, nullIfException));
           }
         }