Thread: [Netcdftools-commit] SF.net SVN: netcdftools:[22] trunk/src

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Revision: 22
          http://netcdftools.svn.sourceforge.net/netcdftools/?rev=22&view=rev
Author:   jdempsey
Date:     2010-06-23 02:23:03 +0000 (Wed, 23 Jun 2010)

Log Message:
-----------
ANDSWRON-690 - Add support for attributes with numeric data types

Modified Paths:
--------------
    trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java
    trunk/src/main/java/au/csiro/netcdf/util/NetCDFUtils.java
    trunk/src/test/java/au/csiro/netcdf/TestNcDefineAttributes.java

Modified: trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java
===================================================================

--- trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java	2010-06-23 00:02:13 UTC (rev 21)
+++ trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java	2010-06-23 02:23:03 UTC (rev 22)
@@ -25,7 +25,9 @@
 import java.io.PrintWriter;
 import java.io.StringWriter;
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.GnuParser;
@@ -36,6 +38,7 @@
 import org.apache.commons.cli.ParseException;
 import org.apache.log4j.Logger;
 
+import ucar.ma2.DataType;
 import ucar.nc2.Attribute;
 import ucar.nc2.NetcdfFileWriteable;
 import ucar.nc2.Variable;
@@ -56,6 +59,8 @@
  */
 public class NcDefineAttributes implements Command
 {
+    private static final String NULL_VALUE = "null";
+
     /**
      * The command name
      */
@@ -96,12 +101,34 @@
      * The pattern for accepted file names where multiple files are accepted.
      */
     public static final String FILENAME_PATTERN = "pattern"; 
+
+    /**
+     * The name of the command line option used for specifying the data type of the attribute.
+     */
+    public static final String ATTRIBUTE_DATA_TYPE = "attributeDataType";
     
     /**
      * Constant that defines the logger to be used.
      */
     private static final Logger LOG = Logger.getLogger(NcDefineAttributes.class.getName());
+
+
+    /**
+     * The only data types that can be used for attributes in netCDF v3 (classic) files.
+     */
+    private static Set<DataType> netCDF3DataTypes = new HashSet<DataType>();
     
+    static 
+    {
+        netCDF3DataTypes.add(DataType.DOUBLE);
+        netCDF3DataTypes.add(DataType.FLOAT);
+        netCDF3DataTypes.add(DataType.INT);
+        netCDF3DataTypes.add(DataType.CHAR);
+        netCDF3DataTypes.add(DataType.SHORT);
+        netCDF3DataTypes.add(DataType.BYTE);
+        netCDF3DataTypes.add(DataType.STRING);
+    }
+    
     /**
      * Command options
      */
@@ -139,6 +166,8 @@
                 .getOptionValue(FILENAME_PATTERN) : "";
         String variableNameArg = (parsedCommandLine.hasOption(VARIABLE_NAME)) ? parsedCommandLine
                         .getOptionValue(VARIABLE_NAME) : "";
+        String attributeDataTypeArg = (parsedCommandLine.hasOption(ATTRIBUTE_DATA_TYPE)) ? parsedCommandLine
+                .getOptionValue(ATTRIBUTE_DATA_TYPE) : "String";
                 
         // check whether large file support is needed
         if (Util.fileExists(outputFilenameArg) 
@@ -162,9 +191,12 @@
                                                                        // value is an empty list.                
         if(!attributesArg.isEmpty())
         {
+            // try getting the variable's data type
+            DataType attributeDataType = NcDefineAttributes.mapStringToDataType(attributeDataTypeArg);
+
             try
             {
-                attributes = NetCDFUtils.mapStringToAttributeValueList(attributesArg);
+                attributes = NetCDFUtils.mapStringToAttributeValueList(attributesArg, attributeDataType);
             }
             catch (IllegalArgumentException iae)
             {
@@ -260,7 +292,7 @@
                     for(Attribute attribute : attributes)
                     {
                         // remove Attribute if the value is "null"                       
-                        if ("null".equalsIgnoreCase(attribute.getStringValue()))
+                        if (NULL_VALUE.equalsIgnoreCase(attribute.getStringValue()))
                         {
                             ncfile.deleteGlobalAttribute(attribute.getName());
                         }
@@ -285,7 +317,7 @@
                         for(Attribute attribute : attributes)
                         {
                             // remove Attribute if the value is "null"                       
-                            if ("null".equalsIgnoreCase(attribute.getStringValue()))
+                            if (NULL_VALUE.equalsIgnoreCase(attribute.getStringValue()))
                             {
                                 variable.removeAttributeIgnoreCase(attribute.getName());
                             }
@@ -444,6 +476,10 @@
                         + "set to define variable attribute.") 
                 .isRequired(false).withLongOpt(VARIABLE_NAME).create("v");     
 
+        Option attributeType = OptionBuilder.withArgName("text").hasArg().withDescription(
+                "8: OPTIONAL, the data type of the attribute(s), e.g. " + NcDefineAttributes.netCDF3DataTypes)
+                .isRequired(false).withLongOpt(ATTRIBUTE_DATA_TYPE).create("t");
+        
         Options options = new Options();
 
         options.addOption(outputFileName);
@@ -453,6 +489,7 @@
         options.addOption(largeFileSupport);
         options.addOption(pattern);
         options.addOption(variableName);
+        options.addOption(attributeType);
 
         return options;
     }
@@ -492,6 +529,8 @@
             boolean isLargeFileSupport = parsedCommandLine.hasOption(IS_LARGE_FILE);  
             String pattern = (parsedCommandLine.hasOption(FILENAME_PATTERN)) ? parsedCommandLine
                     .getOptionValue(FILENAME_PATTERN) : "";
+            String variableDataTypeArg = (parsedCommandLine.hasOption(ATTRIBUTE_DATA_TYPE)) ? parsedCommandLine
+                    .getOptionValue(ATTRIBUTE_DATA_TYPE) : "String";
             
             // check whether large file support is needed
             if (pattern.length() == 0 && Util.fileExists(outputFilenameArg) 
@@ -537,7 +576,12 @@
                             + " value is not a comma separated String of attribute-value pairs: "
                             + attributesArg);
                 }
-            }                    
+            }
+            
+
+            // try getting the variable's data type
+            NcDefineAttributes.mapStringToDataType(variableDataTypeArg);
+            
         }
         catch (ParseException pe)
         {
@@ -550,4 +594,24 @@
 
         return errorMsg;
     }
+
+    /**
+     * Maps a <code>String</code> into a {@link DataType}.
+     * 
+     * @param variableDataType
+     *            a data type description.
+     * @return a {@link DataType}
+     * @throws IllegalArgumentException
+     *             thrown if the <code>String</code> can not be mapped to a {@link DataType}.
+     */
+    public static DataType mapStringToDataType(String variableDataType) throws IllegalArgumentException
+    {
+        DataType dataType = DataType.getType(variableDataType);
+        if (dataType != null && netCDF3DataTypes.contains(dataType))
+        {
+            return dataType;
+        }
+        throw new IllegalArgumentException(NcDefineVariable.VARIABLE_DATA_TYPE + " value is not a valid data type: "
+                + variableDataType + ". Allowed data types are: " + netCDF3DataTypes);
+    }
 }

Modified: trunk/src/main/java/au/csiro/netcdf/util/NetCDFUtils.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/util/NetCDFUtils.java	2010-06-23 00:02:13 UTC (rev 21)
+++ trunk/src/main/java/au/csiro/netcdf/util/NetCDFUtils.java	2010-06-23 02:23:03 UTC (rev 22)
@@ -27,6 +27,7 @@
 import java.util.List;
 
 import ucar.ma2.Array;
+import ucar.ma2.DataType;
 import ucar.nc2.Attribute;
 import ucar.nc2.Dimension;
 import ucar.nc2.NetcdfFile;
@@ -46,6 +47,7 @@
     /** Index value to be returned when the value cannot be found in the array */
     public static final int NOT_FOUND = -1;
 
+    public static final String NULL_VALUE = "null";
 
     /**
      * Lookup the index of a value in a dimension. The dimension to be searched must 
@@ -242,7 +244,7 @@
     }
     
     /**
-     * Converts a comma separated <code>String</code> into an {@link Attribute} list.
+     * Converts a comma separated <code>String</code> into a String {@link Attribute} list.  
      * 
      * @param commaSeparatedAttributeValueString
      *            a list of comma separated attribute-value pairs, e.g. attribute1=value1,attribute2=value2,...
@@ -253,6 +255,22 @@
     public static List<Attribute> mapStringToAttributeValueList(String commaSeparatedAttributeValueString)
             throws IllegalArgumentException
     {
+        return mapStringToAttributeValueList(commaSeparatedAttributeValueString, DataType.STRING);
+    }
+    
+    /**
+     * Converts a comma separated <code>String</code> into an {@link Attribute} list. 
+     * 
+     * @param commaSeparatedAttributeValueString
+     *            a list of comma separated attribute-value pairs, e.g. attribute1=value1,attribute2=value2,...
+     * @param dataType The type of attributes to be created.           
+     * @return an {@link Attribute} list.
+     * @throws IllegalArgumentException
+     *             thrown if the <code>String</code> can not be converted into an {@link Attribute} list.
+     */
+    public static List<Attribute> mapStringToAttributeValueList(String commaSeparatedAttributeValueString, DataType dataType)
+        throws IllegalArgumentException
+    {
         List<Attribute> attributeValues = new ArrayList<Attribute>();
 
         List<String> attributePairs = Util.tokeniseCommaSeparatedString(commaSeparatedAttributeValueString);
@@ -264,8 +282,90 @@
             if (keyValuePair.length == 2 && !keyValuePair[0].isEmpty() && !keyValuePair[1].isEmpty())
             {
                 String key = keyValuePair[0].replaceAll("\\\\,", ",").replaceAll("\\\\=", "=");
-                attributeValues.add(new Attribute(key.trim(),
-                        keyValuePair[1].replaceAll("\\\\,", ",").replaceAll("\\\\=", "=")));
+                key = key.trim();
+                String strVal = keyValuePair[1].replaceAll("\\\\,", ",").replaceAll("\\\\=", "=");
+                Attribute attrib;
+                
+                if (NULL_VALUE.equals(strVal) || dataType == DataType.STRING || dataType == DataType.CHAR)
+                {
+                    attrib = new Attribute(key, strVal);
+                }
+                else if (dataType == DataType.FLOAT)
+                {
+                    Float value;
+                    try
+                    {
+                        value = Float.parseFloat(strVal);
+                    }
+                    catch (NumberFormatException e)
+                    {
+                        throw new IllegalArgumentException("Invalid float value '" + strVal + "' for key "
+                                + key + ".");
+                    }
+                    attrib = new Attribute(key, value);
+                }
+                else if (dataType == DataType.DOUBLE)
+                {
+                    Double value;
+                    try
+                    {
+                        value = Double.parseDouble(strVal);
+                    }
+                    catch (NumberFormatException e)
+                    {
+                        throw new IllegalArgumentException("Invalid double value '" + strVal + "' for key "
+                                + key + ".");
+                    }
+                    attrib = new Attribute(key, value);
+                }
+                else if (dataType == DataType.INT)
+                {
+                    Integer value;
+                    try
+                    {
+                        value = Integer.parseInt(strVal);
+                    }
+                    catch (NumberFormatException e)
+                    {
+                        throw new IllegalArgumentException("Invalid integer value '" + strVal + "' for key "
+                                + key + ".");
+                    }
+                    attrib = new Attribute(key, value);
+                }
+                else if (dataType == DataType.SHORT)
+                {
+                    Short value;
+                    try
+                    {
+                        value = Short.parseShort(strVal);
+                    }
+                    catch (NumberFormatException e)
+                    {
+                        throw new IllegalArgumentException("Invalid short value '" + strVal + "' for key "
+                                + key + ".");
+                    }
+                    attrib = new Attribute(key, value);
+                }
+                else if (dataType == DataType.BYTE)
+                {
+                    Byte value;
+                    try
+                    {
+                        value = Byte.parseByte(strVal);
+                    }
+                    catch (NumberFormatException e)
+                    {
+                        throw new IllegalArgumentException("Invalid byte value '" + strVal + "' for key "
+                                + key + ".");
+                    }
+                    attrib = new Attribute(key, value);
+                }
+                else
+                {
+                    throw new IllegalArgumentException(
+                            "Unexpected datatype of " + dataType + " supplied to mapStringToAttributeValueList.");
+                }
+                attributeValues.add(attrib);
             }
             else
             {

Modified: trunk/src/test/java/au/csiro/netcdf/TestNcDefineAttributes.java
===================================================================
--- trunk/src/test/java/au/csiro/netcdf/TestNcDefineAttributes.java	2010-06-23 00:02:13 UTC (rev 21)
+++ trunk/src/test/java/au/csiro/netcdf/TestNcDefineAttributes.java	2010-06-23 02:23:03 UTC (rev 22)
@@ -33,10 +33,11 @@
 import ucar.nc2.NetcdfFile;
 import au.csiro.netcdf.cli.Command;
 import au.csiro.netcdf.util.NetCDFUtils;
+
 /**
  * This class is a unit test suite to verify that the NcDefineAttributes command operates correctly.
  * <p>
- * Copyright 2010, CSIRO Australia All rights reserved.
+ * Copyright 2010, CSIRO Australia
  * 
  * @author James Dempsey on 23/03/2010
  * @version $Revision: 7130 $ $Date: 2010-06-09 14:23:51 +1000 (Wed, 09 Jun 2010) $
@@ -74,6 +75,12 @@
 
     /** Data for the second Attribute */
     private static final String ATTR2_DATA = "Murray Darling Basin Sustainable Yields (MDBSY)";
+
+    /** Name of the third, float, Attribute */
+    private static final String ATTR3_NAME = "Float Val";
+
+    /** Data for the third, float, Attribute */
+    private static final String ATTR3_DATA = "17.5f";
     
     /** Name for history Attribute */
     private static final String ATTR_HISTORY = "history";
@@ -299,8 +306,141 @@
         }
     }
 
+    /**
+     * Test a valid command creates a netCDF file with a float attribute
+     * @throws Exception If there is an error running the test
+     */
+    public final void testExecuteValidFloatAttr() throws Exception
+    {
+        String[] args = new String[] { ncDefineAttr.getCommandName(), 
+                "-" + OUTPUT_FILE, NC_FILE_NAME,
+                "-" + ATTRIBUTES, ATTR3_NAME + "=" + ATTR3_DATA,
+                "-t", "float"};
 
+        File ncFile = new File(NC_FILE_NAME);
+        if (ncFile.exists())
+        {
+            ncFile.delete();
+        }
+
+        ncDefineAttr.execute(args);
+        assertTrue("The nc file was not created: " + NC_FILE_NAME, ncFile.exists());
+
+        NetcdfFile netcdfFile = NetcdfFile.open(NC_FILE_NAME);
+        Attribute attr = netcdfFile.findGlobalAttribute(ATTR3_NAME);
+        assertTrue("The Attribute was not defined: " + ATTR3_NAME, (attr != null));
+        assertEquals("The Attrbute " + ATTR3_NAME + " had a string value. ",
+                null, attr.getStringValue());
+        assertEquals("The Attrbute had the wrong data: " + ATTR3_NAME,
+                Float.parseFloat(ATTR3_DATA), (Float)attr.getNumericValue(), 0.01f);
+        
+        netcdfFile.close();
+        ncFile.delete();
+    }
+
     /**
+     * Test a valid command creates a netCDF file with a short attribute
+     * @throws Exception If there is an error running the test
+     */
+    public final void testExecuteValidShortAttr() throws Exception
+    {
+        final String shortAttrName = "Short";
+        String[] args = new String[] { ncDefineAttr.getCommandName(), 
+                "-" + OUTPUT_FILE, NC_FILE_NAME,
+                "-" + ATTRIBUTES, shortAttrName + "=57",
+                "-t", "short"};
+
+        File ncFile = new File(NC_FILE_NAME);
+        if (ncFile.exists())
+        {
+            ncFile.delete();
+        }
+
+        ncDefineAttr.execute(args);
+        assertTrue("The nc file was not created: " + NC_FILE_NAME, ncFile.exists());
+
+        NetcdfFile netcdfFile = NetcdfFile.open(NC_FILE_NAME);
+        Attribute attr = netcdfFile.findGlobalAttribute(shortAttrName);
+        assertTrue("The Attribute was not defined: " + shortAttrName, (attr != null));
+        assertEquals("The Attrbute " + shortAttrName + " had a string value. ",
+                null, attr.getStringValue());
+        assertEquals("The Attrbute had the wrong data: " + shortAttrName,
+                (short) 57, (Short)attr.getNumericValue(), 0);
+        
+        netcdfFile.close();
+        ncFile.delete();
+    }
+
+    /**
+     * Test a valid command creates a netCDF file with an integer attribute
+     * @throws Exception If there is an error running the test
+     */
+    public final void testExecuteValidIntAttr() throws Exception
+    {
+        final String intAttrName = "Integer";
+        final int intAttrValue = 67991082;
+        String[] args = new String[] { ncDefineAttr.getCommandName(), 
+                "-" + OUTPUT_FILE, NC_FILE_NAME,
+                "-" + ATTRIBUTES, intAttrName + "=" + String.valueOf(intAttrValue),
+                "-t", "int"};
+
+        File ncFile = new File(NC_FILE_NAME);
+        if (ncFile.exists())
+        {
+            ncFile.delete();
+        }
+
+        ncDefineAttr.execute(args);
+        assertTrue("The nc file was not created: " + NC_FILE_NAME, ncFile.exists());
+
+        NetcdfFile netcdfFile = NetcdfFile.open(NC_FILE_NAME);
+        Attribute attr = netcdfFile.findGlobalAttribute(intAttrName);
+        assertTrue("The Attribute was not defined: " + intAttrName, (attr != null));
+        assertEquals("The Attrbute " + intAttrName + " had a string value. ",
+                null, attr.getStringValue());
+        assertEquals("The Attrbute had the wrong data: " + intAttrName,
+                intAttrValue, (Integer)attr.getNumericValue(), 0);
+        
+        netcdfFile.close();
+        ncFile.delete();
+    }
+
+    /**
+     * Test a valid command creates a netCDF file with an integer attribute
+     * @throws Exception If there is an error running the test
+     */
+    public final void testExecuteInvalidType() throws Exception
+    {
+        final String intAttrName = "Integer";
+        final int intAttrValue = 67991082;
+        String[] args = new String[] { ncDefineAttr.getCommandName(), 
+                "-" + OUTPUT_FILE, NC_FILE_NAME,
+                "-" + ATTRIBUTES, intAttrName + "=" + String.valueOf(intAttrValue),
+                "-t", "integer"};
+
+        File ncFile = new File(NC_FILE_NAME);
+        if (ncFile.exists())
+        {
+            ncFile.delete();
+        }
+
+        try
+        {
+            ncDefineAttr.execute(args);
+            ncFile.delete();
+            fail("Type of integer should have been rejected.");
+        }
+        catch (IllegalArgumentException e)
+        {
+            // We can only test the start of the message as the supported types is a set and thus the order is not deterministic
+            assertTrue("Incorrect error message", e.getMessage().startsWith("variableDataType value is not a valid data type: integer. "
+                    + "Allowed data types are: ["));
+        }
+
+    }
+
+
+    /**
      * Test that required options are reported if missing 
      */
     public final void testMissingRequiredOption()


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.




Thread: [Netcdftools-commit] SF.net SVN: netcdftools:[22] trunk/src

netcdftools-commit