netcdftools-commit

[Netcdftools-commit] SF.net SVN: netcdftools:[84] trunk/src/main/java/au/csiro/netcdf

[<rob...@us...>]

Revision: 84
          http://netcdftools.svn.sourceforge.net/netcdftools/?rev=84&view=rev
Author:   robertbridle
Date:     2010-08-25 05:56:46 +0000 (Wed, 25 Aug 2010)

Log Message:
-----------
ANDSWRON-289 - Moved from using GnuParser to BasicParser. The BasicParser uses a basic flattening method and doesn't allow options that would seem to be invalid. 

Modified Paths:
--------------
    trunk/src/main/java/au/csiro/netcdf/NcCSVExtract.java
    trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java
    trunk/src/main/java/au/csiro/netcdf/NcDefineDimension.java
    trunk/src/main/java/au/csiro/netcdf/NcDefineVariable.java
    trunk/src/main/java/au/csiro/netcdf/NcWriteVariable.java
    trunk/src/main/java/au/csiro/netcdf/wron/MdbsyNetCDF2CSVConverter.java
    trunk/src/main/java/au/csiro/netcdf/wron/MdbsyScenarioAConverter.java
    trunk/src/main/java/au/csiro/netcdf/wron/MdbsyScenarioCConverter.java

Modified: trunk/src/main/java/au/csiro/netcdf/NcCSVExtract.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/NcCSVExtract.java	2010-08-18 05:16:33 UTC (rev 83)
+++ trunk/src/main/java/au/csiro/netcdf/NcCSVExtract.java	2010-08-25 05:56:46 UTC (rev 84)
@@ -22,8 +22,8 @@
 import java.io.PrintWriter;
 import java.io.StringWriter;
 
+import org.apache.commons.cli.BasicParser;
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.GnuParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.OptionBuilder;
@@ -135,7 +135,7 @@
     public void execute(String[] args) throws ParseException, IOException
     {
         // parse the command line arguments
-        CommandLine parsedCommandLine = new GnuParser().parse(options, args);
+        CommandLine parsedCommandLine = new BasicParser().parse(options, args);
 
         String filename = parsedCommandLine.getOptionValue(INPUT_FILE);
         int numRecords = Util.fastFileLineCounter(filename);
@@ -207,7 +207,7 @@
         // check required options are provided
         try
         {
-            parsedCommandLine = new GnuParser().parse(options, commandLine);
+            parsedCommandLine = new BasicParser().parse(options, commandLine);
         }
         catch (ParseException ex)
         {

Modified: trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java	2010-08-18 05:16:33 UTC (rev 83)
+++ trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java	2010-08-25 05:56:46 UTC (rev 84)
@@ -29,8 +29,8 @@
 import java.util.List;
 import java.util.Set;
 
+import org.apache.commons.cli.BasicParser;
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.GnuParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.OptionBuilder;
@@ -151,7 +151,7 @@
     public void execute(String[] args) throws ParseException, IOException, IllegalArgumentException
     {
         // parse the command line arguments
-        CommandLine parsedCommandLine = new GnuParser().parse(this.options, args);
+        CommandLine parsedCommandLine = new BasicParser().parse(this.options, args);
 
         // get the command line argument values
         String outputFilenameArg = (parsedCommandLine.hasOption(OUTPUT_FILE)) ? parsedCommandLine
@@ -523,7 +523,7 @@
         try
         {
             // try parsing the command line, where ParseException can be thrown from
-            CommandLine parsedCommandLine = new GnuParser().parse(this.options, commandLine);
+            CommandLine parsedCommandLine = new BasicParser().parse(this.options, commandLine);
             
             // get the command line argument values
             String outputFilenameArg = (parsedCommandLine.hasOption(OUTPUT_FILE)) ? parsedCommandLine

Modified: trunk/src/main/java/au/csiro/netcdf/NcDefineDimension.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/NcDefineDimension.java	2010-08-18 05:16:33 UTC (rev 83)
+++ trunk/src/main/java/au/csiro/netcdf/NcDefineDimension.java	2010-08-25 05:56:46 UTC (rev 84)
@@ -26,8 +26,8 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import org.apache.commons.cli.BasicParser;
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.GnuParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.OptionBuilder;
@@ -106,7 +106,7 @@
     public void execute(String[] args) throws ParseException, IOException, IllegalArgumentException
     {
         // parse the command line arguments
-        CommandLine parsedCommandLine = new GnuParser().parse(this.options, args);
+        CommandLine parsedCommandLine = new BasicParser().parse(this.options, args);
 
         // get the command line argument values
         String outputFilenameArg = (parsedCommandLine.hasOption(OUTPUT_FILE)) ? parsedCommandLine
@@ -357,7 +357,7 @@
         try
         {
             // try parsing the command line, where ParseException can be thrown from
-            CommandLine parsedCommandLine = new GnuParser().parse(this.options, commandLine);
+            CommandLine parsedCommandLine = new BasicParser().parse(this.options, commandLine);
             
             // get the command line argument values
             String outputFilenameArg = (parsedCommandLine.hasOption(OUTPUT_FILE)) ? parsedCommandLine

Modified: trunk/src/main/java/au/csiro/netcdf/NcDefineVariable.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/NcDefineVariable.java	2010-08-18 05:16:33 UTC (rev 83)
+++ trunk/src/main/java/au/csiro/netcdf/NcDefineVariable.java	2010-08-25 05:56:46 UTC (rev 84)
@@ -30,8 +30,8 @@
 import java.util.Set;
 import java.util.regex.PatternSyntaxException;
 
+import org.apache.commons.cli.BasicParser;
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.GnuParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.OptionBuilder;
@@ -157,7 +157,7 @@
     public void execute(String[] args) throws IllegalArgumentException, IOException, ParseException
     {
         // parse the command line arguments
-        CommandLine parsedCommandLine = new GnuParser().parse(this.options, args);
+        CommandLine parsedCommandLine = new BasicParser().parse(this.options, args);
 
         // get the command line argument values
         String outputFilenameArg = (parsedCommandLine.hasOption(OUTPUT_FILE)) ? parsedCommandLine
@@ -506,7 +506,7 @@
         try
         {
             // try parsing the command line, where ParseException can be thrown from
-            CommandLine parsedCommandLine = new GnuParser().parse(this.options, commandLine);
+            CommandLine parsedCommandLine = new BasicParser().parse(this.options, commandLine);
 
             // try converting command line parameters to their associated types, where IllegalArgumentException can be
             // thrown from

Modified: trunk/src/main/java/au/csiro/netcdf/NcWriteVariable.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/NcWriteVariable.java	2010-08-18 05:16:33 UTC (rev 83)
+++ trunk/src/main/java/au/csiro/netcdf/NcWriteVariable.java	2010-08-25 05:56:46 UTC (rev 84)
@@ -32,8 +32,8 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import org.apache.commons.cli.BasicParser;
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.GnuParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.OptionBuilder;
@@ -117,7 +117,7 @@
     public void execute(String[] args) throws ParseException, IOException
     {
         // parse the command line arguments
-        CommandLine parsedCommandLine = new GnuParser().parse(options, args);
+        CommandLine parsedCommandLine = new BasicParser().parse(options, args);
 
         // get the command line argument values
         String outputFilenameArg = (parsedCommandLine.hasOption(OUTPUT_FILE)) ? parsedCommandLine
@@ -331,7 +331,7 @@
         try
         {
             // try parsing the command line, where ParseException can be thrown from
-            CommandLine parsedCommandLine = new GnuParser().parse(options, args);
+            CommandLine parsedCommandLine = new BasicParser().parse(options, args);
 
             // try converting command line parameters to their associated types, where IllegalArgumentException can be
             // thrown from

Modified: trunk/src/main/java/au/csiro/netcdf/wron/MdbsyNetCDF2CSVConverter.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/wron/MdbsyNetCDF2CSVConverter.java	2010-08-18 05:16:33 UTC (rev 83)
+++ trunk/src/main/java/au/csiro/netcdf/wron/MdbsyNetCDF2CSVConverter.java	2010-08-25 05:56:46 UTC (rev 84)
@@ -27,8 +27,8 @@
 import java.util.Date;
 import java.util.List;
 
+import org.apache.commons.cli.BasicParser;
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.GnuParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.MissingOptionException;
 import org.apache.commons.cli.Option;
@@ -161,7 +161,7 @@
             options.addOption(outputDirectoryName);
 
             // parse the command line arguments
-            CommandLine parsedCommandLine = new GnuParser().parse(options, args);
+            CommandLine parsedCommandLine = new BasicParser().parse(options, args);
 
             String inputDir = parsedCommandLine.getOptionValue(INPUT_DIR);
             String outputDir = parsedCommandLine.getOptionValue(OUTPUT_DIR);

Modified: trunk/src/main/java/au/csiro/netcdf/wron/MdbsyScenarioAConverter.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/wron/MdbsyScenarioAConverter.java	2010-08-18 05:16:33 UTC (rev 83)
+++ trunk/src/main/java/au/csiro/netcdf/wron/MdbsyScenarioAConverter.java	2010-08-25 05:56:46 UTC (rev 84)
@@ -45,8 +45,8 @@
 import java.util.TreeSet;
 import java.util.regex.Pattern;
 
+import org.apache.commons.cli.BasicParser;
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.GnuParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.MissingOptionException;
 import org.apache.commons.cli.Option;
@@ -280,7 +280,7 @@
             options.addOption(endLat);
 
             // parse the command line arguments
-            CommandLine parsedCommandLine = new GnuParser().parse(options, args);
+            CommandLine parsedCommandLine = new BasicParser().parse(options, args);
 
             INPUT_CSV_DIRECTORY = (parsedCommandLine.hasOption("inputDirectory")) ? parsedCommandLine
                     .getOptionValue("inputDirectory") : "";

Modified: trunk/src/main/java/au/csiro/netcdf/wron/MdbsyScenarioCConverter.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/wron/MdbsyScenarioCConverter.java	2010-08-18 05:16:33 UTC (rev 83)
+++ trunk/src/main/java/au/csiro/netcdf/wron/MdbsyScenarioCConverter.java	2010-08-25 05:56:46 UTC (rev 84)
@@ -45,8 +45,8 @@
 import java.util.TreeSet;
 import java.util.regex.Pattern;
 
+import org.apache.commons.cli.BasicParser;
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.GnuParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.MissingOptionException;
 import org.apache.commons.cli.Option;
@@ -308,7 +308,7 @@
             options.addOption(endLat);
 
             // parse the command line arguments
-            CommandLine parsedCommandLine = new GnuParser().parse(options, args);
+            CommandLine parsedCommandLine = new BasicParser().parse(options, args);
 
             INPUT_CSV_DIRECTORY = (parsedCommandLine.hasOption("inputDirectory")) ? parsedCommandLine
                     .getOptionValue("inputDirectory") : "";


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[Netcdftools-commit] SF.net SVN: netcdftools:[85] trunk/src/main/java/au/csiro/netcdf

[<rit...@us...>]

Revision: 85
          http://netcdftools.svn.sourceforge.net/netcdftools/?rev=85&view=rev
Author:   ritacsiro
Date:     2010-08-30 06:10:19 +0000 (Mon, 30 Aug 2010)

Log Message:
-----------
ANDSWRON-462:ANDSWRDM - Conversion Tools - Error handling when fillrange exceeds actual range of values in binary file

Modified Paths:
--------------
    trunk/src/main/java/au/csiro/netcdf/NcWriteVariable.java
    trunk/src/main/java/au/csiro/netcdf/cli/NetCDFTool.java

Modified: trunk/src/main/java/au/csiro/netcdf/NcWriteVariable.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/NcWriteVariable.java	2010-08-25 05:56:46 UTC (rev 84)
+++ trunk/src/main/java/au/csiro/netcdf/NcWriteVariable.java	2010-08-30 06:10:19 UTC (rev 85)
@@ -22,6 +22,7 @@
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.DataInputStream;
+import java.io.EOFException;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
@@ -662,41 +663,49 @@
         int i = 0;
         while (i < buffer.getSize())
         {
-
-            if (isFloat)
+            try
             {
-                buffer.setFloat(i, dataIn.readFloat());
+                if (isFloat)
+                {
+                    buffer.setFloat(i, dataIn.readFloat());
+                }
+                else if (isDouble)
+                {
+                    buffer.setDouble(i, dataIn.readDouble());
+                }
+                else if (isLong)
+                {
+                    buffer.setLong(i, dataIn.readLong());
+                }
+                else if (isInt)
+                {
+                    buffer.setInt(i, dataIn.readInt());
+                }
+                else if (isChar)
+                {
+                    buffer.setChar(i, dataIn.readChar());
+                }
+                else if (isByte)
+                {
+                    buffer.setByte(i, dataIn.readByte());
+                }
+                else if (isBoolean)
+                {
+                    buffer.setBoolean(i, dataIn.readBoolean());
+                }
+                else if (isShort)
+                {
+                    buffer.setShort(i, dataIn.readShort());
+                }
             }
-            else if (isDouble)
+            catch (EOFException e)
             {
-                buffer.setDouble(i, dataIn.readDouble());
+                String error = "Expected block of " + buffer.getSize() + " values but ran out after " + i + ".";
+                System.err.println(error);
+                throw new EOFException(error);
             }
-            else if (isLong)
-            {
-                buffer.setLong(i, dataIn.readLong());
-            }
-            else if (isInt)
-            {
-                buffer.setInt(i, dataIn.readInt());
-            }
-            else if (isChar)
-            {
-                buffer.setChar(i, dataIn.readChar());
-            }
-            else if (isByte)
-            {
-                buffer.setByte(i, dataIn.readByte());
-            }
-            else if (isBoolean)
-            {
-                buffer.setBoolean(i, dataIn.readBoolean());
-            }
-            else if (isShort)
-            {
-                buffer.setShort(i, dataIn.readShort());
-            }
             i++;
         }
-        
+
     }
 }

Modified: trunk/src/main/java/au/csiro/netcdf/cli/NetCDFTool.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/cli/NetCDFTool.java	2010-08-25 05:56:46 UTC (rev 84)
+++ trunk/src/main/java/au/csiro/netcdf/cli/NetCDFTool.java	2010-08-30 06:10:19 UTC (rev 85)
@@ -85,10 +85,9 @@
                 catch (Exception e)
                 {
                     LOG.error(e);
-                    e.printStackTrace();
+//                    e.printStackTrace();
                     System.out.println("Error: " + e.getMessage());
                     System.out.println(command.getUsageString());
-//                    e.printStackTrace();
                     System.exit(2);
                 }
             }


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