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[Netcdftools-commit] SF.net SVN: netcdftools:[29] trunk
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From: <jde...@us...> - 2010-06-24 00:29:14
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Revision: 29
http://netcdftools.svn.sourceforge.net/netcdftools/?rev=29&view=rev
Author: jdempsey
Date: 2010-06-24 00:29:08 +0000 (Thu, 24 Jun 2010)
Log Message:
-----------
ANDSWRON-657 - Allow defineAttributes to manipulate multiple files
- Update to address review feedback and only a single file matching the pattern
Modified Paths:
--------------
trunk/USAGE.txt
trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java
trunk/src/main/java/au/csiro/netcdf/util/Util.java
Added Paths:
-----------
trunk/src/test/java/au/csiro/netcdf/util/UtilTest.java
Modified: trunk/USAGE.txt
===================================================================
--- trunk/USAGE.txt 2010-06-23 08:29:49 UTC (rev 28)
+++ trunk/USAGE.txt 2010-06-24 00:29:08 UTC (rev 29)
@@ -1,19 +1,3 @@
-====
- Copyright 2010, CSIRO Australia.
-
- Licensed under the Apache License, Version 2.0 (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
-====
-
ncextractcsv
Extract a block of data from a CSV file. The data can then be piped into the
ncwritevar command to add the data to a variable in a netCDF file.
@@ -47,7 +31,7 @@
-------------------------------------
-usage: ncdefineAtt
+ncdefineAtt
Define an attribute in a netCDF file.
-o,--outputFileName <file> 1: the filename of the netCDF file to be
created.
@@ -69,10 +53,16 @@
-p,--pattern <filename pattern> 6: OPTIONAL, a pattern to match multiple
existing files, where multiple files should be
processed. If this option is present the
- outptuFilename is expected to be a direcotry
- containing the files to be processed.
+ outputFilename is expected to be a directory
+ containing the files to be processed. The
+ wildcard characters * and ? are supported but
+ may need to be escaped by a \ to avoid
+ processing by the shell. e.g. \*.nc
-v,--variable <text> 7: OPTIONAL, the variable to assign attribute(s)
to, set to define variable attribute.
+-t,--attributeDataType <text> 8: OPTIONAL, the data type of the attribute(s),
+ e.g. [byte, short, String, float, double, int,
+ char]
Example: ncdefineatt -outputFileName ABC.nc -attributes
"netCDF-Java=4.0,Conventions=value with a space,toDelete=null"
@@ -93,8 +83,8 @@
that text containing '=' or ',' characters are
delimited by a backslash.
-v,--variableName <text> 4: the name to be given to the variable.
--t,--variableDataType <text> 5: the data type of the variable, e.g. [int,
- double, char, float, short, byte]
+-t,--variableDataType <text> 5: the data type of the variable, e.g. [byte,
+ short, float, double, int, char]
-a,--variableAttributes <text> 6: a comma separated list of attribute-value
pairs, OPTIONAL, e.g. "units=mm", ensure that
text containing '=' or ',' characters are
Modified: trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java 2010-06-23 08:29:49 UTC (rev 28)
+++ trunk/src/main/java/au/csiro/netcdf/NcDefineAttributes.java 2010-06-24 00:29:08 UTC (rev 29)
@@ -168,17 +168,21 @@
.getOptionValue(VARIABLE_NAME) : "";
String attributeDataTypeArg = (parsedCommandLine.hasOption(ATTRIBUTE_DATA_TYPE)) ? parsedCommandLine
.getOptionValue(ATTRIBUTE_DATA_TYPE) : "String";
+
+ List<String> targetFileNames = Util.getListOfTargetFiles(outputFilenameArg, pattern);
// check whether large file support is needed
- if (Util.fileExists(outputFilenameArg)
- && Util.getExistingFile(outputFilenameArg).length() >= MAX_32BIT_OFFSET_FILE_SIZE
- && !isLargeFileSupport)
+ for (String outputFileName : targetFileNames)
{
- throw new IllegalArgumentException("The netCDF file will be too large, please use " + IS_LARGE_FILE
- + " flag.");
+ if (Util.fileExists(outputFileName)
+ && Util.getExistingFile(outputFileName).length() >= MAX_32BIT_OFFSET_FILE_SIZE
+ && !isLargeFileSupport)
+ {
+ throw new IllegalArgumentException("The netCDF file " + outputFileName
+ + " will be too large, please use " + IS_LARGE_FILE + " flag.");
+ }
}
- List<String> targetFileNames = Util.getListOfTargetFiles(outputFilenameArg, pattern);
// check that if an input file is specified then it actually exists.
if (!inputFilenameArg.isEmpty())
@@ -217,6 +221,7 @@
for (String outputFileName : targetFileNames)
{
+ LOG.debug("Processing file : " + outputFileName);
this.execute(outputFileName, attributes, isLargeFileSupport, variableNameArg);
}
}
@@ -465,9 +470,10 @@
Option pattern = OptionBuilder.withArgName("filename pattern").hasArg().withDescription(
"6: OPTIONAL, a pattern to match multiple existing files, where multiple files should be "
- + "processed. If this option is present the outptuFilename is expected to be a direcotry "
- + "containing the files to be processed.").isRequired(false).withLongOpt(FILENAME_PATTERN)
- .create("p");
+ + "processed. If this option is present the outputFilename is expected to be a directory "
+ + "containing the files to be processed. The wildcard characters * and ? are supported but "
+ + "may need to be escaped by a \\ to avoid processing by the shell. e.g. \\*.nc ").isRequired(
+ false).withLongOpt(FILENAME_PATTERN).create("p");
Option variableName = OptionBuilder
.withArgName("text")
.hasArg()
Modified: trunk/src/main/java/au/csiro/netcdf/util/Util.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/util/Util.java 2010-06-23 08:29:49 UTC (rev 28)
+++ trunk/src/main/java/au/csiro/netcdf/util/Util.java 2010-06-24 00:29:08 UTC (rev 29)
@@ -220,6 +220,7 @@
*/
public static List<String> getListOfTargetFiles(String foldername, String pattern)
{
+ String cleanPat = pattern.replaceAll("\\\\\\*", "*").replaceAll("\\\\\\?", "?");
List<String> fileNameList = new ArrayList<String>();
if (pattern == null || pattern.length() == 0)
{
@@ -233,7 +234,7 @@
return Collections.emptyList();
}
- FileFilter patternFilter = new WildcardFileFilter(pattern);
+ FileFilter patternFilter = new WildcardFileFilter(cleanPat);
File[] files = dir.listFiles(patternFilter);
for (int i = 0; i < files.length; i++)
{
Added: trunk/src/test/java/au/csiro/netcdf/util/UtilTest.java
===================================================================
--- trunk/src/test/java/au/csiro/netcdf/util/UtilTest.java (rev 0)
+++ trunk/src/test/java/au/csiro/netcdf/util/UtilTest.java 2010-06-24 00:29:08 UTC (rev 29)
@@ -0,0 +1,79 @@
+/**
+ * Copyright 2010, CSIRO Australia.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package au.csiro.netcdf.util;
+
+import java.util.List;
+
+import junit.framework.TestCase;
+
+/**
+ * Check the function of the Util class.
+ *
+ * @author James Dempsey on 23/06/2010
+ * @version $Revision$ $Date$
+ */
+public class UtilTest extends TestCase
+{
+
+ /* (non-Javadoc)
+ * @see junit.framework.TestCase#setUp()
+ */
+ protected void setUp() throws Exception
+ {
+ super.setUp();
+ }
+
+ /**
+ * Test method for {@link au.csiro.netcdf.util.Util#getListOfTargetFiles(java.lang.String, java.lang.String)}.
+ */
+ public final void testGetListOfTargetFiles()
+ {
+ List<String> files = Util.getListOfTargetFiles(".", "*.txt");
+ assertNotNull("Files should be a non-empty list", files);
+ assertTrue("Files should be a non-empty list", files.size()>1);
+ boolean hasUsage = false;
+ for (String string : files)
+ {
+ if (string.endsWith("USAGE.txt"))
+ {
+ hasUsage = true;
+ }
+ }
+ assertTrue("Expected to find USAGE.txt in result set.", hasUsage);
+
+ }
+
+ /**
+ * Test method for {@link au.csiro.netcdf.util.Util#getListOfTargetFiles(java.lang.String, java.lang.String)}.
+ */
+ public final void testGetListOfTargetFilesEscaped()
+ {
+ List<String> files = Util.getListOfTargetFiles(".", "\\*.txt");
+ assertNotNull("Files should be a non-empty list", files);
+ assertTrue("Files should be a non-empty list", files.size()>1);
+ boolean hasUsage = false;
+ for (String string : files)
+ {
+ if (string.endsWith("USAGE.txt"))
+ {
+ hasUsage = true;
+ }
+ }
+ assertTrue("Expected to find USAGE.txt in result set.", hasUsage);
+
+ }
+
+}
Property changes on: trunk/src/test/java/au/csiro/netcdf/util/UtilTest.java
___________________________________________________________________
Added: svn:keywords
+ Author Revision Date Id
Added: svn:eol-style
+ native
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