From 1958c7e504081d6800cd3064b86bc63815f26680 Mon Sep 17 00:00:00 2001
From: ribeaudc <ribeaudc>
Date: Thu, 6 Mar 2008 09:38:12 +0000
Subject: [PATCH] change: - 'ILineFilter' and its implementations moved to its
own package 'parser.filter'. add: - 'FileUtilities.loadToStringList' accepts
a 'ILineFilter' parameter (which could be null).
SVN: 4649
---
.../cisd/common/parser/DefaultParser.java | 2 +
.../cisd/common/parser/HeaderLineFilter.java | 3 +
.../systemsx/cisd/common/parser/IParser.java | 2 +
.../cisd/common/parser/ParserUtilities.java | 2 +
.../cisd/common/parser/TabFileLoader.java | 2 +
.../{ => filter}/AlwaysAcceptLineFilter.java | 2 +-
.../ExcludeEmptyAndCommentLineFilter.java | 2 +-
.../parser/{ => filter}/ILineFilter.java | 2 +-
.../cisd/common/utilities/FileUtilities.java | 87 ++++++++++++++-----
.../common/parser/ParserUtilitiesTest.java | 1 +
.../common/utilities/FileUtilitiesTest.java | 27 ++++++
11 files changed, 106 insertions(+), 26 deletions(-)
rename common/source/java/ch/systemsx/cisd/common/parser/{ => filter}/AlwaysAcceptLineFilter.java (90%)
rename common/source/java/ch/systemsx/cisd/common/parser/{ => filter}/ExcludeEmptyAndCommentLineFilter.java (93%)
rename common/source/java/ch/systemsx/cisd/common/parser/{ => filter}/ILineFilter.java (95%)
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java b/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
index 6cc8fee0920..98a6eeefb3b 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
@@ -20,6 +20,8 @@ import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
+import ch.systemsx.cisd.common.parser.filter.ILineFilter;
+
/**
* A default {@link IParser} implementation.
* <p>
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java b/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
index effaf40be6d..6b3d0b08adf 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
@@ -1,5 +1,8 @@
package ch.systemsx.cisd.common.parser;
+import ch.systemsx.cisd.common.parser.filter.ExcludeEmptyAndCommentLineFilter;
+import ch.systemsx.cisd.common.parser.filter.ILineFilter;
+
/**
* A <code>ILineFilter</code> implementation that extends {@link ExcludeEmptyAndCommentLineFilter} by
* excluding the header line (if <code>> 1</code>) as well.
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IParser.java b/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
index 59cbd702d02..28a1f135573 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
@@ -19,6 +19,8 @@ package ch.systemsx.cisd.common.parser;
import java.util.Iterator;
import java.util.List;
+import ch.systemsx.cisd.common.parser.filter.ILineFilter;
+
/**
* <code>IReaderParser</code> is able to parse a given text lines and to return a list of objects of type
* <code>E</code>.
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java b/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
index 9bd5e73c9e4..f07f180a40e 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
@@ -25,6 +25,8 @@ import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.parser.filter.AlwaysAcceptLineFilter;
+import ch.systemsx.cisd.common.parser.filter.ILineFilter;
/**
* Utilities for parsing files.
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java b/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
index 6670c82c742..e1b976886e9 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
@@ -33,6 +33,8 @@ import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.parser.filter.AlwaysAcceptLineFilter;
+import ch.systemsx.cisd.common.parser.filter.ILineFilter;
/**
* Convenient class to load a tab file and deliver a list of beans of type <code>T</code>. The following formats for
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/AlwaysAcceptLineFilter.java b/common/source/java/ch/systemsx/cisd/common/parser/filter/AlwaysAcceptLineFilter.java
similarity index 90%
rename from common/source/java/ch/systemsx/cisd/common/parser/AlwaysAcceptLineFilter.java
rename to common/source/java/ch/systemsx/cisd/common/parser/filter/AlwaysAcceptLineFilter.java
index 486f87e97e2..7ebf9129639 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/AlwaysAcceptLineFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/filter/AlwaysAcceptLineFilter.java
@@ -1,4 +1,4 @@
-package ch.systemsx.cisd.common.parser;
+package ch.systemsx.cisd.common.parser.filter;
/**
* A default line filter that accepts any line.
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ExcludeEmptyAndCommentLineFilter.java b/common/source/java/ch/systemsx/cisd/common/parser/filter/ExcludeEmptyAndCommentLineFilter.java
similarity index 93%
rename from common/source/java/ch/systemsx/cisd/common/parser/ExcludeEmptyAndCommentLineFilter.java
rename to common/source/java/ch/systemsx/cisd/common/parser/filter/ExcludeEmptyAndCommentLineFilter.java
index fc0498aaa58..b0c16d27d0c 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ExcludeEmptyAndCommentLineFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/filter/ExcludeEmptyAndCommentLineFilter.java
@@ -1,4 +1,4 @@
-package ch.systemsx.cisd.common.parser;
+package ch.systemsx.cisd.common.parser.filter;
/**
* A default <code>LineFilter</code> implementation that excludes empty and comment lines.
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ILineFilter.java b/common/source/java/ch/systemsx/cisd/common/parser/filter/ILineFilter.java
similarity index 95%
rename from common/source/java/ch/systemsx/cisd/common/parser/ILineFilter.java
rename to common/source/java/ch/systemsx/cisd/common/parser/filter/ILineFilter.java
index 79981c2cf0e..cef4af9c34e 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ILineFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/filter/ILineFilter.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.common.parser;
+package ch.systemsx.cisd.common.parser.filter;
/**
* A line filter for <code>ReaderParser</code>.
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/FileUtilities.java b/common/source/java/ch/systemsx/cisd/common/utilities/FileUtilities.java
index 378b1e95b32..fdc6442caf0 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/FileUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/FileUtilities.java
@@ -48,6 +48,8 @@ import ch.systemsx.cisd.common.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.logging.ISimpleLogger;
import ch.systemsx.cisd.common.logging.LogLevel;
+import ch.systemsx.cisd.common.parser.filter.AlwaysAcceptLineFilter;
+import ch.systemsx.cisd.common.parser.filter.ILineFilter;
/**
* Some useful utility methods for files and directories.
@@ -178,15 +180,30 @@ public final class FileUtilities
* @return The content of the file line by line.
* @throws CheckedExceptionTunnel for wrapping an {@link IOException}, e.g. if the file does not exist.
*/
- public static List<String> loadToStringList(File file) throws CheckedExceptionTunnel
+ public final static List<String> loadToStringList(final File file) throws CheckedExceptionTunnel
{
- assert file != null;
+ return loadToStringList(file, null);
+ }
+
+ /**
+ * Loads a text file line by line to a {@link List} of {@link String}s.
+ *
+ * @param file the file that should be loaded. This method asserts that given <code>File</code> is not
+ * <code>null</code>.
+ * @param lineFilterOrNull a line filter if you are not interested in all lines. May be <code>null</code>.
+ * @return The content of the file line by line.
+ * @throws CheckedExceptionTunnel for wrapping an {@link IOException}, e.g. if the file does not exist.
+ */
+ public final static List<String> loadToStringList(final File file, final ILineFilter lineFilterOrNull)
+ throws CheckedExceptionTunnel
+ {
+ assert file != null : "Unspecified file.";
FileReader fileReader = null;
try
{
fileReader = new FileReader(file);
- return readStringList(new BufferedReader(fileReader));
+ return readStringList(new BufferedReader(fileReader), lineFilterOrNull);
} catch (IOException ex)
{
throw new CheckedExceptionTunnel(ex);
@@ -215,8 +232,8 @@ public final class FileUtilities
BufferedReader reader = null;
try
{
- reader = getBufferedReader(clazz, resource);
- return readString(reader);
+ reader = tryGetBufferedReader(clazz, resource);
+ return reader == null ? null : readString(reader);
} catch (IOException ex)
{
throw new CheckedExceptionTunnel(ex);
@@ -230,23 +247,43 @@ public final class FileUtilities
* Loads a text file line by line to a {@link List} of {@link String}s.
* <p>
* A non-existent resource will result in a return value of <code>null</code>.
+ * </p>
*
* @param clazz Class for which <code>getResource()</code> will be invoked.
- * @param resource Absolute path of the resource (will be the argument of <code>getResource()</code>).
+ * @param resource absolute path of the resource (will be the argument of <code>getResource()</code>).
* @return The content of the resource line by line.
* @throws CheckedExceptionTunnel for wrapping an {@link IOException}, e.g. if the file does not exist.
*/
- public static List<String> loadToStringList(final Class<?> clazz, final String resource)
+ public final static List<String> loadToStringList(final Class<?> clazz, final String resource)
throws CheckedExceptionTunnel
+ {
+ return loadToStringList(clazz, resource, null);
+ }
+
+ /**
+ * Loads a text file line by line to a {@link List} of {@link String}s.
+ * <p>
+ * A non-existent resource will result in a return value of <code>null</code>.
+ * </p>
+ *
+ * @param clazz Class for which <code>getResource()</code> will be invoked.
+ * @param resource absolute path of the resource (will be the argument of <code>getResource()</code>).
+ * @param lineFilterOrNull a line filter if you are not interested in all lines. May be <code>null</code>.
+ * @return The content of the resource line by line or <code>null</code> if given <var>resource</var> can not be
+ * found.
+ * @throws CheckedExceptionTunnel for wrapping an {@link IOException}, e.g. if the file does not exist.
+ */
+ public final static List<String> loadToStringList(final Class<?> clazz, final String resource,
+ final ILineFilter lineFilterOrNull) throws CheckedExceptionTunnel
{
assert clazz != null : "Given class can not be null.";
- assert resource != null && resource.length() > 0 : "Given resource can not be null.";
+ assert StringUtils.isNotEmpty(resource) : "Given resource can not be empty.";
BufferedReader reader = null;
try
{
- reader = getBufferedReader(clazz, resource);
- return readStringList(reader);
+ reader = tryGetBufferedReader(clazz, resource);
+ return reader == null ? null : readStringList(reader, lineFilterOrNull);
} catch (IOException ex)
{
throw new CheckedExceptionTunnel(ex);
@@ -256,7 +293,7 @@ public final class FileUtilities
}
}
- private final static BufferedReader getBufferedReader(final Class<?> clazz, final String resource)
+ private final static BufferedReader tryGetBufferedReader(final Class<?> clazz, final String resource)
throws FileNotFoundException
{
final URL url = clazz.getResource(resource);
@@ -273,13 +310,9 @@ public final class FileUtilities
}
}
- private static String readString(BufferedReader reader) throws IOException
+ private static String readString(final BufferedReader reader) throws IOException
{
- if (reader == null)
- {
- return null;
- }
-
+ assert reader != null : "Unspecified BufferedReader.";
final StringBuilder builder = new StringBuilder();
String line;
while ((line = reader.readLine()) != null)
@@ -289,18 +322,26 @@ public final class FileUtilities
return builder.toString();
}
- private static List<String> readStringList(BufferedReader reader) throws IOException
+ private final static List<String> readStringList(final BufferedReader reader, final ILineFilter lineFilterOrNull)
+ throws IOException
{
- if (reader == null)
+ assert reader != null : "Unspecified BufferedReader.";
+ final ILineFilter lineFilter;
+ if (lineFilterOrNull == null)
{
- return null;
+ lineFilter = AlwaysAcceptLineFilter.INSTANCE;
+ } else
+ {
+ lineFilter = lineFilterOrNull;
}
-
final List<String> list = new ArrayList<String>();
String line;
- while ((line = reader.readLine()) != null)
+ for (int lineNumber = 0; (line = reader.readLine()) != null; lineNumber++)
{
- list.add(line);
+ if (lineFilter.acceptLine(line, lineNumber))
+ {
+ list.add(line);
+ }
}
return list;
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java
index dce574df6d6..f2af1aa96ec 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java
@@ -30,6 +30,7 @@ import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.logging.LogInitializer;
+import ch.systemsx.cisd.common.parser.filter.ExcludeEmptyAndCommentLineFilter;
/**
* Test cases for corresponding {@link ParserUtilities} class.
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java
index 95449dd3761..68e3079d203 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java
@@ -40,6 +40,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.common.Constants;
import ch.systemsx.cisd.common.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.parser.filter.ExcludeEmptyAndCommentLineFilter;
/**
* Test cases for the {@link FileUtilities}.
@@ -215,6 +216,32 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
assertEquals(Arrays.asList("Hello", "World!"), text);
}
+ @Test
+ public final void testLoadToStringListFileWithLineFilter() throws Exception
+ {
+ final File file = new File(workingDirectory, "test.txt");
+ final FileWriter writer = new FileWriter(file);
+ try
+ {
+ writer.write("\nHello\nWorld!\n\n");
+ } finally
+ {
+ writer.close();
+ }
+ // With no line filter.
+ List<String> text = FileUtilities.loadToStringList(file);
+ assertEquals(4, text.size());
+ assertEquals(Arrays.asList("", "Hello", "World!", ""), text);
+ // With null line filter.
+ text = FileUtilities.loadToStringList(file, null);
+ assertEquals(4, text.size());
+ assertEquals(Arrays.asList("", "Hello", "World!", ""), text);
+ // With a correct line filter.
+ text = FileUtilities.loadToStringList(file, ExcludeEmptyAndCommentLineFilter.INSTANCE);
+ assertEquals(2, text.size());
+ assertEquals(Arrays.asList("Hello", "World!"), text);
+ }
+
@Test
public final void testRemovePrefixFromFileName()
{
--
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