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 e2a7fc8f76616c9acbafc3b2f1fa0c456990c8b4..7b18b9cef3745774b95723dbfdca223d1962f810 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
@@ -58,23 +58,6 @@ public class DefaultParser<E> implements IParser<E>
return factory.createObject(tokens);
}
- /**
- * Parses given <code>line</code> into an element.
- * <p>
- * Uses <code>ILineTokenizer</code> to do its job.
- * </p>
- *
- * @param lineNumber line number.
- */
- private final String[] parseLine(final int lineNumber, final String line)
- {
- return lineTokenizer.tokenize(line);
- }
-
- //
- // Parser
- //
-
public final List<E> parse(final Iterator<Line> lineIterator, final ILineFilter lineFilter,
final int headerLength) throws ParsingException
{
@@ -89,12 +72,8 @@ public class DefaultParser<E> implements IParser<E>
final int number = line.getNumber();
if (lineFilter.acceptLine(nextLine, number))
{
- final String[] tokens = parseLine(number, nextLine);
E object = null;
- if (tokens.length != headerLength)
- {
- throw new ColumnSizeMismatchException(tokens, number, headerLength);
- }
+ String[] tokens = parseLine(number, nextLine, headerLength);
try
{
object = createObject(tokens);
@@ -108,11 +87,30 @@ public class DefaultParser<E> implements IParser<E>
lineTokenizer.destroy();
return elements;
}
-
}
public final void setObjectFactory(final IParserObjectFactory<E> factory)
{
this.factory = factory;
}
-}
\ No newline at end of file
+
+ private String[] parseLine(final int lineNumber, final String nextLine, final int headerLength)
+ {
+ String[] tokens = lineTokenizer.tokenize(nextLine);
+ if (tokens.length > headerLength)
+ {
+ throw new ColumnSizeMismatchException(tokens, lineNumber, headerLength);
+ }
+ if (tokens.length < headerLength)
+ {
+ String[] newTokens = new String[headerLength];
+ System.arraycopy(tokens, 0, newTokens, 0, tokens.length);
+ for (int i = tokens.length; i < headerLength; i++)
+ {
+ newTokens[i] = "";
+ }
+ tokens = newTokens;
+ }
+ return tokens;
+ }
+}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java
index 688145ca88375b8ae93888df2e8fa13b8451b6ae..4cb61a6bacb9d3a2d6e205cbaeb98cedfe89f5b8 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java
@@ -37,6 +37,16 @@ public final class DefaultParserTest
"Charles\tDarwin\tHumboldt Ave. 1865\t4242 Somewhere",
"Albert\tEinstein\tNewton Road 1905\t4711 Princton");
+ private final static List<String> textWithTab =
+ Arrays.asList("", "# This is a comment", "firstName\tlastName\taddress\tcity",
+ "Charles\tDarwin\tHumboldt Ave. 1865\t4242 Somewhere",
+ "Albert\t\tNewton Road 1905\t");
+
+ private final static List<String> textWithMissingLastCells =
+ Arrays.asList("", "# This is a comment", "firstName\tlastName\taddress\tcity",
+ "\tDarwin\tHumboldt Ave. 1865",
+ "Albert\tEinstein");
+
private final static int HEADER_LENGTH = 4;
private final static IParser<String[]> createParser()
@@ -51,7 +61,7 @@ public final class DefaultParserTest
{
final IParser<String[]> parser = createParser();
final List<String[]> result =
- parser.parse(createLineIterator(), new HeaderLineFilter(), HEADER_LENGTH);
+ parser.parse(createLineIterator(text), new HeaderLineFilter(), HEADER_LENGTH);
assertEquals(3, result.size());
assertEquals(result.get(0)[0], "firstName");
assertEquals(result.get(1)[1], "Darwin");
@@ -64,11 +74,41 @@ public final class DefaultParserTest
{
final IParser<String[]> parser = createParser();
final List<String[]> result =
- parser.parse(createLineIterator(), new HeaderLineFilter(3), HEADER_LENGTH);
+ parser.parse(createLineIterator(text), new HeaderLineFilter(3), HEADER_LENGTH);
assertEquals(2, result.size());
assertEquals(result.get(0)[0], "Charles");
assertEquals(result.get(1)[1], "Einstein");
}
+
+ @Test
+ public final void testParseFileWithTabs()
+ {
+ final IParser<String[]> parser = createParser();
+ final List<String[]> result =
+ parser.parse(createLineIterator(textWithTab), new HeaderLineFilter(), HEADER_LENGTH);
+ assertEquals(3, result.size());
+ assertEquals("Albert", result.get(2)[0]);
+ assertEquals("", result.get(2)[1]);
+ assertEquals("Newton Road 1905", result.get(2)[2]);
+ assertEquals("", result.get(2)[3]);
+ }
+
+ @Test
+ public final void testParseFileWithMissingLastCells()
+ {
+ final IParser<String[]> parser = createParser();
+ final List<String[]> result =
+ parser.parse(createLineIterator(textWithMissingLastCells), new HeaderLineFilter(), HEADER_LENGTH);
+ assertEquals(3, result.size());
+ assertEquals("", result.get(1)[0]);
+ assertEquals("Darwin", result.get(1)[1]);
+ assertEquals("Humboldt Ave. 1865", result.get(1)[2]);
+ assertEquals("", result.get(1)[3]);
+ assertEquals("Albert", result.get(2)[0]);
+ assertEquals("Einstein", result.get(2)[1]);
+ assertEquals("", result.get(2)[2]);
+ assertEquals("", result.get(2)[3]);
+ }
@Test
public final void testParseWithColumnSizeMismatching()
@@ -76,7 +116,7 @@ public final class DefaultParserTest
final IParser<String[]> parser = createParser();
try
{
- parser.parse(createLineIterator(), new HeaderLineFilter(3), HEADER_LENGTH + 1);
+ parser.parse(createLineIterator(text), new HeaderLineFilter(3), HEADER_LENGTH + 1);
} catch (final ColumnSizeMismatchException ex)
{
assertEquals(
@@ -104,7 +144,7 @@ public final class DefaultParserTest
parser.setObjectFactory(IParserObjectFactory.STRING_ARRAY_OBJECT_FACTORY);
try
{
- parser.parse(createLineIterator(), new HeaderLineFilter(2), HEADER_LENGTH);
+ parser.parse(createLineIterator(text), new HeaderLineFilter(2), HEADER_LENGTH);
fail(String.format("'%s' exception expected.", ParsingException.class));
} catch (final ParsingException ex)
{
@@ -115,11 +155,11 @@ public final class DefaultParserTest
}
}
- private Iterator<Line> createLineIterator()
+ private Iterator<Line> createLineIterator(final List<String> lines)
{
return new Iterator<Line>()
{
- private final Iterator<String> iterator = text.iterator();
+ private final Iterator<String> iterator = lines.iterator();
private int lineNumber;