diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AbstractValidator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AbstractValidator.java
index 35b0d85f594480a20dd3d6010e5c9088b64ddfa2..867417a5563b35773cc9a3395a3d34b2cf95eec9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AbstractValidator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AbstractValidator.java
@@ -21,7 +21,7 @@ import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
- *
+ * Super class for validators which handles empty cells in the same way.
*
* @author Franz-Josef Elmer
*/
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/ColumnDefinition.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/ColumnDefinition.java
index 84c298db50b312e8d6d879c8a10905df517bd8c9..fa6a47bcbf42a63de5f91e69ec07bd5a62c73c3f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/ColumnDefinition.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/ColumnDefinition.java
@@ -24,7 +24,7 @@ import ch.systemsx.cisd.common.utilities.ClassUtils;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
/**
- *
+ * Definition of a column used by {@link DataSetValidatorForTSV}.
*
* @author Franz-Josef Elmer
*/
@@ -35,17 +35,20 @@ class ColumnDefinition
static final String HEADER_VALIDATOR_KEY = "header-validator";
static final String HEADER_PATTERN_KEY = "header-pattern";
static final String VALUE_VALIDATOR_KEY = "value-validator";
+ static final String CAN_DEFINE_MULTIPLE_COLUMNS_KEY = "can-define-multiple-columns";
private final String name;
private final IColumnHeaderValidator headerValidator;
private final IValidatorFactory valueValidatorFactory;
private final boolean mandatory;
private final Integer orderOrNull;
+ private final boolean canDefineMultipleColumns;
static ColumnDefinition create(String name, Properties properties)
{
boolean mandatory = PropertyUtils.getBoolean(properties, MANDATORY_KEY, false);
Integer order = null;
+ boolean canDefineMultipleColumns;
if (properties.getProperty(ORDER_KEY) != null)
{
order = PropertyUtils.getInt(properties, ORDER_KEY, 0);
@@ -53,6 +56,11 @@ class ColumnDefinition
{
throw new ConfigurationFailureException("Order value has to be positive: " + order);
}
+ canDefineMultipleColumns = false;
+ } else
+ {
+ canDefineMultipleColumns =
+ PropertyUtils.getBoolean(properties, CAN_DEFINE_MULTIPLE_COLUMNS_KEY, false);
}
String headerValidatorName = properties.getProperty(HEADER_VALIDATOR_KEY);
IColumnHeaderValidator headerValidator;
@@ -71,17 +79,25 @@ class ColumnDefinition
.getName());
IValidatorFactory factory =
ClassUtils.create(IValidatorFactory.class, validatorFactoryName, properties);
- return new ColumnDefinition(name, headerValidator, factory, mandatory, order);
+ return new ColumnDefinition(name, headerValidator, factory, mandatory, order,
+ canDefineMultipleColumns);
}
private ColumnDefinition(String name, IColumnHeaderValidator headerValidator,
- IValidatorFactory valueValidatorFactory, boolean mandatory, Integer orderOrNull)
+ IValidatorFactory valueValidatorFactory, boolean mandatory, Integer orderOrNull,
+ boolean canDefineMultipleColumns)
{
this.name = name;
this.headerValidator = headerValidator;
this.valueValidatorFactory = valueValidatorFactory;
this.mandatory = mandatory;
this.orderOrNull = orderOrNull;
+ this.canDefineMultipleColumns = canDefineMultipleColumns;
+ }
+
+ boolean canDefineMultipleColumns()
+ {
+ return canDefineMultipleColumns;
}
boolean isMandatory()
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSV.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSV.java
index 01f80ac901132f8d6c268979cdb181d9c44b959b..b6927b51128744e19fcedc0ae9b57452a7ece2c6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSV.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSV.java
@@ -20,6 +20,7 @@ import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.LinkedList;
@@ -41,8 +42,14 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.utils.PropertyParametersUtil.
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
/**
- * Validator for data sets containing TAB-separated value (TSV) files.
- *
+ * Validator for data sets containing TAB-separated value (TSV) files. Such a file is valid if
+ * <ul>
+ * <li>All column headers are unique.
+ * <li>For each column a {@link ColumnDefinition} as specified by the properties are found.
+ * <li>All values of a column are valid in accordance to the {@link IValidator} created by the
+ * {@link ColumnDefinition} instance of the column.
+ * </ul>
+ *
* @author Franz-Josef Elmer
*/
class DataSetValidatorForTSV implements IDataSetValidator
@@ -128,6 +135,7 @@ class DataSetValidatorForTSV implements IDataSetValidator
throw new IOException("Empty file '" + file);
}
String[] headers = getRowCells(lineIterator.nextLine());
+ assertUniqueHeaders(headers);
ColumnDefinition[] definitions = findColumnDefinitions(headers);
IValidator[] validators = new IValidator[definitions.length];
for (int i = 0; i < validators.length; i++)
@@ -166,7 +174,19 @@ class DataSetValidatorForTSV implements IDataSetValidator
{
IOUtils.closeQuietly(reader);
}
-
+ }
+
+ private void assertUniqueHeaders(String[] headers)
+ {
+ HashSet<String> headerSet = new HashSet<String>();
+ for (String header : headers)
+ {
+ if (headerSet.contains(header))
+ {
+ throw new UserFailureException("Column header '" + header + "' appeared twice.");
+ }
+ headerSet.add(header);
+ }
}
private ColumnDefinition[] findColumnDefinitions(String[] columnHeaders)
@@ -239,7 +259,10 @@ class DataSetValidatorForTSV implements IDataSetValidator
ColumnDefinition columnDefinition = iterator.next();
if (columnDefinition.isValidHeader(columnHeader))
{
- iterator.remove();
+ if (columnDefinition.canDefineMultipleColumns() == false)
+ {
+ iterator.remove();
+ }
return columnDefinition;
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DefaultValueValidatorFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DefaultValueValidatorFactory.java
index fa127b029b01e176829dd45a985fa5c4986a65e3..c6241da68ec8ad3d528145584d46c6acb6c347dd 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DefaultValueValidatorFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DefaultValueValidatorFactory.java
@@ -21,7 +21,7 @@ import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
/**
- *
+ * Default factory for {@link IValidator} intances.
*
* @author Franz-Josef Elmer
*/
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IColumnHeaderValidator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IColumnHeaderValidator.java
index 590915b4e7ea841744df0280f09bbb354da647a1..3c96effebac8722b7e137ea1002bde55777579fe 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IColumnHeaderValidator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IColumnHeaderValidator.java
@@ -17,11 +17,14 @@
package ch.systemsx.cisd.etlserver.validation;
/**
- *
+ * Interface of a validator for the header of a column.
*
* @author Franz-Josef Elmer
*/
public interface IColumnHeaderValidator
{
+ /**
+ * Returns <code>true</code> if the specified header is valid.
+ */
public boolean isValidHeader(String header);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IValidator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IValidator.java
index 644a7c87dbc2f8a8e0db10e42f13cac4143450de..4e2b3cf188dd04317631b54cadbdf9156c7fe08e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IValidator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IValidator.java
@@ -16,12 +16,19 @@
package ch.systemsx.cisd.etlserver.validation;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
/**
- *
+ * Interface for a validator of a table cell value.
*
* @author Franz-Josef Elmer
*/
public interface IValidator
{
+ /**
+ * Asserts valid table cell value.
+ *
+ * @throws UserFailureException if the specified value is not valid.
+ */
public void assertValid(String value);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IValidatorFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IValidatorFactory.java
index d770118b1de305b37d98f949870da260ad1c9580..4e42035830d4badc2e0472032cf3052c4b1edff2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IValidatorFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/IValidatorFactory.java
@@ -17,11 +17,15 @@
package ch.systemsx.cisd.etlserver.validation;
/**
- *
+ * Factory for table cell validators.
*
* @author Franz-Josef Elmer
*/
public interface IValidatorFactory
{
+ /**
+ * Creates a validator. The same instance can be returned as in a previous call if the
+ * validator object is immutable.
+ */
public IValidator createValidator();
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSVTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSVTest.java
index 0807d3f6f1e7a62b2b2a9a39c946908e8a9e5e8a..5bdc717b6f1006b2c58e7ab3e1237bd73ff9f66b 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSVTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSVTest.java
@@ -307,6 +307,53 @@ public class DataSetValidatorForTSVTest extends AbstractFileSystemTestCase
MockValidatorFactory.assertSatisfied();
}
+ @Test
+ public void testUniqueColumnHeaders()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(DataSetValidatorForTSV.PATH_PATTERNS_KEY, "*");
+ DataSetValidatorForTSV validator = new DataSetValidatorForTSV(properties);
+ FileUtilities.writeToFile(new File(workingDirectory, "a.txt"), "A\tA\n");
+
+ try
+ {
+ validator.assertValidDataSet(null, workingDirectory);
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Column header 'A' appeared twice.", ex.getMessage());
+ }
+
+ MockValidatorFactory.assertSatisfied();
+ }
+
+ @Test
+ public void testColumnDefinitionWhichCanBeUsedToDefineMultipleColumnsOrder()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(DataSetValidatorForTSV.PATH_PATTERNS_KEY, "a.txt");
+ properties.setProperty(DataSetValidatorForTSV.COLUMNS_KEY, "c1, c2, c3, c4");
+ properties.setProperty("c1." + ColumnDefinition.HEADER_PATTERN_KEY, "ID");
+ properties.setProperty("c1." + ColumnDefinition.MANDATORY_KEY, "yes");
+ properties.setProperty("c1." + ColumnDefinition.ORDER_KEY, "1");
+ properties.setProperty("c1." + ColumnDefinition.VALUE_VALIDATOR_KEY, MOCK_FACTORY);
+ properties.setProperty("c1." + NAME_KEY, "c1");
+ properties.setProperty("c1." + EXPECTED_VALUES_KEY, "1,2");
+ properties.setProperty("c2." + ColumnDefinition.HEADER_PATTERN_KEY, "A[0-9]*");
+ properties.setProperty("c2." + ColumnDefinition.CAN_DEFINE_MULTIPLE_COLUMNS_KEY, "true");
+ properties.setProperty("c2." + ColumnDefinition.VALUE_VALIDATOR_KEY, MOCK_FACTORY);
+ properties.setProperty("c2." + NAME_KEY, "c2");
+ properties.setProperty("c2." + EXPECTED_VALUES_KEY, "a,b,c,d");
+ DataSetValidatorForTSV validator = new DataSetValidatorForTSV(properties);
+
+ FileUtilities.writeToFile(new File(workingDirectory, "a.txt"), "ID\tA6\tA42\n"
+ + "1\ta\tb\n" + "2\tc\td\n");
+
+ validator.assertValidDataSet(null, workingDirectory);
+
+ MockValidatorFactory.assertSatisfied();
+ }
+
@Test
public void testMissingColumnWithOrder()
{