From f2346394dc9ad33cfdb69c7c1d160979da7e1ca2 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 7 Jun 2010 13:38:51 +0000
Subject: [PATCH] BaSysBio needs: log CIFEX data set upload info, allow moving
to error for CIFEX Storage Processor, log data set type of message of data
set validator, allow trailing empty cells in TSV viewer
SVN: 16303
---
.../cisd/etlserver/CifexStorageProcessor.java | 6 ++++-
.../cifex/CifexDataSetInfoExtractor.java | 10 ++++++++
.../validation/DataSetValidator.java | 10 +++++++-
.../AbstractFileTableReportingPlugin.java | 24 +++++++++++++++++--
4 files changed, 46 insertions(+), 4 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java
index 715cce6d454..682edd656e4 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java
@@ -54,9 +54,12 @@ public class CifexStorageProcessor extends AbstractDelegatingStorageProcessor
LogFactory.getLogger(LogCategory.NOTIFY, CifexStorageProcessor.class);
public static final String KEEP_FILE_REGEX_KEY = "keep-file-regex";
+ public static final String MOVE_TO_ERROR_FOLDER_KEY = "move-to-error-folder";
private final String keepFileRegex;
+ private final boolean moveToErrorFolder;
+
private File dirToRestore;
private File fileToMove;
@@ -67,6 +70,7 @@ public class CifexStorageProcessor extends AbstractDelegatingStorageProcessor
{
super(properties);
keepFileRegex = PropertyUtils.getProperty(properties, KEEP_FILE_REGEX_KEY);
+ moveToErrorFolder = PropertyUtils.getBoolean(properties, MOVE_TO_ERROR_FOLDER_KEY, false);
}
@Override
@@ -92,7 +96,7 @@ public class CifexStorageProcessor extends AbstractDelegatingStorageProcessor
dirToRestore);
}
super.rollback(incomingDataSetDirectory, storedDataDirectory, exception);
- return UnstoreDataAction.DELETE;
+ return moveToErrorFolder ? UnstoreDataAction.MOVE_TO_ERROR : UnstoreDataAction.DELETE;
}
@Private
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
index c1cf70d420a..e123b578199 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
@@ -22,9 +22,13 @@ import java.io.File;
import java.util.Arrays;
import java.util.Properties;
+import org.apache.log4j.Logger;
+
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -42,6 +46,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
*/
public class CifexDataSetInfoExtractor implements IDataSetInfoExtractor
{
+ private final static Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, CifexDataSetInfoExtractor.class);
@Private
static final String DATA_SET_PROPERTIES_FILE_NAME_KEY =
@@ -62,6 +68,10 @@ public class CifexDataSetInfoExtractor implements IDataSetInfoExtractor
assert incomingDataSetPath != null : "Incoming data set path can not be null.";
DataSetUploadInfo info = CifexExtractorHelper.getDataSetUploadInfo(incomingDataSetPath);
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info("Data set upload info: " + info);
+ }
final DataSetInformation dataSetInformation = new DataSetInformation();
// either sample is specified or experiment (with optional data set parents)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidator.java
index 3b10f29a5b4..c4ba370c9bd 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidator.java
@@ -24,6 +24,7 @@ import java.util.Properties;
import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.utilities.ClassUtils;
@@ -101,7 +102,14 @@ public class DataSetValidator implements IDataSetValidator
IDataSetValidator validator = validators.get(dataSetType.getCode());
if (validator != null)
{
- validator.assertValidDataSet(dataSetType, incomingDataSetFileOrFolder);
+ try
+ {
+ validator.assertValidDataSet(dataSetType, incomingDataSetFileOrFolder);
+ } catch (Exception ex)
+ {
+ throw new UserFailureException("Data set of type '" + dataSetType.getCode()
+ + "' is invalid: " + ex.getMessage(), ex);
+ }
if (operationLog.isInfoEnabled())
{
operationLog.info("Data set [" + incomingDataSetFileOrFolder + "] of type '"
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractFileTableReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractFileTableReportingPlugin.java
index 752632a855b..cbd73d334f5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractFileTableReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractFileTableReportingPlugin.java
@@ -56,6 +56,8 @@ abstract public class AbstractFileTableReportingPlugin extends AbstractDatastore
private static final String SEPARATOR_PROPERTY_KEY = "separator";
private static final String IGNORE_COMMENTS_PROPERTY_KEY = "ignore-comments";
+
+ private static final String IGNORE_TRAILING_EMPTY_CELLS_PROPERTY_KEY = "ignore-trailing-empty-cells";
// if the line starts with this character and comments should be ignored, the line is ignored
private static final char COMMENT = '#';
@@ -64,6 +66,8 @@ abstract public class AbstractFileTableReportingPlugin extends AbstractDatastore
private final boolean ignoreComments;
+ private final boolean ignoreTrailingEmptyCells;
+
protected AbstractFileTableReportingPlugin(Properties properties, File storeRoot,
char defaultSeparator)
{
@@ -72,6 +76,9 @@ abstract public class AbstractFileTableReportingPlugin extends AbstractDatastore
PropertyUtils.getChar(properties, SEPARATOR_PROPERTY_KEY, defaultSeparator);
this.ignoreComments =
PropertyUtils.getBoolean(properties, IGNORE_COMMENTS_PROPERTY_KEY, true);
+ ignoreTrailingEmptyCells =
+ PropertyUtils.getBoolean(properties, IGNORE_TRAILING_EMPTY_CELLS_PROPERTY_KEY,
+ false);
}
@@ -143,10 +150,11 @@ abstract public class AbstractFileTableReportingPlugin extends AbstractDatastore
return new DatasetFileLines(file, dataset, lines);
}
- protected static TableModel createTableModel(DatasetFileLines lines)
+ protected TableModel createTableModel(DatasetFileLines lines)
{
SimpleTableModelBuilder tableBuilder = new SimpleTableModelBuilder();
- for (String title : lines.getHeaderTokens())
+ String[] headerTokens = lines.getHeaderTokens();
+ for (String title : headerTokens)
{
tableBuilder.addHeader(title);
}
@@ -157,6 +165,18 @@ abstract public class AbstractFileTableReportingPlugin extends AbstractDatastore
{
row.add(TableCellUtil.createTableCell(token));
}
+ if (ignoreTrailingEmptyCells)
+ {
+ while (row.size() > headerTokens.length)
+ {
+ ISerializableComparable cell = row.get(row.size() - 1);
+ if (cell.toString().length() > 0)
+ {
+ break;
+ }
+ row.remove(row.size() - 1);
+ }
+ }
tableBuilder.addRow(row);
}
return tableBuilder.getTableModel();
--
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