From db41fdba0c0d197bc3ccfa727d15ea364acd9326 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 8 Jun 2010 08:35:08 +0000
Subject: [PATCH] test and bug fixing of TSVViewReportingPlugin
SVN: 16320
---
.../dss/generic/server/AutoResolveUtils.java | 18 ++-
.../AbstractFileTableReportingPlugin.java | 21 +--
.../plugins/tasks/DatasetFileLines.java | 28 +++-
.../standard/TSVViewReportingPluginTest.java | 122 ++++++++++++++++++
4 files changed, 165 insertions(+), 24 deletions(-)
create mode 100644 datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/TSVViewReportingPluginTest.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AutoResolveUtils.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AutoResolveUtils.java
index ddb1f3fcb90..0cc113544de 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AutoResolveUtils.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AutoResolveUtils.java
@@ -148,15 +148,23 @@ public class AutoResolveUtils
return;
} else
{
- for (File f : startingPoint.listFiles(filter))
+ File[] filteredFiles = startingPoint.listFiles(filter);
+ if (filteredFiles != null)
{
- result.add(f);
+ for (File f : filteredFiles)
+ {
+ result.add(f);
+ }
}
- for (File d : startingPoint.listFiles())
+ File[] files = startingPoint.listFiles();
+ if (files != null)
{
- if (d.isDirectory())
+ for (File d : files)
{
- findFiles(d, filter, result);
+ if (d.isDirectory())
+ {
+ findFiles(d, filter, result);
+ }
}
}
}
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 cbd73d334f5..2dccf3dd3c8 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
@@ -55,9 +55,9 @@ abstract public class AbstractFileTableReportingPlugin extends AbstractDatastore
private static final String SEPARATOR_PROPERTY_KEY = "separator";
- private static final String IGNORE_COMMENTS_PROPERTY_KEY = "ignore-comments";
+ public static final String IGNORE_COMMENTS_PROPERTY_KEY = "ignore-comments";
- private static final String IGNORE_TRAILING_EMPTY_CELLS_PROPERTY_KEY = "ignore-trailing-empty-cells";
+ public 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 = '#';
@@ -147,14 +147,13 @@ abstract public class AbstractFileTableReportingPlugin extends AbstractDatastore
{
lines.add(reader.getValues());
}
- return new DatasetFileLines(file, dataset, lines);
+ return new DatasetFileLines(file, dataset.getDatasetCode(), lines, ignoreTrailingEmptyCells);
}
protected TableModel createTableModel(DatasetFileLines lines)
{
SimpleTableModelBuilder tableBuilder = new SimpleTableModelBuilder();
- String[] headerTokens = lines.getHeaderTokens();
- for (String title : headerTokens)
+ for (String title : lines.getHeaderTokens())
{
tableBuilder.addHeader(title);
}
@@ -165,18 +164,6 @@ 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();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/DatasetFileLines.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/DatasetFileLines.java
index dc9b4139318..8183906d728 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/DatasetFileLines.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/DatasetFileLines.java
@@ -20,6 +20,8 @@ import java.io.File;
import java.util.ArrayList;
import java.util.List;
+import org.apache.commons.lang.StringUtils;
+
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
@@ -42,6 +44,11 @@ public class DatasetFileLines
}
public DatasetFileLines(File file, String datasetCode, List<String[]> lines)
+ {
+ this(file, datasetCode, lines, false);
+ }
+
+ public DatasetFileLines(File file, String datasetCode, List<String[]> lines, boolean ignoreTrailingEmptyCells)
{
this.file = file;
if (lines.size() < 2)
@@ -54,18 +61,35 @@ public class DatasetFileLines
dataLines = new ArrayList<String[]>(lines.size());
for (int i = 1; i < lines.size(); i++)
{
- String[] dataTokens = lines.get(i);
+ String[] dataTokens = getTokens(lines.get(i), ignoreTrailingEmptyCells);
if (headerTokens.length != dataTokens.length)
{
throw UserFailureException.fromTemplate(
"Number of columns in header (%s) does not match number of columns "
- + "in %d data row (%s) in Data Set '%s' file.",
+ + "in %d. data row (%s) in Data Set '%s' file.",
headerTokens.length, i, dataTokens.length, datasetCode);
}
dataLines.add(dataTokens);
}
}
+ private String[] getTokens(String[] dataTokens, boolean ignoreTrailingEmptyCells)
+ {
+ if (ignoreTrailingEmptyCells)
+ {
+ int indexOfLastNonEmptyCell = dataTokens.length - 1;
+ while (indexOfLastNonEmptyCell >= headerTokens.length
+ && StringUtils.isBlank(dataTokens[indexOfLastNonEmptyCell]))
+ {
+ indexOfLastNonEmptyCell--;
+ }
+ String[] newDataTopkens = new String[indexOfLastNonEmptyCell + 1];
+ System.arraycopy(dataTokens, 0, newDataTopkens, 0, newDataTopkens.length);
+ return newDataTopkens;
+ }
+ return dataTokens;
+ }
+
public final File getFile()
{
return file;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/TSVViewReportingPluginTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/TSVViewReportingPluginTest.java
new file mode 100644
index 00000000000..a821150aa3e
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/TSVViewReportingPluginTest.java
@@ -0,0 +1,122 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * 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 ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard;
+
+import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractFileTableReportingPlugin.IGNORE_COMMENTS_PROPERTY_KEY;
+import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractFileTableReportingPlugin.IGNORE_TRAILING_EMPTY_CELLS_PROPERTY_KEY;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Properties;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class TSVViewReportingPluginTest extends AbstractFileSystemTestCase
+{
+ private static final String TEST_FILE = "test.txt";
+
+ private File store;
+
+ private File dataSetInStore;
+
+ private DatasetDescription datasetDescription;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ store = new File(workingDirectory, "store");
+ store.mkdirs();
+ dataSetInStore = new File(store, "dataset");
+ dataSetInStore.mkdirs();
+ datasetDescription = new DatasetDescription();
+ datasetDescription.setDatasetCode("ds1");
+ datasetDescription.setMainDataSetPattern(".*");
+ datasetDescription.setDataSetLocation(dataSetInStore.getName());
+ }
+
+ @Test
+ public void testCreateReport()
+ {
+ FileUtilities.writeToFile(new File(dataSetInStore, TEST_FILE), "a\tb\n1\t2\n\t4");
+ TSVViewReportingPlugin plugin = new TSVViewReportingPlugin(new Properties(), store);
+ TableModel tableModel = plugin.createReport(Arrays.asList(datasetDescription));
+
+ assertEquals("[a, b]", tableModel.getHeader().toString());
+ List<TableModelRow> rows = tableModel.getRows();
+ assertEquals("[1, 2]", rows.get(0).getValues().toString());
+ assertEquals("[, 4]", rows.get(1).getValues().toString());
+ assertEquals(2, rows.size());
+ }
+
+ @Test
+ public void testCreateReportFailingBecauseOfInvalidNumberOfCells()
+ {
+ FileUtilities.writeToFile(new File(dataSetInStore, TEST_FILE), "a\tb\n1\t2\t3\t\n");
+ Properties properties = new Properties();
+ properties.setProperty(IGNORE_TRAILING_EMPTY_CELLS_PROPERTY_KEY, "true");
+ TSVViewReportingPlugin plugin = new TSVViewReportingPlugin(properties, store);
+
+ try
+ {
+ plugin.createReport(Arrays.asList(datasetDescription));
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Number of columns in header (2) does not match number of columns in "
+ + "1. data row (3) in Data Set 'ds1' file.", ex.getMessage());
+ }
+ }
+
+ @Test
+ public void testIgnoringCommentAndTrailingEmptyCells()
+ {
+ FileUtilities.writeToFile(new File(dataSetInStore, TEST_FILE),
+ "a\tb\n" +
+ "#comment\n" +
+ "1\ta\t\t\n" +
+ "2\tb\t\n" +
+ "3\tc\n" +
+ "4\t\n");
+ Properties properties = new Properties();
+ properties.setProperty(IGNORE_COMMENTS_PROPERTY_KEY, "true");
+ properties.setProperty(IGNORE_TRAILING_EMPTY_CELLS_PROPERTY_KEY, "true");
+ TSVViewReportingPlugin plugin = new TSVViewReportingPlugin(properties, store);
+ TableModel tableModel = plugin.createReport(Arrays.asList(datasetDescription));
+
+ assertEquals("[a, b]", tableModel.getHeader().toString());
+ List<TableModelRow> rows = tableModel.getRows();
+ assertEquals("[1, a]", rows.get(0).getValues().toString());
+ assertEquals("[2, b]", rows.get(1).getValues().toString());
+ assertEquals("[3, c]", rows.get(2).getValues().toString());
+ assertEquals("[4, ]", rows.get(3).getValues().toString());
+ assertEquals(4, rows.size());
+ }
+}
--
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