From b35ca1318ed56a1ac75dcb2ea2bb10f23df62f38 Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Tue, 17 May 2011 09:11:03 +0000
Subject: [PATCH] [LMS-2104]: change the DemoProcessing + DemoReporting plugins
to use hierarchical content abstraction. This can be used to prove virtual
data sets are working in processing/reporting.
SVN: 21334
---
.../dataset-1/sample-image.png | Bin 0 -> 400 bytes
.../dataset-1/sample-text-file.txt | 2 +
.../plugins/demo/DemoProcessingPlugin.java | 48 +++++++--
.../plugins/demo/DemoReportingPlugin.java | 102 +++++++++---------
.../HierarchicalContentTraverseUtil.java | 69 ++++++++++++
.../IHierarchicalContentNodeVisitor.java | 33 ++++++
.../tasks/PluginTaskParametersTest.java | 70 ++++++++++--
.../shared/basic/dto/ImageTableCell.java | 11 ++
8 files changed, 268 insertions(+), 67 deletions(-)
create mode 100644 datastore_server/resource/test-data/PluginTaskParametersTest/dataset-1/sample-image.png
create mode 100644 datastore_server/resource/test-data/PluginTaskParametersTest/dataset-1/sample-text-file.txt
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentTraverseUtil.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IHierarchicalContentNodeVisitor.java
diff --git a/datastore_server/resource/test-data/PluginTaskParametersTest/dataset-1/sample-image.png b/datastore_server/resource/test-data/PluginTaskParametersTest/dataset-1/sample-image.png
new file mode 100644
index 0000000000000000000000000000000000000000..37f668e270eb93778f13a53f52eff954c1938382
GIT binary patch
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diff --git a/datastore_server/resource/test-data/PluginTaskParametersTest/dataset-1/sample-text-file.txt b/datastore_server/resource/test-data/PluginTaskParametersTest/dataset-1/sample-text-file.txt
new file mode 100644
index 00000000000..822498f04cc
--- /dev/null
+++ b/datastore_server/resource/test-data/PluginTaskParametersTest/dataset-1/sample-text-file.txt
@@ -0,0 +1,2 @@
+Sample test file
+used for test purposeses.
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java
index ef4b7d5a4c6..ddc3f42bf9b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java
@@ -20,9 +20,19 @@ import java.io.File;
import java.util.List;
import java.util.Properties;
+import org.apache.commons.lang.StringUtils;
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.common.io.IHierarchicalContentNode;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.HierarchicalContentTraverseUtil;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentNodeVisitor;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.ProcessingStatus;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
/**
@@ -34,6 +44,9 @@ public class DemoProcessingPlugin implements IProcessingPluginTask
{
private static final long serialVersionUID = 1L;
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ DemoProcessingPlugin.class);
+
public DemoProcessingPlugin(Properties properties, File storeRoot)
{
}
@@ -41,16 +54,33 @@ public class DemoProcessingPlugin implements IProcessingPluginTask
public ProcessingStatus process(List<DatasetDescription> datasets,
DataSetProcessingContext context)
{
- System.out.println("Processing of the following datasets has been requested: " + datasets);
- System.out.println("sleeping for 2 sec");
- try
- {
- Thread.sleep(2000);
- } catch (InterruptedException ex)
- {
- ex.printStackTrace();
+ operationLog.info("Processing of the following datasets has been requested: " + datasets);
+ IHierarchicalContentProvider contentProvider =
+ ServiceProvider.getHierarchicalContentProvider();
+
+ for (DatasetDescription dataset : datasets) {
+ String dataSetCode = dataset.getDataSetCode();
+ IHierarchicalContentNodeVisitor printingVisitor = createPrintingVisitor(dataSetCode);
+ HierarchicalContentTraverseUtil.traverse(contentProvider, dataSetCode, printingVisitor);
}
- System.out.println("Processing done.");
+ operationLog.info("Processing done.");
return null;
}
+
+ private IHierarchicalContentNodeVisitor createPrintingVisitor(final String datasetCode)
+ {
+ return new IHierarchicalContentNodeVisitor()
+ {
+ public void visit(IHierarchicalContentNode node)
+ {
+ String relativePath = node.getRelativePath();
+ String fullPath = datasetCode + "/";
+ if (false == StringUtils.isBlank(relativePath))
+ {
+ fullPath += relativePath;
+ }
+ operationLog.info("Processing " + node.getRelativePath());
+ }
+ };
+ }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java
index 8484019c0d0..490069f8d5d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java
@@ -22,11 +22,13 @@ import java.util.Date;
import java.util.List;
import java.util.Properties;
-import org.apache.commons.io.FileUtils;
-
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.io.IHierarchicalContentNode;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractTableModelReportingPlugin;
import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.HierarchicalContentTraverseUtil;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentNodeVisitor;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DateTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DoubleTableCell;
@@ -61,77 +63,73 @@ public class DemoReportingPlugin extends AbstractTableModelReportingPlugin
builder.addHeader("Size");
for (DatasetDescription dataset : datasets)
{
- File file = getDataSubDir(context.getDirectoryProvider(), dataset);
- if (file.isDirectory())
- {
- describe(builder, dataset, file);
- } else
- {
- describeUnknown(builder, dataset, file);
- }
+ describe(builder, dataset);
}
return builder.getTableModel();
}
- private static void describe(SimpleTableModelBuilder builder, DatasetDescription dataset,
- File file)
+ private void describe(SimpleTableModelBuilder builder, DatasetDescription dataset)
{
- if (file.isFile())
- {
- describeFile(builder, dataset, file);
- } else
- {
- File[] datasetFiles = FileUtilities.listFiles(file);
- for (File datasetFile : datasetFiles)
- {
- describe(builder, dataset, datasetFile);
- }
- }
+ IHierarchicalContentNodeVisitor visitor =
+ createFileDescribingVisitor(builder, dataset);
+ IHierarchicalContentProvider provider = ServiceProvider.getHierarchicalContentProvider();
+ HierarchicalContentTraverseUtil.traverse(provider, dataset.getDataSetCode(), visitor);
}
- private void describeUnknown(SimpleTableModelBuilder builder, DatasetDescription dataset,
- File file)
+ private IHierarchicalContentNodeVisitor createFileDescribingVisitor(
+ final SimpleTableModelBuilder builder, final DatasetDescription dataset)
{
- String datasetCode = dataset.getDataSetCode();
- ISerializableComparable image = createImageCell(dataset, file);
- List<ISerializableComparable> row =
- Arrays.<ISerializableComparable> asList(new StringTableCell(datasetCode), image,
- new StringTableCell(file.getName()),
- new DateTableCell(new Date(file.lastModified())), new DoubleTableCell(0));
- builder.addRow(row);
+ return new IHierarchicalContentNodeVisitor()
+ {
+
+ public void visit(IHierarchicalContentNode node)
+ {
+ if (false == node.isDirectory())
+ {
+ describeFileNode(builder, dataset, node);
+ }
+ }
+ };
}
- private static ISerializableComparable createImageCell(DatasetDescription dataset, File file)
+ private void describeFileNode(SimpleTableModelBuilder builder, DatasetDescription dataset,
+ IHierarchicalContentNode fileNode)
{
- if (ImageUtil.isImageFile(file))
+ ISerializableComparable image = createPathOrImageCell(dataset, fileNode);
+ long lastModified = 0;
+ try
+ {
+ lastModified = fileNode.getFile().lastModified();
+ } catch (UnsupportedOperationException uoe)
{
- String code = dataset.getDataSetCode();
- String location = dataset.getDataSetLocation();
- return new ImageTableCell(code, location, file.getPath(), 100, 60);
+ // ignore exceptions
}
- return new StringTableCell(file.getName());
- }
-
- private static void describeFile(SimpleTableModelBuilder builder, DatasetDescription dataset,
- File file)
- {
- ISerializableComparable image = createImageCell(dataset, file);
List<ISerializableComparable> row =
Arrays.<ISerializableComparable> asList(
new StringTableCell(dataset.getDataSetCode()), image, new StringTableCell(
- file.getName()), new DateTableCell(new Date(file.lastModified())),
- new DoubleTableCell(getSize(file)));
+ fileNode.getName()), new DateTableCell(new Date(lastModified)),
+ new DoubleTableCell(fileNode.getFileLength()));
builder.addRow(row);
}
- private static long getSize(File file)
+ private ISerializableComparable createPathOrImageCell(DatasetDescription dataset,
+ IHierarchicalContentNode fileNode)
{
- if (file.isFile())
+ File fileOnDisk = null;
+ try
{
- return file.length();
- } else
+ fileOnDisk = fileNode.getFile();
+ } catch (UnsupportedOperationException uoe)
{
- return FileUtils.sizeOfDirectory(file);
+ // do not break
}
+
+ if (fileOnDisk != null && ImageUtil.isImageFile(fileOnDisk))
+ {
+ return new ImageTableCell(dataset.getDataSetCode(), fileNode.getRelativePath(), 100,
+ 60);
+ }
+ return new StringTableCell(fileNode.getName());
}
+
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentTraverseUtil.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentTraverseUtil.java
new file mode 100644
index 00000000000..c50a3bfc6e6
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentTraverseUtil.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2011 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.shared;
+
+import ch.systemsx.cisd.common.io.IHierarchicalContent;
+import ch.systemsx.cisd.common.io.IHierarchicalContentNode;
+
+/**
+ * A utility class to abstract traversing of {@link IHierarchicalContentNode}-s.
+ *
+ * @author Kaloyan Enimanev
+ */
+public class HierarchicalContentTraverseUtil
+{
+
+ /**
+ * Traverses all {@link IHierarchicalContentNode}-s within a data set specified by a data set
+ * code.
+ *
+ * @param provider a provider class used to construct {@link IHierarchicalContent}.
+ * @param dataSetCode the code of the data set to be traversed
+ * @param visitor a visitor that will be invoked for every traversed
+ * {@link IHierarchicalContentNode}.
+ */
+ public static void traverse(IHierarchicalContentProvider provider, String dataSetCode,
+ IHierarchicalContentNodeVisitor visitor)
+ {
+ IHierarchicalContent content = null;
+ try
+ {
+ content = provider.asContent(dataSetCode);
+ visit(content.getRootNode(), visitor);
+ } finally
+ {
+ if (content != null)
+ {
+ content.close();
+ }
+ }
+
+ }
+
+ private static void visit(IHierarchicalContentNode node, IHierarchicalContentNodeVisitor visitor)
+ {
+ visitor.visit(node);
+ if (node.isDirectory())
+ {
+ for (IHierarchicalContentNode child : node.getChildNodes())
+ {
+ visit(child, visitor);
+ }
+ }
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IHierarchicalContentNodeVisitor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IHierarchicalContentNodeVisitor.java
new file mode 100644
index 00000000000..5f030954f08
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IHierarchicalContentNodeVisitor.java
@@ -0,0 +1,33 @@
+/*
+ * Copyright 2011 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.shared;
+
+import ch.systemsx.cisd.common.io.IHierarchicalContentNode;
+
+/**
+ * A visitor for {@link IHierarchicalContentNode}-s.
+ *
+ * @author Kaloyan Enimanev
+ */
+public interface IHierarchicalContentNodeVisitor
+{
+ /**
+ * Visits a node.
+ */
+ void visit(IHierarchicalContentNode node);
+
+}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java
index 9a79b0aa939..cedbef02952 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java
@@ -26,16 +26,26 @@ import java.util.List;
import java.util.Properties;
import org.apache.commons.io.IOUtils;
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.springframework.beans.factory.BeanFactory;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.io.DefaultFileBasedHierarchicalContentFactory;
+import ch.systemsx.cisd.common.io.IHierarchicalContent;
+import ch.systemsx.cisd.common.utilities.IDelegatedAction;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoProcessingPlugin;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoReportingPlugin;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.MockDataSetDirectoryProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProviderTestWrapper;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IDatasetLocation;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
/**
@@ -47,8 +57,55 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
{ PluginTaskProviders.class, AbstractPluginTaskFactory.class })
public class PluginTaskParametersTest extends AbstractFileSystemTestCase
{
- private static final String SHARE_ID = "42";
- private static final File STORE_ROOT = new File(".");
+ private static final File STORE_ROOT = new File("./resource/test-data/"
+ + PluginTaskParametersTest.class.getSimpleName());
+
+ private Mockery context;
+
+ private IHierarchicalContentProvider contentProvider;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ context = new Mockery();
+ contentProvider = new IHierarchicalContentProvider()
+ {
+
+ public IHierarchicalContent asContent(String dataSetCode)
+ {
+ File dataSetFolder = new File(STORE_ROOT, dataSetCode);
+ return new DefaultFileBasedHierarchicalContentFactory().asHierarchicalContent(
+ dataSetFolder, IDelegatedAction.DO_NOTHING);
+ }
+
+ public IHierarchicalContent asContent(File datasetDirectory)
+ {
+ return null;
+ }
+
+ public IHierarchicalContent asContent(IDatasetLocation datasetLocation)
+ {
+ return null;
+ }
+ };
+ final BeanFactory beanFactory = context.mock(BeanFactory.class);
+ ServiceProviderTestWrapper.setApplicationContext(beanFactory);
+
+ context.checking(new Expectations()
+ {
+ {
+ allowing(beanFactory).getBean("hierarchical-content-provider");
+ will(returnValue(contentProvider));
+ }
+ });
+
+ }
+
+ @AfterMethod
+ public void afterTest()
+ {
+ ServiceProviderTestWrapper.restoreApplicationContext();
+ }
@Test
public void testCreateReportingPluginsFactories() throws Exception
@@ -71,7 +128,7 @@ public class PluginTaskParametersTest extends AbstractFileSystemTestCase
factories.logConfigurations();
IReportingPluginTask pluginInstance1 = factories.getPluginInstance(plugin1);
pluginInstance1.createReport(createDatasetDescriptions(), new DataSetProcessingContext(
- new MockDataSetDirectoryProvider(STORE_ROOT, SHARE_ID), null, null, null));
+ null, null, null, null));
List<DatastoreServiceDescription> descriptions = factories.getPluginDescriptions();
assertEquals(2, descriptions.size());
@@ -145,8 +202,9 @@ public class PluginTaskParametersTest extends AbstractFileSystemTestCase
private static List<DatasetDescription> createDatasetDescriptions()
{
DatasetDescription description = new DatasetDescription();
- description.setDatasetCode(".");
- description.setDataSetLocation("3123123123-123");
+ final String dataSetCode = "dataset-1";
+ description.setDatasetCode(dataSetCode);
+ description.setDataSetLocation(dataSetCode);
description.setSampleCode("sampleCode");
description.setSpaceCode("groupCode");
description.setProjectCode("projCode");
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ImageTableCell.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ImageTableCell.java
index 1c8bc5ea0e7..187fa068246 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ImageTableCell.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ImageTableCell.java
@@ -49,6 +49,17 @@ public class ImageTableCell implements ISerializableComparable
this(getPath(dataSetCode, dataSetLocation, originalPath), maxThumbnailWidth, maxThumbnailHeight);
}
+ /**
+ * @param relativePathFromDataSetRoot the relative path to this image file starting from the
+ * data set root.
+ */
+ public ImageTableCell(String dataSetCode, String relativePathFromDataSetRoot,
+ int maxThumbnailWidth,
+ int maxThumbnailHeight)
+ {
+ this(dataSetCode + relativePathFromDataSetRoot, maxThumbnailWidth, maxThumbnailHeight);
+ }
+
public ImageTableCell(String path, int maxThumbnailWidth, int maxThumbnailHeight)
{
this.path = path;
--
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