From 3090086a487604cd1011d74623f2843eec8ca115 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 21 Jun 2011 08:33:11 +0000
Subject: [PATCH] LMS-2286 handle uploading to cifex even for container data
sets. IHierachicalContentNode by method getLastModified().
SVN: 21759
---
...faultFileBasedHierarchicalContentNode.java | 5 ++
...ContainerBasedHierarchicalContentNode.java | 10 +++
.../common/io/IHierarchicalContentNode.java | 8 ++
.../common/io/VirtualHierarchicalContent.java | 5 ++
.../AbstractHierarchicalContentNodeTest.java | 10 +++
...faultFileBasedHierarchicalContentTest.java | 10 ++-
.../cisd/common/io/VirtualNodeTest.java | 17 ++++
.../dss/generic/server/UploadingCommand.java | 90 ++++++++++---------
...hInfoProviderBasedHierarchicalContent.java | 5 ++
.../generic/server/UploadingCommandTest.java | 64 +++++++++++--
.../server/business/bo/DataSetTable.java | 74 ++++++++-------
11 files changed, 213 insertions(+), 85 deletions(-)
diff --git a/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentNode.java
index 04677f257c3..ab414f19eca 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentNode.java
@@ -83,6 +83,11 @@ class DefaultFileBasedHierarchicalContentNode extends AbstractHierarchicalConten
return file.isDirectory();
}
+ public long getLastModified()
+ {
+ return file.lastModified();
+ }
+
@Override
public List<IHierarchicalContentNode> doGetChildNodes()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/io/HDF5ContainerBasedHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/HDF5ContainerBasedHierarchicalContentNode.java
index e870f861fdf..63a89f40c7b 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/HDF5ContainerBasedHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/HDF5ContainerBasedHierarchicalContentNode.java
@@ -187,6 +187,11 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
return true;
}
+ public long getLastModified()
+ {
+ return file.lastModified();
+ }
+
public File getFile() throws UnsupportedOperationException
{
throw new UnsupportedOperationException("This is not a normal directory node.");
@@ -267,6 +272,11 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
return false;
}
+ public long getLastModified()
+ {
+ return file.lastModified();
+ }
+
public File getFile() throws UnsupportedOperationException
{
throw new UnsupportedOperationException("This is not a normal file node.");
diff --git a/common/source/java/ch/systemsx/cisd/common/io/IHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/IHierarchicalContentNode.java
index 32a88091f09..ff27ec822d5 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/IHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/IHierarchicalContentNode.java
@@ -51,6 +51,14 @@ public interface IHierarchicalContentNode
* otherwise.
*/
boolean isDirectory();
+
+ /**
+ * Returns the time this node or the persistent object containing this node has been modified.
+ *
+ * @return A long value representing the time of last modification, measured in milliseconds
+ * since the epoch (00:00:00 GMT, January 1, 1970).
+ */
+ long getLastModified();
/**
* List of child nodes of this node.
diff --git a/common/source/java/ch/systemsx/cisd/common/io/VirtualHierarchicalContent.java b/common/source/java/ch/systemsx/cisd/common/io/VirtualHierarchicalContent.java
index ce4300bc420..9a4335ba702 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/VirtualHierarchicalContent.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/VirtualHierarchicalContent.java
@@ -391,6 +391,11 @@ class VirtualHierarchicalContent implements IHierarchicalContent
return lastNode().isDirectory();
}
+ public long getLastModified()
+ {
+ return lastNode().getLastModified();
+ }
+
public List<IHierarchicalContentNode> getChildNodes() throws UnsupportedOperationException
{
IVirtualNodeListMerger listMerger = nodeMergerFactory.createNodeListMerger();
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/io/AbstractHierarchicalContentNodeTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/io/AbstractHierarchicalContentNodeTest.java
index 25be091d582..b32a35f474f 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/io/AbstractHierarchicalContentNodeTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/io/AbstractHierarchicalContentNodeTest.java
@@ -152,6 +152,11 @@ public class AbstractHierarchicalContentNodeTest extends AssertJUnit
return false;
}
+ public long getLastModified()
+ {
+ return 0;
+ }
+
@Override
protected InputStream doGetInputStream()
{
@@ -209,6 +214,11 @@ public class AbstractHierarchicalContentNodeTest extends AssertJUnit
return false;
}
+ public long getLastModified()
+ {
+ return 0;
+ }
+
@Override
protected InputStream doGetInputStream()
{
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentTest.java
index eaf3c7034bb..bd3ace20c5e 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentTest.java
@@ -491,8 +491,9 @@ public class DefaultFileBasedHierarchicalContentTest extends AbstractFileSystemT
assertEquals("This is not a normal file node.", ex.getMessage());
}
// file info access
- assertEquals(expectedFile.getName(), fileNode.getName());
- assertEquals(expectedFile.length(), fileNode.getFileLength());
+ assertEquals("File: " + expectedFile, expectedFile.getName(), fileNode.getName());
+ assertEquals("File: " + expectedFile, expectedFile.length(), fileNode.getFileLength());
+ assertEquals("File: " + expectedFile, expectedFile.lastModified(), fileNode.getLastModified());
final String expectedFileData = expectedFile.getName() + " data";
// check random access to file content
@@ -571,6 +572,11 @@ public class DefaultFileBasedHierarchicalContentTest extends AbstractFileSystemT
return file.exists();
}
+ public long getLastModified()
+ {
+ return file.lastModified();
+ }
+
public long getFileLength() throws UnsupportedOperationException
{
throw new UnsupportedOperationException(METHOD_NOT_IMPLEMENTED);
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/io/VirtualNodeTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/io/VirtualNodeTest.java
index 011eff97ee0..380bfd63d1b 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/io/VirtualNodeTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/io/VirtualNodeTest.java
@@ -271,6 +271,23 @@ public class VirtualNodeTest extends AbstractFileSystemTestCase
context.assertIsSatisfied();
}
+
+ @Test
+ public void testLastModified()
+ {
+ final IHierarchicalContentNode virtualNode = createVirtualNode();
+ context.checking(new Expectations()
+ {
+ {
+ one(node1).getLastModified();
+ will(returnValue(42L));
+ }
+ });
+
+ assertEquals(42, virtualNode.getLastModified());
+
+ context.assertIsSatisfied();
+ }
@Test
public void testGetChildNodes()
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java
index fdf4ebceba0..79a3f1e9bd5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.io.ByteArrayInputStream;
import java.io.File;
-import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
@@ -40,6 +39,8 @@ import ch.systemsx.cisd.cifex.rpc.client.ICIFEXComponent;
import ch.systemsx.cisd.cifex.rpc.client.ICIFEXUploader;
import ch.systemsx.cisd.cifex.rpc.client.gui.IProgressListener;
import ch.systemsx.cisd.cifex.shared.basic.Constants;
+import ch.systemsx.cisd.common.io.IHierarchicalContent;
+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.common.mail.IMailClient;
@@ -48,7 +49,8 @@ import ch.systemsx.cisd.common.mail.MailClientParameters;
import ch.systemsx.cisd.common.types.BooleanOrUnknown;
import ch.systemsx.cisd.common.utilities.TokenGenerator;
import ch.systemsx.cisd.openbis.dss.generic.shared.IDataSetDirectoryProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
@@ -57,8 +59,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
import de.schlichtherle.util.zip.ZipEntry;
import de.schlichtherle.util.zip.ZipOutputStream;
@@ -285,6 +285,8 @@ class UploadingCommand implements IDataSetCommand
@Private
boolean deleteAfterUploading = true;
+ @Private transient IHierarchicalContentProvider hierarchicalContentProvider;
+
UploadingCommand(ICIFEXRPCServiceFactory cifexServiceFactory,
MailClientParameters mailClientParameters, List<ExternalData> dataSets,
DataSetUploadContext context, String cifexAdminUserOrNull,
@@ -412,37 +414,34 @@ class UploadingCommand implements IDataSetCommand
zipOutputStream = new ZipOutputStream(outputStream);
for (ExternalData externalData : dataSets)
{
- DataSet dataSet = externalData.tryGetAsDataSet();
- assert dataSet != null : "container datasets are currently not supported by DSS client";
-
- DatasetDescription dataSetDescription =
- DataSetTranslator.translateToDescription(dataSet);
- File dataSetFile = dataSetDirectoryProvider.getDataSetDirectory(dataSetDescription);
- if (dataSetFile.exists() == false)
- {
- notificationLog.error("Data set '" + dataSetFile + "' does not exist.");
- return false;
- }
- String newRootPath = createRootPath(dataSet);
+ String newRootPath = createRootPath(externalData) + "/";
try
{
- addEntry(zipOutputStream, newRootPath + "/meta-data.tsv",
+ addEntry(zipOutputStream, newRootPath + "meta-data.tsv",
System.currentTimeMillis(),
- new ByteArrayInputStream(createMetaData(dataSet).getBytes()));
+ new ByteArrayInputStream(createMetaData(externalData).getBytes()));
} catch (IOException ex)
{
notificationLog.error(
- "Couldn't add meta date for data set '" + dataSet.getCode()
+ "Couldn't add meta date for data set '" + externalData.getCode()
+ "' to zip file.", ex);
return false;
}
+ IHierarchicalContent root = null;
+ try
+ {
+ root = getHierarchicalContentProvider().asContent(externalData.getCode());
+ } catch (Exception ex)
+ {
+ notificationLog.error("Data set " + externalData.getCode() + " does not exist.", ex);
+ return false;
+ }
try
{
- addTo(zipOutputStream, dataSetFile.getCanonicalPath().length(), newRootPath,
- dataSetFile);
+ addTo(zipOutputStream, newRootPath, root.getRootNode());
} catch (IOException ex)
{
- notificationLog.error("Couldn't add data set '" + dataSetFile
+ notificationLog.error("Couldn't add data set '" + externalData.getCode()
+ "' to zip file.", ex);
return false;
}
@@ -466,8 +465,35 @@ class UploadingCommand implements IDataSetCommand
}
}
}
+
+ private IHierarchicalContentProvider getHierarchicalContentProvider()
+ {
+ if (hierarchicalContentProvider == null)
+ {
+ hierarchicalContentProvider = ServiceProvider.getHierarchicalContentProvider();
+ }
+ return hierarchicalContentProvider;
+ }
+
+ private void addTo(ZipOutputStream zipOutputStream, String newRootPath,
+ IHierarchicalContentNode node) throws IOException
+ {
+ if (node.isDirectory())
+ {
+ List<IHierarchicalContentNode> childNodes = node.getChildNodes();
+ for (IHierarchicalContentNode childNode : childNodes)
+ {
+ addTo(zipOutputStream, newRootPath, childNode);
+ }
+ } else
+ {
+ addEntry(zipOutputStream, newRootPath + node.getRelativePath(), node.getLastModified(),
+ node.getInputStream());
+ }
+ }
- private String createMetaData(DataSet dataSet)
+ @SuppressWarnings("deprecation")
+ private String createMetaData(ExternalData dataSet)
{
MetaDataBuilder builder = new MetaDataBuilder();
builder.dataSet("code", dataSet.getCode());
@@ -525,24 +551,6 @@ class UploadingCommand implements IDataSetCommand
+ "/" + (sample == null ? "" : sample.getCode() + "/") + dataSet.getCode();
}
- private void addTo(ZipOutputStream zipOutputStream, int oldRootPathLength, String newRootPath,
- File file) throws IOException
- {
- if (file.isFile())
- {
- String zipEntryPath =
- newRootPath + file.getCanonicalPath().substring(oldRootPathLength);
- addEntry(zipOutputStream, zipEntryPath, file.lastModified(), new FileInputStream(file));
- } else
- {
- File[] files = file.listFiles();
- for (File childFile : files)
- {
- addTo(zipOutputStream, oldRootPathLength, newRootPath, childFile);
- }
- }
- }
-
private void addEntry(ZipOutputStream zipOutputStream, String zipEntryPath, long lastModified,
InputStream in) throws IOException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
index cfa2fb14865..5705ef4d4e1 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
@@ -207,6 +207,11 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
return pathInfo.isDirectory();
}
+ public long getLastModified()
+ {
+ return System.currentTimeMillis();
+ }
+
@Override
protected String doGetRelativePath()
{
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
index 3be648335bc..a7abb605823 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
@@ -47,9 +47,13 @@ import ch.systemsx.cisd.cifex.rpc.client.ICIFEXUploader;
import ch.systemsx.cisd.cifex.rpc.client.gui.IProgressListener;
import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.io.DefaultFileBasedHierarchicalContentFactory;
+import ch.systemsx.cisd.common.io.IHierarchicalContent;
import ch.systemsx.cisd.common.logging.BufferedAppender;
import ch.systemsx.cisd.common.mail.MailClientParameters;
+import ch.systemsx.cisd.common.utilities.IDelegatedAction;
import ch.systemsx.cisd.openbis.dss.generic.shared.IDataSetDirectoryProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IDatasetLocation;
@@ -74,11 +78,48 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
@Friend(toClasses = UploadingCommand.class)
public class UploadingCommandTest extends AssertJUnit
{
+
private static final File TEST_FOLDER = new File("targets/upload-test");
private static final File STORE = new File(TEST_FOLDER, "store");
private static final String SHARE_ID = "share-id";
+
+ private static final String LOCATION_PREFIX = "ds";
+
+ private static final IHierarchicalContentProvider HIERARCHICAL_CONTENT_PROVIDER =
+ new IHierarchicalContentProvider()
+ {
+ private DefaultFileBasedHierarchicalContentFactory hierarchicalContentFactory =
+ new DefaultFileBasedHierarchicalContentFactory();
+
+ public IHierarchicalContent asContent(File datasetDirectory)
+ {
+ return hierarchicalContentFactory.asHierarchicalContent(datasetDirectory,
+ IDelegatedAction.DO_NOTHING);
+ }
+
+ public IHierarchicalContent asContent(IDatasetLocation datasetLocation)
+ {
+ return getContent(datasetLocation.getDataSetLocation());
+ }
+
+ public IHierarchicalContent getContent(String location)
+ {
+ return asContent(new File(new File(STORE, SHARE_ID), location));
+ }
+
+ public IHierarchicalContent asContent(ExternalData dataSet)
+ {
+ return getContent(dataSet.getCode());
+ }
+
+ public IHierarchicalContent asContent(String dataSetCode)
+ throws IllegalArgumentException
+ {
+ return getContent(LOCATION_PREFIX + dataSetCode);
+ }
+ };
private static final class MockDataSetDirectoryProvider implements IDataSetDirectoryProvider
{
@@ -110,9 +151,9 @@ public class UploadingCommandTest extends AssertJUnit
private static final File EMAILS = new File(TEST_FOLDER, "emails");
- private static final String LOCATION1 = "ds1";
+ private static final String LOCATION1 = LOCATION_PREFIX + "1";
- private static final String LOCATION2 = "ds2";
+ private static final String LOCATION2 = LOCATION_PREFIX + "2";
private static final String SESSION_TOKEN = "session42";
@@ -183,33 +224,36 @@ public class UploadingCommandTest extends AssertJUnit
createTestData(LOCATION1);
ds2 = createTestData(LOCATION2);
ExternalData dataSet1 =
- DataSetTranslator.translate(createDataSet("1", LOCATION1), "?",
+ DataSetTranslator.translate(createDataSet("1"), "?",
ExperimentTranslator.LoadableFields.PROPERTIES);
System.out.println("ds1:" + dataSet1.getExperiment().getProperties());
ExternalData dataSet2 =
- DataSetTranslator.translate(createDataSet("2", LOCATION2), "?",
+ DataSetTranslator.translate(createDataSet("2"), "?",
ExperimentTranslator.LoadableFields.PROPERTIES);
dataSets = Arrays.<ExternalData> asList(dataSet1, dataSet2);
command =
new UploadingCommand(factory, mailClientParameters, dataSets, uploadContext, null,
null);
+ command.hierarchicalContentProvider = HIERARCHICAL_CONTENT_PROVIDER;
commandAdminSession =
new UploadingCommand(factory, mailClientParameters, dataSets,
uploadContextNoPasswordAuthenticated, "admin", "admpwd");
+ commandAdminSession.hierarchicalContentProvider = HIERARCHICAL_CONTENT_PROVIDER;
commandAdminSessionNotAuthenticated =
new UploadingCommand(factory, mailClientParameters, dataSets,
uploadContextNoPasswordNotAuthenticated, "admin", "admpwd");
+ commandAdminSessionNotAuthenticated.hierarchicalContentProvider = HIERARCHICAL_CONTENT_PROVIDER;
command.deleteAfterUploading = false;
commandAdminSession.deleteAfterUploading = false;
commandAdminSessionNotAuthenticated.deleteAfterUploading = false;
}
- private ExternalDataPE createDataSet(String code, String location)
+ private ExternalDataPE createDataSet(String code)
{
ExternalDataPE externalData = new ExternalDataPE();
externalData.setCode(code);
externalData.setShareId(SHARE_ID);
- externalData.setLocation(location);
+ externalData.setLocation(LOCATION_PREFIX + code);
externalData.setDerived(true); // measured == (derived == false)
DataSetTypePE dataSetTypePE = new DataSetTypePE();
dataSetTypePE.setCode("D");
@@ -283,7 +327,8 @@ public class UploadingCommandTest extends AssertJUnit
private String getNormalizedLogContent()
{
- return logRecorder.getLogContent().replaceAll(" [^ ]*\\.zip", " <zipfile>");
+ return logRecorder.getLogContent().replaceAll(" [^ ]*\\.zip", " <zipfile>")
+ .replaceAll("\n\ta.*\\)", "").replaceAll("[^:]*" + TEST_FOLDER.getPath(), "");
}
@AfterMethod
@@ -438,8 +483,9 @@ public class UploadingCommandTest extends AssertJUnit
command.execute(directoryProvider);
checkEmail("Couldn't create zip file");
- assertEquals("ERROR NOTIFY.UploadingCommand"
- + " - Data set 'targets/upload-test/store/share-id/ds2' does not exist."
+ assertEquals("ERROR NOTIFY.UploadingCommand - Data set 2 does not exist."
+ + OSUtilities.LINE_SEPARATOR
+ + "java.lang.IllegalArgumentException:/store/share-id/ds2 doesn't exist"
+ OSUtilities.LINE_SEPARATOR + INFO_MAIL_PREFIX
+ "Sending message from 'a@bc.de' to recipients '[user@bc.de]'",
getNormalizedLogContent());
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
index f7c0ec246ba..43af0d7af2f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
@@ -23,7 +23,6 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -129,7 +128,7 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
List<String> notAvailableDatasets = new ArrayList<String>();
for (DataPE dataSet : datasets)
{
- if (dataSet.isAvailable() == false)
+ if (dataSet.isExternalData() && dataSet.isAvailable() == false)
{
notAvailableDatasets.add(dataSet.getCode());
}
@@ -327,21 +326,20 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
public String uploadLoadedDataSetsToCIFEX(DataSetUploadContext uploadContext)
{
assertDatasetsAreAvailable(dataSets);
- Map<DataStorePE, List<ExternalDataPE>> map = groupExternalDataByDataStores();
+ Map<DataStorePE, List<DataPE>> map = groupDataByDataStores();
assertDataSetsAreKnown(map);
- assertNoContainerDataSets(map);
uploadContext.setUserEMail(session.getPrincipal().getEmail());
uploadContext.setSessionUserID(session.getUserName());
if (StringUtils.isBlank(uploadContext.getComment()))
{
uploadContext.setComment(createUploadComment(dataSets));
}
- List<ExternalDataPE> dataSetsWithUnknownDSS = new ArrayList<ExternalDataPE>();
- for (Map.Entry<DataStorePE, List<ExternalDataPE>> entry : map.entrySet())
+ List<DataPE> dataSetsWithUnknownDSS = new ArrayList<DataPE>();
+ for (Map.Entry<DataStorePE, List<DataPE>> entry : map.entrySet())
{
DataStorePE dataStore = entry.getKey();
- List<ExternalDataPE> externalDatas = entry.getValue();
- for (ExternalDataPE dataSet : externalDatas)
+ List<DataPE> dataSetsOfStore = entry.getValue();
+ for (DataPE dataSet : dataSetsOfStore)
{
HibernateUtils.initialize(dataSet.getParents());
HibernateUtils.initialize(dataSet.getProperties());
@@ -359,35 +357,35 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
}
if (StringUtils.isBlank(dataStore.getRemoteUrl()))
{
- dataSetsWithUnknownDSS.addAll(externalDatas);
+ dataSetsWithUnknownDSS.addAll(dataSetsOfStore);
} else
{
- uploadDataSetsToCIFEX(dataStore, externalDatas, uploadContext);
+ uploadDataSetsToCIFEX(dataStore, dataSetsOfStore, uploadContext);
}
}
StringBuilder builder = new StringBuilder();
if (dataSetsWithUnknownDSS.isEmpty() == false)
{
builder.append("The following data sets couldn't been uploaded because of unkown data store:");
- for (ExternalDataPE externalDataPE : dataSetsWithUnknownDSS)
+ for (DataPE dataSet : dataSetsWithUnknownDSS)
{
- builder.append(' ').append(externalDataPE.getCode());
+ builder.append(' ').append(dataSet.getCode());
}
}
return builder.toString();
}
- private void assertDataSetsAreKnown(Map<DataStorePE, List<ExternalDataPE>> map)
+ private <D extends DataPE> void assertDataSetsAreKnown(Map<DataStorePE, List<D>> map)
{
// Set<String> knownLocations = new LinkedHashSet<String>();
List<String> unknownDataSets = new ArrayList<String>();
- for (Map.Entry<DataStorePE, List<ExternalDataPE>> entry : map.entrySet())
+ for (Map.Entry<DataStorePE, List<D>> entry : map.entrySet())
{
DataStorePE dataStore = entry.getKey();
- List<ExternalDataPE> externalDatas = entry.getValue();
+ List<ExternalDataPE> externalDatas = filterRealDataSets(entry.getValue());
Set<String> knownLocations =
getKnownDataSets(dataStore, createDatasetDescriptions(externalDatas));
- for (ExternalDataPE dataSet : entry.getValue())
+ for (ExternalDataPE dataSet : externalDatas)
{
if (dataSet.getStatus() == DataSetArchivingStatus.ARCHIVED)
{
@@ -407,34 +405,44 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
+ unknownDataSets);
}
}
-
- private void assertNoContainerDataSets(Map<DataStorePE, List<ExternalDataPE>> map)
+
+ private List<ExternalDataPE> filterRealDataSets(List<? extends DataPE> mixedDataSets)
{
- Set<String> containerDataSets = new LinkedHashSet<String>();
- for (Map.Entry<DataStorePE, List<ExternalDataPE>> entry : map.entrySet())
+ List<ExternalDataPE> realDataSets = new ArrayList<ExternalDataPE>();
+ for (DataPE dataSet : mixedDataSets)
{
- for (ExternalDataPE dataSet : entry.getValue())
+ if (dataSet instanceof ExternalDataPE)
{
- if (dataSet.isContainer())
- {
- containerDataSets.add(dataSet.getCode());
- }
+ realDataSets.add((ExternalDataPE) dataSet);
}
}
+ return realDataSets;
+ }
- if (false == containerDataSets.isEmpty())
+ /** groups data sets by data stores */
+ private Map<DataStorePE, List<DataPE>> groupDataByDataStores()
+ {
+ Map<DataStorePE, List<DataPE>> map =
+ new LinkedHashMap<DataStorePE, List<DataPE>>();
+ for (DataPE dataSet : dataSets)
{
- throw new UserFailureException(
- "The following data sets are container data sets and cannot be uploaded to CIFEX. "
- + containerDataSets);
+ DataStorePE dataStore = dataSet.getDataStore();
+ List<DataPE> list = map.get(dataStore);
+ if (list == null)
+ {
+ list = new ArrayList<DataPE>();
+ map.put(dataStore, list);
+ }
+ list.add(dataSet);
}
+ return map;
}
- /** groups data sets by data stores filtering out virtual data sets */
+ /** groups data sets by data stores filtering out container data sets */
private Map<DataStorePE, List<ExternalDataPE>> groupExternalDataByDataStores()
{
Map<DataStorePE, List<ExternalDataPE>> map =
- new LinkedHashMap<DataStorePE, List<ExternalDataPE>>();
+ new LinkedHashMap<DataStorePE, List<ExternalDataPE>>();
for (DataPE dataSet : dataSets)
{
if (dataSet.isExternalData())
@@ -451,7 +459,7 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
}
return map;
}
-
+
/** groups all data sets (both virtual and non-virtual) by data stores */
private Map<DataStorePE, List<DataPE>> groupDataSetsByDataStores()
{
@@ -470,7 +478,7 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
return map;
}
- private void uploadDataSetsToCIFEX(DataStorePE dataStore, List<ExternalDataPE> list,
+ private void uploadDataSetsToCIFEX(DataStorePE dataStore, List<DataPE> list,
DataSetUploadContext context)
{
IDataStoreService service = dssFactory.create(dataStore.getRemoteUrl());
--
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