From 46f6efbbf91dbf77b4dcb530dc88ca26138c50b4 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 6 Jan 2010 15:21:06 +0000
Subject: [PATCH] LMS-1328 performance of fetching the content of one file from
DSS: do not fetch dataset metadata, just check the access rights
SVN: 14177
---
.../etlserver/IdentifiedDataStrategy.java | 19 +-
.../generic/server/CommandQueueLister.java | 3 +-
.../dss/generic/server/ConfigParameters.java | 7 +-
.../server/DatasetDownloadServlet.java | 200 +++++++++++----
.../server/EncapsulatedOpenBISService.java | 11 +-
.../shared/IEncapsulatedOpenBISService.java | 8 +-
.../shared/utils/DatasetLocationUtil.java | 57 +++++
.../server/DatasetDownloadServletTest.java | 232 ++++++++++--------
.../openbis/generic/server/ETLService.java | 22 +-
.../generic/server/ETLServiceLogger.java | 39 +--
.../generic/shared/IETLLIMSService.java | 16 +-
.../shared/IETLLIMSService.java.expected | 16 +-
12 files changed, 420 insertions(+), 210 deletions(-)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetLocationUtil.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
index b1402dc264e..a46fccb117c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
@@ -20,8 +20,8 @@ import java.io.File;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.utilities.MD5ChecksumCalculator;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
/**
@@ -64,22 +64,7 @@ public final class IdentifiedDataStrategy implements IDataStoreStrategy
{
String dataSetCode = dataSetInfo.getDataSetCode();
final String instanceUUID = dataSetInfo.getInstanceUUID();
- final File instanceDir = new File(baseDir, instanceUUID);
- final File shardingDir = createShardingDir(instanceDir, dataSetCode);
- final File datasetDir = new File(shardingDir, dataSetCode);
- return datasetDir;
- }
-
- // In order not to overwhelm the file system implementation, we won't use a completely flat
- // hierarchy, but instead a structure called 'data sharding'. 'Data sharding' ensures that there
- // are no directories with an extremely large number of data sets.
- private static File createShardingDir(File parentDir, String dataSetCode)
- {
- String checksum = MD5ChecksumCalculator.calculate(dataSetCode);
- final File dirLevel1 = new File(parentDir, checksum.substring(0, 2));
- final File dirLevel2 = new File(dirLevel1, checksum.substring(2, 4));
- final File dirLevel3 = new File(dirLevel2, checksum.substring(4, 6));
- return dirLevel3;
+ return DatasetLocationUtil.getDatasetLocationPath(baseDir, dataSetCode, instanceUUID);
}
//
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/CommandQueueLister.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/CommandQueueLister.java
index 6b04bc22482..2a0c14a5970 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/CommandQueueLister.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/CommandQueueLister.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.dss.generic.server;
-import java.io.File;
/**
* A class that provides a lister for the commands in the command queue of the store.
@@ -33,6 +32,6 @@ public final class CommandQueueLister
public static void listQueuedCommand()
{
final ConfigParameters configParams = DataStoreServer.getConfigParameters();
- DataSetCommandExecutor.listQueuedCommands(new File(configParams.getStorePath()));
+ DataSetCommandExecutor.listQueuedCommands(configParams.getStorePath());
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java
index 362d70a70eb..59fb213febd 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.dss.generic.server;
+import java.io.File;
import java.util.Properties;
import org.apache.log4j.Logger;
@@ -52,7 +53,7 @@ final class ConfigParameters
static final String KEYSTORE_KEY_PASSWORD_KEY = KEYSTORE + "key-password";
- private final String storePath;
+ private final File storePath;
private final int port;
@@ -73,7 +74,7 @@ final class ConfigParameters
*/
public ConfigParameters(final Properties properties)
{
- storePath = PropertyUtils.getMandatoryProperty(properties, STOREROOT_DIR_KEY);
+ storePath = new File(PropertyUtils.getMandatoryProperty(properties, STOREROOT_DIR_KEY));
port = getMandatoryIntegerProperty(properties, PORT_KEY);
serverURL = PropertyUtils.getMandatoryProperty(properties, SERVER_URL_KEY);
sessionTimeout = getMandatoryIntegerProperty(properties, SESSION_TIMEOUT_KEY) * 60;
@@ -97,7 +98,7 @@ final class ConfigParameters
}
}
- public final String getStorePath()
+ public final File getStorePath()
{
return storePath;
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServlet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServlet.java
index 7dfd76fca81..24a2ffa78ed 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServlet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServlet.java
@@ -57,9 +57,10 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
/**
* @author Franz-Josef Elmer
@@ -97,9 +98,11 @@ public class DatasetDownloadServlet extends HttpServlet
private static final String THUMBNAIL_MODE_DISPLAY = "thumbnail";
- static final String DATA_SET_KEY = "data-set";
+ static final String DATABASE_INSTANCE_SESSION_KEY = "database-instance";
- static final String DATASET_CODE_KEY = "dataSetCode";
+ static final String DATA_SET_ACCESS_SESSION_KEY = "data-set-access";
+
+ static final String DATA_SET_SESSION_KEY = "data-set";
static final String SESSION_ID_KEY = "sessionID";
@@ -237,10 +240,7 @@ public class DatasetDownloadServlet extends HttpServlet
parseRequestURL(request, DATA_STORE_SERVER_WEB_APPLICATION_NAME);
rendererFactory = createRendererFactory(requestParams.getDisplayMode());
- obtainDataSetFromServer(requestParams.getDataSetCode(),
- requestParams.tryGetSessionId(), request);
-
- HttpSession session = request.getSession(false);
+ HttpSession session = tryGetOrCreateSession(request, requestParams);
if (session == null)
{
printSessionExpired(response);
@@ -263,16 +263,18 @@ public class DatasetDownloadServlet extends HttpServlet
throws UnsupportedEncodingException, IOException
{
String dataSetCode = requestParams.getDataSetCode();
- ExternalData dataSet = tryToGetDataSet(session, dataSetCode);
- if (dataSet == null)
- {
- throw new UserFailureException("Unknown data set '" + dataSetCode + "'.");
- }
- File rootDir = createDataSetRootDirectory(dataSet);
+ RenderingContext context = createRenderingContext(requestParams, dataSetCode, session);
+ renderPage(rendererFactory, response, dataSetCode, context, requestParams, session);
+ }
+
+ private RenderingContext createRenderingContext(RequestParams requestParams,
+ String dataSetCode, HttpSession session)
+ {
+ File rootDir = createDataSetRootDirectory(dataSetCode, session);
RenderingContext context =
new RenderingContext(rootDir, requestParams.getURLPrefix(), requestParams
.getPathInfo());
- renderPage(rendererFactory, response, dataSet, context, requestParams);
+ return context;
}
private IRendererFactory createRendererFactory(String displayMode)
@@ -351,20 +353,29 @@ public class DatasetDownloadServlet extends HttpServlet
}
private void renderPage(IRendererFactory rendererFactory, HttpServletResponse response,
- ExternalData dataSet, RenderingContext renderingContext, RequestParams requestParams)
- throws IOException
+ String dataSetCode, RenderingContext renderingContext, RequestParams requestParams,
+ HttpSession session) throws IOException
{
File file = renderingContext.getFile();
if (file.exists() == false)
{
throw new EnvironmentFailureException("File '" + file.getName() + "' does not exist.");
}
+ // If we want to browse a directory, we need a whole dataset metadata from openbis to
+ // display them for the user. But if just a file is needed, then it's much faster to just
+ // check the access rights in openbis.
+ String sessionIdOrNull = requestParams.tryGetSessionId();
if (file.isDirectory())
{
+ ExternalData dataSet = getDataSet(dataSetCode, sessionIdOrNull, session);
createPage(rendererFactory, response, dataSet, renderingContext, file);
} else
{
- deliverFile(response, dataSet, file, requestParams.getDisplayMode());
+ if (isDatasetAccessible(dataSetCode, sessionIdOrNull, session) == false)
+ {
+ throw new UserFailureException("Data set '" + dataSetCode + "' is not accessible.");
+ }
+ deliverFile(response, dataSetCode, file, requestParams.getDisplayMode());
}
}
@@ -415,7 +426,7 @@ public class DatasetDownloadServlet extends HttpServlet
}
}
- private void deliverFile(final HttpServletResponse response, ExternalData dataSet, File file,
+ private void deliverFile(final HttpServletResponse response, String dataSetCode, File file,
String displayMode) throws IOException, FileNotFoundException
{
ServletOutputStream outputStream = null;
@@ -445,7 +456,7 @@ public class DatasetDownloadServlet extends HttpServlet
}
if (operationLog.isInfoEnabled())
{
- operationLog.info("For data set '" + dataSet.getCode() + "' deliver file "
+ operationLog.info("For data set '" + dataSetCode + "' deliver file "
+ file.getAbsolutePath() + infoPostfix);
}
response.setContentLength(size);
@@ -491,53 +502,137 @@ public class DatasetDownloadServlet extends HttpServlet
writer.close();
}
- private void obtainDataSetFromServer(String dataSetCode, String sessionIdOrNull,
- final HttpServletRequest request)
+ private ExternalData getDataSet(String dataSetCode, String sessionIdOrNull, HttpSession session)
+ {
+ ExternalData dataset = tryToGetCachedDataSet(session, dataSetCode);
+ if (dataset != null)
+ {
+ return dataset;
+ }
+ ensureSessionIdSpecified(sessionIdOrNull);
+ ExternalData dataSet = tryGetDataSetFromServer(dataSetCode, sessionIdOrNull);
+ if (dataSet != null)
+ {
+ putDataSetToMap(session, dataSetCode, dataSet);
+ return dataSet;
+ } else
+ {
+ throw new UserFailureException("Unknown data set '" + dataSetCode + "'.");
+ }
+ }
+
+ private void ensureSessionIdSpecified(String sessionIdOrNull)
+ {
+ if (sessionIdOrNull == null)
+ {
+ throw new EnvironmentFailureException("Session id not specified in the URL");
+ }
+ }
+
+ private ExternalData tryGetDataSetFromServer(String dataSetCode, String sessionIdOrNull)
+ {
+ IEncapsulatedOpenBISService dataSetService = applicationContext.getDataSetService();
+ ExternalData dataSet = dataSetService.tryGetDataSet(sessionIdOrNull, dataSetCode);
+ if (operationLog.isInfoEnabled())
+ {
+ String actionDesc = (dataSet != null) ? "obtained from" : "not found in";
+ operationLog.info(String.format("Data set '%s' %s openBIS server.", dataSetCode,
+ actionDesc));
+ }
+ return dataSet;
+ }
+
+ private HttpSession tryGetOrCreateSession(final HttpServletRequest request,
+ RequestParams requestParams)
{
HttpSession session = request.getSession(false);
- if (session != null && tryToGetDataSet(session, dataSetCode) != null)
+ if (session == null && requestParams.tryGetSessionId() == null)
{
- return; // dataset is already in the cache
+ // a) The session is expired and b) we do not have openbis session id provided.
+ // So a) metadata about datasets are not in the session and b) we cannot get them from
+ // openbis.
+ return null;
}
- if (sessionIdOrNull != null)
+ if (session == null)
{
- IEncapsulatedOpenBISService dataSetService = applicationContext.getDataSetService();
- ExternalData dataSet = dataSetService.tryGetDataSet(sessionIdOrNull, dataSetCode);
- if (operationLog.isInfoEnabled())
+ session = request.getSession(true);
+ ConfigParameters configParameters = applicationContext.getConfigParameters();
+ session.setMaxInactiveInterval(configParameters.getSessionTimeout());
+ }
+ return session;
+ }
+
+ private File createDataSetRootDirectory(String dataSetCode, HttpSession session)
+ {
+ DatabaseInstance databaseInstance = getDatabaseInstance(session);
+ File storeDir = applicationContext.getConfigParameters().getStorePath();
+ File dataSetRootDirectory =
+ DatasetLocationUtil.getDatasetLocationPath(storeDir, dataSetCode, databaseInstance
+ .getUuid());
+ if (dataSetRootDirectory.exists() == false)
+ {
+ throw new UserFailureException("Data set '" + dataSetCode + "' not found in the store.");
+ }
+ return dataSetRootDirectory;
+ }
+
+ // ---
+
+ private DatabaseInstance getDatabaseInstance(HttpSession session)
+ {
+ DatabaseInstance databaseInstance =
+ (DatabaseInstance) session.getAttribute(DATABASE_INSTANCE_SESSION_KEY);
+ if (databaseInstance == null)
+ {
+ databaseInstance = applicationContext.getDataSetService().getHomeDatabaseInstance();
+ session.setAttribute(DATABASE_INSTANCE_SESSION_KEY, databaseInstance);
+ }
+ return databaseInstance;
+ }
+
+ // ---
+
+ private boolean isDatasetAccessible(String dataSetCode, String sessionIdOrNull,
+ HttpSession session)
+ {
+ Boolean access = getDataSetAccess(session).get(dataSetCode);
+ if (access == null)
+ {
+ if (tryToGetCachedDataSet(session, dataSetCode) != null)
{
- String actionDesc = (dataSet != null) ? "obtained from" : "not found in";
- operationLog.info(String.format("Data set '%s' %s openBIS server.", dataSetCode,
- actionDesc));
+ return true; // access already checked and granted
}
-
- ConfigParameters configParameters = applicationContext.getConfigParameters();
- if (session == null)
+ if (operationLog.isInfoEnabled())
{
- session = request.getSession(true);
- session.setMaxInactiveInterval(configParameters.getSessionTimeout());
+ operationLog.info(String.format(
+ "Check access to the data set '%s' at openBIS server.", dataSetCode));
}
- if (dataSet != null)
+ IEncapsulatedOpenBISService dataSetService = applicationContext.getDataSetService();
+ ensureSessionIdSpecified(sessionIdOrNull);
+ try
+ {
+ dataSetService.checkDataSetAccess(sessionIdOrNull, dataSetCode);
+ access = true;
+ } catch (UserFailureException ex)
{
- putDataSetToMap(session, dataSetCode, dataSet);
+ access = false;
}
+ getDataSetAccess(session).put(dataSetCode, access);
}
+ return access;
}
- private File createDataSetRootDirectory(ExternalData dataSet)
+ @SuppressWarnings("unchecked")
+ private Map<String, Boolean> getDataSetAccess(HttpSession session)
{
- String path = dataSet.getLocation();
- LocatorType locatorType = dataSet.getLocatorType();
- if (locatorType.getCode().equals(LocatorType.DEFAULT_LOCATOR_TYPE_CODE))
- {
- path = applicationContext.getConfigParameters().getStorePath() + "/" + path;
- }
- File dataSetRootDirectory = new File(path);
- if (dataSetRootDirectory.exists() == false)
+ Map<String, Boolean> map =
+ (Map<String, Boolean>) session.getAttribute(DATA_SET_ACCESS_SESSION_KEY);
+ if (map == null)
{
- throw new UserFailureException("Data set '" + dataSet.getCode()
- + "' not found in store at '" + dataSetRootDirectory.getAbsolutePath() + "'.");
+ map = new HashMap<String, Boolean>();
+ session.setAttribute(DATA_SET_ACCESS_SESSION_KEY, map);
}
- return dataSetRootDirectory;
+ return map;
}
private void putDataSetToMap(HttpSession session, String dataSetCode, ExternalData dataSet)
@@ -545,7 +640,7 @@ public class DatasetDownloadServlet extends HttpServlet
getDataSets(session).put(dataSetCode, dataSet);
}
- private ExternalData tryToGetDataSet(HttpSession session, String dataSetCode)
+ private ExternalData tryToGetCachedDataSet(HttpSession session, String dataSetCode)
{
return getDataSets(session).get(dataSetCode);
}
@@ -554,13 +649,12 @@ public class DatasetDownloadServlet extends HttpServlet
private Map<String, ExternalData> getDataSets(HttpSession session)
{
Map<String, ExternalData> map =
- (Map<String, ExternalData>) session.getAttribute(DATA_SET_KEY);
+ (Map<String, ExternalData>) session.getAttribute(DATA_SET_SESSION_KEY);
if (map == null)
{
map = new HashMap<String, ExternalData>();
- session.setAttribute(DATA_SET_KEY, map);
+ session.setAttribute(DATA_SET_SESSION_KEY, map);
}
return map;
}
-
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
index 306d9fa496a..ae7b6e0fa10 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
@@ -297,7 +297,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return service.getSampleType(sessionToken, sampleTypeCode);
}
}
-
+
synchronized public DataSetTypeWithVocabularyTerms getDataSetType(String dataSetTypeCode)
{
checkSessionToken();
@@ -324,7 +324,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
authenticate();
return service.listDataSetsBySampleID(sessionToken, id, showOnlyDirectlyConnected);
}
- }
+ }
synchronized public long registerSample(NewSample newSample) throws UserFailureException
{
@@ -433,6 +433,13 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return service.tryGetDataSet(sToken, dataSetCode);
}
+ synchronized public void checkDataSetAccess(String sToken, String dataSetCode)
+ throws UserFailureException
+ {
+ checkSessionToken();
+ service.checkDataSetAccess(sToken, dataSetCode);
+ }
+
synchronized public List<SimpleDataSetInformationDTO> listDataSets()
throws UserFailureException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
index bc43254b797..e438ec76c20 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
@@ -52,6 +52,12 @@ public interface IEncapsulatedOpenBISService
public ExternalData tryGetDataSet(final String sessionToken, final String dataSetCode)
throws UserFailureException;
+ /**
+ * Checks if the current user has access rights to a dataset with the specified data set code.
+ */
+ public void checkDataSetAccess(final String sessionToken, final String dataSetCode)
+ throws UserFailureException;
+
/**
* Tries to get the experiment of specified identifier or <code>null</code> if not found.
*/
@@ -91,7 +97,7 @@ public interface IEncapsulatedOpenBISService
*/
public List<ExternalData> listDataSetsBySampleID(long sampleID,
boolean showOnlyDirectlyConnected) throws UserFailureException;
-
+
/**
* Registers the specified sample.
*
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetLocationUtil.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetLocationUtil.java
new file mode 100644
index 00000000000..575c17a7ab6
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetLocationUtil.java
@@ -0,0 +1,57 @@
+/*
+ * 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.shared.utils;
+
+import java.io.File;
+
+import ch.systemsx.cisd.common.utilities.MD5ChecksumCalculator;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class DatasetLocationUtil
+{
+ /** Creates a location where a dataset can be found in a specified base directory. */
+ public static File getDatasetLocationPath(final File baseDir, String dataSetCode,
+ final String instanceUUID)
+ {
+ return new File(baseDir, getDatasetRelativeLocationPath(dataSetCode, instanceUUID));
+ }
+
+ /** returns path relative to the store */
+ public static String getDatasetRelativeLocationPath(String dataSetCode,
+ final String instanceUUID)
+ {
+ final File instanceDir = new File(instanceUUID);
+ final File shardingDir = createShardingDir(instanceDir, dataSetCode);
+ final File datasetDir = new File(shardingDir, dataSetCode);
+ return datasetDir.getPath();
+ }
+
+ // In order not to overwhelm the file system implementation, we won't use a completely flat
+ // hierarchy, but instead a structure called 'data sharding'. 'Data sharding' ensures that there
+ // are no directories with an extremely large number of data sets.
+ private static File createShardingDir(File parentDir, String dataSetCode)
+ {
+ String checksum = MD5ChecksumCalculator.calculate(dataSetCode);
+ final File dirLevel1 = new File(parentDir, checksum.substring(0, 2));
+ final File dirLevel2 = new File(dirLevel1, checksum.substring(2, 4));
+ final File dirLevel3 = new File(dirLevel2, checksum.substring(4, 6));
+ return dirLevel3;
+ }
+
+}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java
index 3ce565f8ae1..d6b22c8a07d 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java
@@ -50,7 +50,8 @@ import ch.systemsx.cisd.base.utilities.OSUtilities;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.logging.BufferedAppender;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
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.Group;
@@ -58,7 +59,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
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.dto.ExternalDataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
/**
* @author Franz-Josef Elmer
@@ -77,12 +77,14 @@ public class DatasetDownloadServletTest
private static final String LOG_ERROR = "ERROR " + LOGGER_NAME + " - ";
+ private static final String DATABASE_INSTANCE_UUID = "db-uuid";
+
private static final File TEST_FOLDER = new File("targets/unit-test/store");
- private static final String EXAMPLE_DATA_SET_FOLDER_NAME = "data set #123";
+ private static final String EXAMPLE_DATA_SET_CODE = "1234-1";
private static final File EXAMPLE_DATA_SET_FOLDER =
- new File(TEST_FOLDER, EXAMPLE_DATA_SET_FOLDER_NAME);
+ getDatasetDirectoryLocation(TEST_FOLDER, EXAMPLE_DATA_SET_CODE);
private static final String EXAMPLE_FILE_NAME = "read me @home.txt";
@@ -100,8 +102,6 @@ public class DatasetDownloadServletTest
private static final String EXAMPLE_SESSION_ID = "AV76CF";
- private static final String EXAMPLE_DATA_SET_CODE = "1234-1";
-
private static final String SAMPLE_CODE = "SAMPLE-S";
private static final String EXPERIMENT_CODE = "EPERIMENT-E";
@@ -144,7 +144,7 @@ public class DatasetDownloadServletTest
dataSetService = context.mock(IEncapsulatedOpenBISService.class);
httpSession = context.mock(HttpSession.class);
TEST_FOLDER.mkdirs();
- EXAMPLE_DATA_SET_FOLDER.mkdir();
+ EXAMPLE_DATA_SET_FOLDER.mkdirs();
FileUtilities.writeToFile(EXAMPLE_FILE, EXAMPLE_FILE_CONTENT);
EXAMPLE_DATA_SET_SUB_FOLDER.mkdir();
}
@@ -199,7 +199,7 @@ public class DatasetDownloadServletTest
+ OSUtilities.LINE_SEPARATOR + "", writer.toString());
assertEquals(LOG_INFO + "Data set '1234-1' obtained from openBIS server."
+ OSUtilities.LINE_SEPARATOR + LOG_INFO
- + "For data set '1234-1' show directory <wd>/data set #123",
+ + "For data set '1234-1' show directory <wd>/db-uuid/0a/28/59/1234-1",
getNormalizedLogContent());
context.assertIsSatisfied();
@@ -234,7 +234,7 @@ public class DatasetDownloadServletTest
+ OSUtilities.LINE_SEPARATOR + "", writer.toString());
assertEquals(LOG_INFO + "Data set '1234-1' obtained from openBIS server."
+ OSUtilities.LINE_SEPARATOR + LOG_INFO
- + "For data set '1234-1' show directory <wd>/data set #123",
+ + "For data set '1234-1' show directory <wd>/db-uuid/0a/28/59/1234-1",
getNormalizedLogContent());
context.assertIsSatisfied();
@@ -259,15 +259,18 @@ public class DatasetDownloadServletTest
{
final StringWriter writer = new StringWriter();
final ExternalData externalData = createExternalData();
- LocatorType locatorType = new LocatorType();
- locatorType.setCode("unknown");
- externalData.setLocatorType(locatorType);
prepareParseRequestURL();
- prepareForObtainingDataSetFromServer(externalData);
+ prepareCreateSession();
context.checking(new Expectations()
{
{
- prepareForGettingDataSetFromSession(this, externalData, "blabla");
+ prepareGetRequestURI(this, externalData, "blabla");
+
+ one(request).getRequestURL();
+ will(returnValue(new StringBuffer("requestURL")));
+
+ one(request).getQueryString();
+ will(returnValue("queryString"));
one(response).setContentType("text/html");
one(response).getWriter();
@@ -278,7 +281,7 @@ public class DatasetDownloadServletTest
DatasetDownloadServlet servlet = createServlet();
servlet.doGet(request, response);
String pageContent = writer.toString();
- String snippet = "Data set '1234-1' not found in store";
+ String snippet = "File 'blabla' does not exist.";
assertEquals("Text snippet >" + snippet + "< not found in following page content: "
+ pageContent, true, pageContent.indexOf(snippet) > 0);
String logContent = logRecorder.getLogContent();
@@ -292,22 +295,14 @@ public class DatasetDownloadServletTest
public void testDoGetButUnknownDataSetCode() throws Exception
{
final StringWriter writer = new StringWriter();
- final ExternalData externalData = createExternalData();
prepareParseRequestURL();
- prepareForObtainingDataSetFromServer(externalData);
+ prepareCreateSession();
+ prepareTryGetDataset(null);
context.checking(new Expectations()
{
{
- one(request).getSession(false);
- will(returnValue(httpSession));
-
- one(httpSession).getAttribute(DatasetDownloadServlet.DATA_SET_KEY);
- Map<String, NewExternalData> map = new HashMap<String, NewExternalData>();
- will(returnValue(map));
-
one(request).getRequestURI();
- String codeAndPath = externalData.getCode();
- will(returnValue(REQUEST_URI_PREFIX + codeAndPath));
+ will(returnValue(REQUEST_URI_PREFIX + EXAMPLE_DATA_SET_CODE));
one(response).setContentType("text/html");
one(response).getWriter();
@@ -321,7 +316,7 @@ public class DatasetDownloadServletTest
+ "Unknown data set '1234-1'." + OSUtilities.LINE_SEPARATOR + "</body></html>"
+ OSUtilities.LINE_SEPARATOR, writer.toString());
String logContent = logRecorder.getLogContent();
- assertEquals(LOG_INFO + "Data set '1234-1' obtained from openBIS server."
+ assertEquals(LOG_INFO + "Data set '1234-1' not found in openBIS server."
+ OSUtilities.LINE_SEPARATOR + LOG_INFO
+ "User failure: Unknown data set '1234-1'.", logContent);
@@ -338,8 +333,13 @@ public class DatasetDownloadServletTest
{
prepareParseRequestURLNoSession(this);
- one(request).getSession(false);
- will(returnValue(null));
+ allowing(request).getSession(false);
+ will(returnValue(httpSession));
+
+ DatabaseInstance databaseInstance = new DatabaseInstance();
+ databaseInstance.setUuid(DATABASE_INSTANCE_UUID);
+ getSessionAttribute(this, DatasetDownloadServlet.DATABASE_INSTANCE_SESSION_KEY,
+ databaseInstance);
prepareForGettingDataSetFromSession(this, externalData,
ESCAPED_EXAMPLE_DATA_SET_SUB_FOLDER_NAME);
@@ -363,7 +363,8 @@ public class DatasetDownloadServletTest
+ OSUtilities.LINE_SEPARATOR
+ "</table> </div> <div class=\'footer\'>Copyright © 2008 ETHZ - <a href=\'http://www.cisd.systemsx.ethz.ch/\'>CISD</a> </div> </body></html>"
+ OSUtilities.LINE_SEPARATOR, writer.toString());
- assertEquals(LOG_INFO + "For data set '1234-1' show directory <wd>/data set #123/"
+ assertEquals(LOG_INFO
+ + "For data set '1234-1' show directory <wd>/db-uuid/0a/28/59/1234-1/"
+ EXAMPLE_DATA_SET_SUB_FOLDER_NAME, getNormalizedLogContent());
context.assertIsSatisfied();
@@ -375,15 +376,13 @@ public class DatasetDownloadServletTest
final ExternalData externalData = createExternalData();
final ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+ prepareCreateSession();
+ prepareCheckDatasetAccess();
+ prepareParseRequestURL();
context.checking(new Expectations()
{
{
- prepareParseRequestURLNoSession(this);
-
- one(request).getSession(false);
- will(returnValue(null));
-
- prepareForGettingDataSetFromSession(this, externalData, EXAMPLE_FILE_NAME);
+ prepareGetRequestURI(this, externalData, EXAMPLE_FILE_NAME);
one(response).setContentType("text/plain");
one(response).setContentLength(EXAMPLE_FILE_CONTENT.length());
@@ -404,8 +403,10 @@ public class DatasetDownloadServletTest
DatasetDownloadServlet servlet = createServlet();
servlet.doGet(request, response);
assertEquals("Hello world!", outputStream.toString());
- assertEquals(LOG_INFO + "For data set '1234-1' deliver file "
- + "<wd>/data set #123/read me @home.txt (12 bytes).", getNormalizedLogContent());
+ assertEquals(LOG_INFO + "Check access to the data set '1234-1' at openBIS server."
+ + OSUtilities.LINE_SEPARATOR + LOG_INFO + "For data set '1234-1' deliver file "
+ + "<wd>/db-uuid/0a/28/59/1234-1/read me @home.txt (12 bytes).",
+ getNormalizedLogContent());
context.assertIsSatisfied();
}
@@ -415,9 +416,9 @@ public class DatasetDownloadServletTest
{
BufferedImage image = new BufferedImage(100, 200, BufferedImage.TYPE_INT_RGB);
ImageIO.write(image, "png", EXAMPLE_FILE);
- final ExternalData externalData = createExternalData();
prepareParseRequestURLForThumbnail(100, 50);
- prepareForObtainingDataSetFromServer(externalData);
+ prepareCreateSession();
+ prepareCheckDatasetAccess();
final ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
context.checking(new Expectations()
{
@@ -426,14 +427,6 @@ public class DatasetDownloadServletTest
will(returnValue(REQUEST_URI_PREFIX + EXAMPLE_DATA_SET_CODE + "/"
+ EXAMPLE_FILE_NAME));
- one(request).getSession(false);
- will(returnValue(httpSession));
-
- one(httpSession).getAttribute(DatasetDownloadServlet.DATA_SET_KEY);
- Map<String, ExternalData> map = new HashMap<String, ExternalData>();
- map.put(externalData.getCode(), externalData);
- will(returnValue(map));
-
one(response).setContentType("image/png");
one(response).setContentLength(84);
one(response).setHeader("Content-Disposition",
@@ -456,10 +449,13 @@ public class DatasetDownloadServletTest
ImageIO.read(new ByteArrayInputStream(outputStream.toByteArray()));
assertEquals(25, thumbnail.getWidth());
assertEquals(50, thumbnail.getHeight());
- assertEquals(LOG_INFO + "Data set '1234-1' obtained from openBIS server."
- + OSUtilities.LINE_SEPARATOR + LOG_INFO
- + "For data set '1234-1' deliver file <wd>/data set #123/read me @home.txt "
- + "as a thumbnail.", getNormalizedLogContent());
+ assertEquals(
+ LOG_INFO
+ + "Check access to the data set '1234-1' at openBIS server."
+ + OSUtilities.LINE_SEPARATOR
+ + LOG_INFO
+ + "For data set '1234-1' deliver file <wd>/db-uuid/0a/28/59/1234-1/read me @home.txt "
+ + "as a thumbnail.", getNormalizedLogContent());
context.assertIsSatisfied();
}
@@ -469,15 +465,12 @@ public class DatasetDownloadServletTest
{
final StringWriter writer = new StringWriter();
final ExternalData externalData = createExternalData();
+ prepareParseRequestURL();
+ prepareCreateSession();
context.checking(new Expectations()
{
{
- prepareParseRequestURLNoSession(this);
-
- one(request).getSession(false);
- will(returnValue(null));
-
- prepareForGettingDataSetFromSession(this, externalData, "blabla");
+ prepareGetRequestURI(this, externalData, "blabla");
one(request).getRequestURL();
will(returnValue(new StringBuffer("requestURL")));
@@ -566,36 +559,6 @@ public class DatasetDownloadServletTest
context.assertIsSatisfied();
}
- @Test
- public void testDoGetForPathInfoStartingWithSeparator() throws Exception
- {
- final StringWriter writer = new StringWriter();
- final ExternalData externalData = createExternalData();
- prepareParseRequestURL();
- prepareForObtainingDataSetFromServer(externalData);
- context.checking(new Expectations()
- {
- {
- one(request).getRequestURI();
- will(returnValue(REQUEST_URI_PREFIX + EXAMPLE_DATA_SET_CODE));
-
- one(request).getSession(false);
- will(returnValue(null));
-
- one(response).getWriter();
- will(returnValue(new PrintWriter(writer)));
- }
- });
-
- DatasetDownloadServlet servlet = createServlet();
- servlet.doGet(request, response);
- assertEquals(EXPIRATION_MESSAGE, writer.toString());
- assertEquals(LOG_INFO + "Data set '1234-1' obtained from openBIS server.",
- getNormalizedLogContent());
-
- context.assertIsSatisfied();
- }
-
private void prepareForGettingDataSetFromSession(final ExternalData externalData,
final String path)
{
@@ -610,23 +573,20 @@ public class DatasetDownloadServletTest
private void prepareForGettingDataSetFromSession(Expectations exp,
final ExternalData externalData, final String path)
{
- exp.one(request).getSession(false);
- exp.will(Expectations.returnValue(httpSession));
-
- exp.one(httpSession).getAttribute(DatasetDownloadServlet.DATA_SET_KEY);
+ exp.one(httpSession).getAttribute(DatasetDownloadServlet.DATA_SET_SESSION_KEY);
Map<String, ExternalData> map = new HashMap<String, ExternalData>();
map.put(externalData.getCode(), externalData);
exp.will(Expectations.returnValue(map));
+ prepareGetRequestURI(exp, externalData, path);
+ }
+
+ private void prepareGetRequestURI(Expectations exp, final ExternalData externalData,
+ final String path)
+ {
exp.one(request).getRequestURI();
String codeAndPath = REQUEST_URI_PREFIX + externalData.getCode() + "/" + path;
exp.will(Expectations.returnValue(codeAndPath));
-
- exp.allowing(request).getRequestURI();
- exp.will(Expectations
- .returnValue(GenericSharedConstants.DATA_STORE_SERVER_WEB_APPLICATION_NAME + "/"
- + codeAndPath));
-
}
private void prepareParseRequestURLNoSession(Expectations exp)
@@ -653,29 +613,82 @@ public class DatasetDownloadServletTest
}
private void prepareForObtainingDataSetFromServer(final ExternalData externalData)
+ {
+ prepareCreateSession();
+ prepareTryGetDataset(externalData);
+ }
+
+ private void prepareCreateSession()
{
context.checking(new Expectations()
{
{
- one(dataSetService).tryGetDataSet(EXAMPLE_SESSION_ID, EXAMPLE_DATA_SET_CODE);
- will(returnValue(externalData));
-
- one(request).getSession(false);
+ allowing(request).getSession(false);
will(returnValue(null));
one(request).getSession(true);
will(returnValue(httpSession));
one(httpSession).setMaxInactiveInterval(120);
- one(httpSession).getAttribute(DatasetDownloadServlet.DATA_SET_KEY);
- will(returnValue(null));
- one(httpSession).setAttribute(DatasetDownloadServlet.DATA_SET_KEY,
+ DatabaseInstance databaseInstance = new DatabaseInstance();
+ databaseInstance.setUuid(DATABASE_INSTANCE_UUID);
+ one(dataSetService).getHomeDatabaseInstance();
+ will(returnValue(databaseInstance));
+ checkAndSetAttribute(this,
+ DatasetDownloadServlet.DATABASE_INSTANCE_SESSION_KEY, databaseInstance);
+
+ }
+ });
+ }
+
+ private void prepareTryGetDataset(final ExternalData externalData)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ HashMap<String, ExternalDataPE> map = new HashMap<String, ExternalDataPE>();
+ checkAndSetAttribute(this, DatasetDownloadServlet.DATA_SET_SESSION_KEY, map);
+
+ one(dataSetService).tryGetDataSet(EXAMPLE_SESSION_ID, EXAMPLE_DATA_SET_CODE);
+ will(returnValue(externalData));
+ }
+ });
+ }
+
+ private void prepareCheckDatasetAccess()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ getSessionAttribute(this, DatasetDownloadServlet.DATA_SET_SESSION_KEY,
new HashMap<String, ExternalDataPE>());
+
+ Map<String, Boolean> map = new HashMap<String, Boolean>();
+ checkAndSetAttribute(this, DatasetDownloadServlet.DATA_SET_ACCESS_SESSION_KEY,
+ map);
+
+ one(dataSetService).checkDataSetAccess(EXAMPLE_SESSION_ID,
+ EXAMPLE_DATA_SET_CODE);
+
+ getSessionAttribute(this, DatasetDownloadServlet.DATA_SET_ACCESS_SESSION_KEY,
+ map);
}
});
}
+ private void checkAndSetAttribute(Expectations exp, String attributeKey, Object newValue)
+ {
+ getSessionAttribute(exp, attributeKey, null);
+ exp.one(httpSession).setAttribute(attributeKey, newValue);
+ }
+
+ private void getSessionAttribute(Expectations exp, String attributeKey, Object value)
+ {
+ exp.one(httpSession).getAttribute(attributeKey);
+ exp.will(Expectations.returnValue(value));
+ }
+
private void prepareForCreatingHTML(final StringWriter writer) throws IOException
{
context.checking(new Expectations()
@@ -716,10 +729,17 @@ public class DatasetDownloadServletTest
LocatorType locatorType = new LocatorType();
locatorType.setCode(LocatorType.DEFAULT_LOCATOR_TYPE_CODE);
externalData.setLocatorType(locatorType);
- externalData.setLocation(EXAMPLE_DATA_SET_FOLDER_NAME);
+ externalData.setLocation(DatasetLocationUtil.getDatasetRelativeLocationPath(
+ EXAMPLE_DATA_SET_CODE, DATABASE_INSTANCE_UUID));
return externalData;
}
+ private static File getDatasetDirectoryLocation(final File baseDir, String dataSetCode)
+ {
+ return DatasetLocationUtil.getDatasetLocationPath(baseDir, dataSetCode,
+ DATABASE_INSTANCE_UUID);
+ }
+
private DatasetDownloadServlet createServlet()
{
Properties properties = new Properties();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
index e405d8c8574..ab333e57df4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
@@ -345,12 +345,13 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
throws UserFailureException
{
checkSession(sessionToken);
-
+
ISampleTypeDAO sampleTypeDAO = getDAOFactory().getSampleTypeDAO();
SampleTypePE sampleType = sampleTypeDAO.tryFindSampleTypeByCode(sampleTypeCode);
if (sampleType == null)
{
- throw new UserFailureException("No sample type found with code '" + sampleTypeCode + "'.");
+ throw new UserFailureException("No sample type found with code '" + sampleTypeCode
+ + "'.");
}
HibernateUtils.initialize(sampleType.getSampleTypePropertyTypes());
return SampleTypeTranslator.translate(sampleType, null);
@@ -360,16 +361,18 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
throws UserFailureException
{
checkSession(sessionToken);
-
+
IDataSetTypeDAO dataSetTypeDAO = getDAOFactory().getDataSetTypeDAO();
DataSetTypePE dataSetType = dataSetTypeDAO.tryToFindDataSetTypeByCode(dataSetTypeCode);
if (dataSetType == null)
{
- throw new UserFailureException("No data set type found with code '" + dataSetTypeCode + "'.");
+ throw new UserFailureException("No data set type found with code '" + dataSetTypeCode
+ + "'.");
}
DataSetTypeWithVocabularyTerms result = new DataSetTypeWithVocabularyTerms();
result.setCode(dataSetType.getCode());
- Set<DataSetTypePropertyTypePE> dataSetTypePropertyTypes = dataSetType.getDataSetTypePropertyTypes();
+ Set<DataSetTypePropertyTypePE> dataSetTypePropertyTypes =
+ dataSetType.getDataSetTypePropertyTypes();
HibernateUtils.initialize(dataSetTypePropertyTypes);
for (DataSetTypePropertyTypePE dataSetTypePropertyTypePE : dataSetTypePropertyTypes)
{
@@ -387,7 +390,7 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
}
return result;
}
-
+
public List<ExternalData> listDataSetsBySampleID(final String sessionToken,
final TechId sampleId, final boolean showOnlyDirectlyConnected)
{
@@ -502,6 +505,13 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
return ExternalDataTranslator.translate(externalDataBO.getExternalData(),
dataStoreBaseURLProvider.getDataStoreBaseURL(), session.getBaseIndexURL());
}
+
+ public void checkDataSetAccess(String sessionToken, String dataSetCode)
+ throws UserFailureException
+ {
+ checkSession(sessionToken);
+ // do nothing, the access rights specified in method annotations are checked by a proxy
+ }
public List<Sample> listSamplesByCriteria(String sessionToken,
ListSamplesByPropertyCriteria criteria) throws UserFailureException
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
index ad5db863c47..ae159cbc323 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
@@ -43,7 +43,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public class ETLServiceLogger extends AbstractServerLogger implements IETLService
{
@@ -56,7 +56,7 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
public String createDataSetCode(String sessionToken) throws UserFailureException
{
- logTracking(sessionToken, "create_data_set_code", "");
+ logTracking(sessionToken, "createDataSetCode", "");
return null;
}
@@ -74,7 +74,7 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
DatastoreServiceDescriptions services = info.getServicesDescriptions();
logTracking(
sessionToken,
- "register_data_store_server_session_token",
+ "registerDataStoreServer",
"CODE(%s) DOWNLOAD-URL(%s) PORT(%s) DSS-TOKEN(%s) REPORTING_PLUGINS(%s), PROCESSING_PLUGINS(%s)",
code, downloadUrl, port, dssSessionToken, services
.getReportingServiceDescriptions(), services
@@ -84,7 +84,7 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
public long registerSample(String sessionToken, NewSample newSample)
throws UserFailureException
{
- logTracking(sessionToken, "register_sample", "SAMPLE_TYPE(%s) SAMPLE(%S)", newSample
+ logTracking(sessionToken, "registerSample", "SAMPLE_TYPE(%s) SAMPLE(%S)", newSample
.getSampleType(), newSample.getIdentifier());
return 0;
}
@@ -92,71 +92,78 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
public void registerDataSet(String sessionToken, SampleIdentifier sampleIdentifier,
NewExternalData externalData) throws UserFailureException
{
- logTracking(sessionToken, "register_data_set", "SAMPLE(%s) DATA_SET(%s)", sampleIdentifier,
+ logTracking(sessionToken, "registerDataSet", "SAMPLE(%s) DATA_SET(%s)", sampleIdentifier,
externalData);
}
public void registerDataSet(String sessionToken, ExperimentIdentifier experimentIdentifier,
NewExternalData externalData) throws UserFailureException
{
- logTracking(sessionToken, "register_data_set", "EXPERIMENT(%s) DATA_SET(%s)",
+ logTracking(sessionToken, "registerDataSet", "EXPERIMENT(%s) DATA_SET(%s)",
experimentIdentifier, externalData);
}
public Experiment tryToGetExperiment(String sessionToken,
ExperimentIdentifier experimentIdentifier) throws UserFailureException
{
- logAccess(sessionToken, "get_experiment", "EXPERIMENT(%s)", experimentIdentifier);
+ logAccess(sessionToken, "tryToGetExperiment", "EXPERIMENT(%s)", experimentIdentifier);
return null;
}
public List<Sample> listSamples(String sessionToken, ListSampleCriteria criteria)
{
- logAccess(sessionToken, "list_samples", "CRITERIA(%s)", criteria);
+ logAccess(sessionToken, "listSamples", "CRITERIA(%s)", criteria);
return null;
}
public Sample tryGetSampleWithExperiment(String sessionToken, SampleIdentifier sampleIdentifier)
throws UserFailureException
{
- logAccess(sessionToken, "get_sample_with_experiment", "SAMPLE(%s)", sampleIdentifier);
+ logAccess(sessionToken, "tryGetSampleWithExperiment", "SAMPLE(%s)", sampleIdentifier);
return null;
}
public SampleType getSampleType(String sessionToken, String sampleTypeCode)
throws UserFailureException
{
- logAccess(sessionToken, "get_sample_type", "SAMPLE_TYPE(%s)", sampleTypeCode);
+ logAccess(sessionToken, "getSampleType", "SAMPLE_TYPE(%s)", sampleTypeCode);
return null;
}
public DataSetTypeWithVocabularyTerms getDataSetType(String sessionToken, String dataSetTypeCode)
{
- logAccess(sessionToken, "get_data_set_type", "DATA_SET_TYPE(%s)", dataSetTypeCode);
+ logAccess(sessionToken, "getDataSetType", "DATA_SET_TYPE(%s)", dataSetTypeCode);
return null;
}
public List<ExternalData> listDataSetsBySampleID(final String sessionToken,
final TechId sampleId, final boolean showOnlyDirectlyConnected)
{
- logAccess(sessionToken, "list_data_sets_by_sample_id", "SAMPLE_ID(%s)", sampleId);
+ logAccess(sessionToken, "listDataSetsBySampleID", "SAMPLE_ID(%s)", sampleId);
return null;
}
public IEntityProperty[] tryToGetPropertiesOfTopSampleRegisteredFor(String sessionToken,
SampleIdentifier sampleIdentifier) throws UserFailureException
{
- logAccess(sessionToken, "get_properties_of_top_sample", "SAMPLE(%s)", sampleIdentifier);
+ logAccess(sessionToken, "tryToGetPropertiesOfTopSampleRegisteredFor", "SAMPLE(%s)",
+ sampleIdentifier);
return null;
}
+ public void checkDataSetAccess(String sessionToken, String dataSetCode)
+ throws UserFailureException
+ {
+ logAccess(sessionToken, "checkDataSetAccess", "DATA_SET(%s)", dataSetCode);
+ }
+
public ExternalData tryGetDataSet(String sessionToken, String dataSetCode)
throws UserFailureException
{
- logAccess(sessionToken, "try_get_data_set", "DATA_SET(%s)", dataSetCode);
+ logAccess(sessionToken, "tryGetDataSet", "DATA_SET(%s)", dataSetCode);
return null;
}
-
+
public List<Sample> listSamplesByCriteria(String sessionToken,
ListSamplesByPropertyCriteria criteria) throws UserFailureException
{
@@ -174,7 +181,7 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
public SamplePE getSampleWithProperty(String sessionToken, String propertyTypeCode,
GroupIdentifier groupIdentifier, String propertyValue)
{
- logAccess(sessionToken, "get_sample_with_property",
+ logAccess(sessionToken, "getSampleWithProperty",
"PROPERTY_TYPE(%s) GROUP(%s) PROPERTY_VALUE(%s)", propertyTypeCode,
groupIdentifier, propertyValue);
return null;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
index 8731a062eaf..34959e61638 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
@@ -25,6 +25,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.ISessionProvider;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.GroupIdentifierPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ListSampleCriteriaPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ListSamplesByPropertyPredicate;
@@ -115,7 +116,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@RolesAllowed(RoleSet.ETL_SERVER)
public DataSetTypeWithVocabularyTerms getDataSetType(String sessionToken, String dataSetTypeCode)
throws UserFailureException;
-
+
/**
* For given sample {@link TechId} returns the corresponding list of {@link ExternalData}.
*
@@ -201,12 +202,23 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) final ExperimentIdentifier experimentIdentifier,
final NewExternalData externalData) throws UserFailureException;
+ /**
+ * Does nothing besides checking that the current user has rights to access the content of the
+ * dataset.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.OBSERVER)
+ public void checkDataSetAccess(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode)
+ throws UserFailureException;
+
/**
* Tries to return the data set specified by its code.
*/
@Transactional
@RolesAllowed(RoleSet.OBSERVER)
- public ExternalData tryGetDataSet(String sessionToken, String dataSetCode)
+ public ExternalData tryGetDataSet(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode)
throws UserFailureException;
/**
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
index 8731a062eaf..34959e61638 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
@@ -25,6 +25,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.ISessionProvider;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.GroupIdentifierPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ListSampleCriteriaPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ListSamplesByPropertyPredicate;
@@ -115,7 +116,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@RolesAllowed(RoleSet.ETL_SERVER)
public DataSetTypeWithVocabularyTerms getDataSetType(String sessionToken, String dataSetTypeCode)
throws UserFailureException;
-
+
/**
* For given sample {@link TechId} returns the corresponding list of {@link ExternalData}.
*
@@ -201,12 +202,23 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) final ExperimentIdentifier experimentIdentifier,
final NewExternalData externalData) throws UserFailureException;
+ /**
+ * Does nothing besides checking that the current user has rights to access the content of the
+ * dataset.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.OBSERVER)
+ public void checkDataSetAccess(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode)
+ throws UserFailureException;
+
/**
* Tries to return the data set specified by its code.
*/
@Transactional
@RolesAllowed(RoleSet.OBSERVER)
- public ExternalData tryGetDataSet(String sessionToken, String dataSetCode)
+ public ExternalData tryGetDataSet(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode)
throws UserFailureException;
/**
--
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