From 297a88337552f9a25053b9fa1d72027c5fb847bb Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Fri, 13 Aug 2010 10:03:12 +0000
Subject: [PATCH] [LMS-1691] got rid of dataStoreBaseURL in most places in
openbis
SVN: 17442
---
.../server/EncapsulatedOpenBISService.java | 11 +++++--
.../generic/server/UploadingCommandTest.java | 4 +--
openbis/dist/server/service.properties | 2 +-
.../web/server/AbstractClientService.java | 5 ----
.../web/server/CommonClientService.java | 1 -
.../generic/server/AbstractCommonServer.java | 2 +-
.../generic/server/AbstractServer.java | 12 ++++----
.../server/CommonBusinessObjectFactory.java | 5 ++--
.../openbis/generic/server/CommonServer.java | 6 ++--
.../openbis/generic/server/ETLService.java | 6 ++--
.../generic/server/TrackingServer.java | 3 +-
.../bo/ICommonBusinessObjectFactory.java | 2 +-
.../bo/datasetlister/DatasetLister.java | 24 +++++----------
.../basic/IDataStoreBaseURLProvider.java | 1 -
.../translator/DataStoreTranslator.java | 17 ++++-------
.../translator/ExternalDataTranslator.java | 16 ++++------
openbis/source/java/service.properties | 6 ++--
.../web/server/CommonClientServiceTest.java | 3 +-
.../generic/server/CommonServerTest.java | 12 +++-----
.../bo/datasetlister/DatasetListerTest.java | 8 ++---
.../ExternalDataTranslatorTest.java | 28 +++++++++++------
.../server/RawDataServiceInternal.java | 26 ++++++++--------
.../server/RawDataServiceInternalTest.java | 4 +--
.../plugin/screening/client/cli/Login.java | 5 ++--
.../IScreeningBusinessObjectFactory.java | 2 +-
.../ScreeningBusinessObjectFactory.java | 5 ++--
.../screening/server/ScreeningServer.java | 16 +++++-----
.../logic/FeatureVectorDatasetLoader.java | 9 +++---
.../logic/GenePlateLocationsLoader.java | 30 +++++++------------
.../server/logic/ImageDatasetLoader.java | 6 ++--
.../server/logic/PlateContentLoader.java | 29 +++++++-----------
.../server/logic/PlateDatasetLoader.java | 10 ++-----
.../server/logic/ScreeningApiImpl.java | 27 ++++++++---------
.../server/logic/ScreeningApiImplTest.java | 12 ++++----
34 files changed, 155 insertions(+), 200 deletions(-)
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 d5fe2d712bb..80d566b2d2f 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
@@ -28,6 +28,7 @@ import ch.systemsx.cisd.common.exceptions.InvalidSessionException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskProviders;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -204,6 +205,11 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
dataStoreServerInfo.setPort(port);
dataStoreServerInfo.setUseSSL(useSSL);
dataStoreServerInfo.setDataStoreCode(dataStoreCode);
+ if (StringUtils.isBlank(downloadUrl))
+ {
+ final String msg = "'download-url' has to be set.";
+ throw new ConfigurationFailureException(msg);
+ }
dataStoreServerInfo.setDownloadUrl(downloadUrl);
dataStoreServerInfo.setSessionToken(sessionTokenManager.drawSessionToken());
dataStoreServerInfo.setServicesDescriptions(pluginTaskDescriptions);
@@ -316,7 +322,8 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
}
}
- synchronized public SampleIdentifier tryToGetSampleIdentifier(String samplePermID) throws UserFailureException
+ synchronized public SampleIdentifier tryToGetSampleIdentifier(String samplePermID)
+ throws UserFailureException
{
checkSessionToken();
try
@@ -467,7 +474,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
+ ".");
}
}
-
+
synchronized public void deleteDataSet(String dataSetCode, String reason)
throws UserFailureException
{
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 823cd013dd1..398193702ac 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
@@ -157,11 +157,11 @@ public class UploadingCommandTest extends AssertJUnit
createTestData(LOCATION1);
ds2 = createTestData(LOCATION2);
ExternalData dataSet1 =
- ExternalDataTranslator.translate(createDataSet("1", LOCATION1), "?", "?",
+ ExternalDataTranslator.translate(createDataSet("1", LOCATION1), "?",
ExperimentTranslator.LoadableFields.PROPERTIES);
System.out.println("ds1:" + dataSet1.getExperiment().getProperties());
ExternalData dataSet2 =
- ExternalDataTranslator.translate(createDataSet("2", LOCATION2), "?", "?",
+ ExternalDataTranslator.translate(createDataSet("2", LOCATION2), "?",
ExperimentTranslator.LoadableFields.PROPERTIES);
dataSets = Arrays.<ExternalData> asList(dataSet1, dataSet2);
command =
diff --git a/openbis/dist/server/service.properties b/openbis/dist/server/service.properties
index 5d9725ac91b..f47274d851c 100644
--- a/openbis/dist/server/service.properties
+++ b/openbis/dist/server/service.properties
@@ -65,7 +65,7 @@ ldap.attributenames.last.name =
database-instance = TEST
# Base URL of the Data Store Server.
-# Will be used only for data sets registered in an openBIS server version before 14.04.2009 (or revision 10665)
+# Will be used only by DSS client trying to register data sets.
data-store-server-base-url =
# The URL of the CIFEX server
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/AbstractClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/AbstractClientService.java
index 55d483bce03..eceaaa26465 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/AbstractClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/AbstractClientService.java
@@ -98,11 +98,6 @@ public abstract class AbstractClientService implements IClientService,
this.requestContextProvider = requestContextProvider;
}
- protected String getDataStoreBaseURL()
- {
- return commonClientService.getDataStoreBaseURL();
- }
-
@SuppressWarnings("unchecked")
protected final <K> IResultSetManager<K> getResultSetManager()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
index 316b53868ad..a0e3ed67ea8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
@@ -165,7 +165,6 @@ public final class CommonClientService extends AbstractClientService implements
this.commonServer = commonServer;
}
- @Override
public String getDataStoreBaseURL()
{
return this.dataStoreBaseURL;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
index ecd022ecf33..00501c2733f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
@@ -109,7 +109,7 @@ abstract class AbstractCommonServer<T extends IServer> extends AbstractServer<T>
protected IDatasetLister createDatasetLister(Session session)
{
- return businessObjectFactory.createDatasetLister(session, getDataStoreBaseURL());
+ return businessObjectFactory.createDatasetLister(session);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
index 41f2114590e..9722ddaece6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
@@ -66,10 +66,10 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
{
@Resource(name = ResourceNames.SAMPLE_PLUGIN_REGISTRY)
private SampleServerPluginRegistry sampleServerPluginRegistry;
-
+
@Resource(name = ResourceNames.DATA_SET_PLUGIN_REGISTRY)
private DataSetServerPluginRegistry dataSetServerPluginRegistry;
-
+
// For testing purpose.
private ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin;
@@ -133,8 +133,7 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
{
return sampleTypeSlaveServerPlugin;
}
- return sampleServerPluginRegistry.getPlugin(EntityKind.SAMPLE, sampleType)
- .getSlaveServer();
+ return sampleServerPluginRegistry.getPlugin(EntityKind.SAMPLE, sampleType).getSlaveServer();
}
protected final IDataSetTypeSlaveServerPlugin getDataSetTypeSlaveServerPlugin(
@@ -144,7 +143,8 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
{
return dataSetTypeSlaveServerPlugin;
}
- return dataSetServerPluginRegistry.getPlugin(EntityKind.DATA_SET, dataSetType).getSlaveServer();
+ return dataSetServerPluginRegistry.getPlugin(EntityKind.DATA_SET, dataSetType)
+ .getSlaveServer();
}
private final RoleAssignmentPE createInstanceAdminRoleAssigment(final PersonPE registrator,
@@ -202,7 +202,7 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
return daoFactory;
}
- protected final String getDataStoreBaseURL()
+ protected final String getDefaultDataStoreBaseURL()
{
return dataStoreBaseURLProvider.getDataStoreBaseURL();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
index c115ab7aed7..922b79e6280 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
@@ -109,10 +109,9 @@ public final class CommonBusinessObjectFactory extends AbstractBusinessObjectFac
return SampleLister.create(getDaoFactory(), session.getBaseIndexURL());
}
- public IDatasetLister createDatasetLister(Session session, String defaultDataStoreBaseURL)
+ public IDatasetLister createDatasetLister(Session session)
{
- return DatasetLister.create(getDaoFactory(), session.getBaseIndexURL(),
- defaultDataStoreBaseURL);
+ return DatasetLister.create(getDaoFactory(), session.getBaseIndexURL());
}
public IMaterialLister createMaterialLister(Session session)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index 20706791274..665dc9aff2c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -774,8 +774,7 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
datasetBO.enrichWithChildren();
datasetBO.enrichWithProperties();
final ExternalDataPE dataset = datasetBO.getExternalData();
- return ExternalDataTranslator.translate(dataset, getDataStoreBaseURL(), session
- .getBaseIndexURL(), false);
+ return ExternalDataTranslator.translate(dataset, session.getBaseIndexURL(), false);
}
public List<ExternalData> listRelatedDataSets(String sessionToken,
@@ -790,8 +789,7 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
final List<ExternalData> list = new ArrayList<ExternalData>(resultSet.size());
for (final ExternalDataPE hit : resultSet)
{
- list.add(ExternalDataTranslator.translate(hit, getDataStoreBaseURL(), session
- .getBaseIndexURL(), false));
+ list.add(ExternalDataTranslator.translate(hit, session.getBaseIndexURL(), false));
}
return list;
} catch (final DataAccessException ex)
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 1a12cf2951e..42ce9feeae2 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
@@ -643,8 +643,7 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
ExternalDataPE externalDataPE = externalDataBO.tryExternalData();
if (null == externalDataPE)
return null;
- return ExternalDataTranslator.translate(externalDataPE, dataStoreBaseURLProvider
- .getDataStoreBaseURL(), session.getBaseIndexURL());
+ return ExternalDataTranslator.translate(externalDataPE, session.getBaseIndexURL());
}
public void checkDataSetAccess(String sessionToken, String dataSetCode)
@@ -718,7 +717,8 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
public String getDefaultDataStoreBaseURL(String sessionToken)
{
// See DataStoreApiUrlUtilities
- String url = getDataStoreBaseURL();
+ // TODO 2010-08-13, Piotr Buczek: get directly from properties
+ String url = getDefaultDataStoreBaseURL();
// Strip the web application name from the URL
if (url.endsWith("/" + DATA_STORE_SERVER_WEB_APPLICATION_NAME))
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java
index 64357994dca..ce18b126ce6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java
@@ -84,8 +84,7 @@ public final class TrackingServer extends AbstractServer<ITrackingServer> implem
// retrieve data sets connected to samples of type specified in criteria
// (these samples don't have properties loaded but ids are loaded)
- final IDatasetLister datasetLister =
- businessObjectFactory.createDatasetLister(session, getDataStoreBaseURL());
+ final IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
final List<ExternalData> dataSets = datasetLister.listByTrackingCriteria(criteria);
// retrieve samples enriched with their dependent samples and properties
// (drawback - samples directly connected to data sets are retrieved twice)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
index a9647462cc1..2ff1099aa89 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
@@ -77,7 +77,7 @@ public interface ICommonBusinessObjectFactory
public ISampleLister createSampleLister(Session session);
- public IDatasetLister createDatasetLister(Session session, String defaultDataStoreBaseURL);
+ public IDatasetLister createDatasetLister(Session session);
public IMaterialLister createMaterialLister(Session session);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
index c37a39d27a5..fef98587ae9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
@@ -83,8 +83,6 @@ public class DatasetLister implements IDatasetLister
private final String baseIndexURL;
- private final String defaultDataStoreBaseURL;
-
//
// Working interfaces
//
@@ -108,30 +106,28 @@ public class DatasetLister implements IDatasetLister
private final Map<Long, LocatorType> locatorTypes = new HashMap<Long, LocatorType>();
- public static IDatasetLister create(IDAOFactory daoFactory, String baseIndexURL,
- String defaultDataStoreBaseURL)
+ public static IDatasetLister create(IDAOFactory daoFactory, String baseIndexURL)
{
DatasetListerDAO dao = DatasetListerDAO.create(daoFactory);
SecondaryEntityDAO referencedEntityDAO = SecondaryEntityDAO.create(daoFactory);
- return create(dao, referencedEntityDAO, baseIndexURL, defaultDataStoreBaseURL);
+ return create(dao, referencedEntityDAO, baseIndexURL);
}
static IDatasetLister create(DatasetListerDAO dao, SecondaryEntityDAO referencedEntityDAO,
- String baseIndexURL, String defaultDataStoreBaseURL)
+ String baseIndexURL)
{
IDatasetListingQuery query = dao.getQuery();
EntityPropertiesEnricher propertiesEnricher =
new EntityPropertiesEnricher(query, dao.getPropertySetQuery());
return new DatasetLister(dao.getDatabaseInstanceId(), dao.getDatabaseInstance(), query,
- propertiesEnricher, referencedEntityDAO, baseIndexURL, defaultDataStoreBaseURL);
+ propertiesEnricher, referencedEntityDAO, baseIndexURL);
}
// For unit tests
DatasetLister(final long databaseInstanceId, final DatabaseInstance databaseInstance,
final IDatasetListingQuery query, IEntityPropertiesEnricher propertiesEnricher,
- SecondaryEntityDAO referencedEntityDAO, String baseIndexURL,
- String defaultDataStoreBaseURL)
+ SecondaryEntityDAO referencedEntityDAO, String baseIndexURL)
{
assert databaseInstance != null;
assert query != null;
@@ -142,7 +138,6 @@ public class DatasetLister implements IDatasetLister
this.propertiesEnricher = propertiesEnricher;
this.referencedEntityDAO = referencedEntityDAO;
this.baseIndexURL = baseIndexURL;
- this.defaultDataStoreBaseURL = defaultDataStoreBaseURL;
}
public List<ExternalData> listBySampleTechId(TechId sampleId, boolean showOnlyDirectlyConnected)
@@ -491,7 +486,7 @@ public class DatasetLister implements IDatasetLister
dataStores.clear();
for (DataStoreRecord code : query.getDataStores(databaseInstanceId))
{
- dataStores.put(code.id, createDataStore(code, defaultDataStoreBaseURL));
+ dataStores.put(code.id, createDataStore(code));
}
}
@@ -500,14 +495,11 @@ public class DatasetLister implements IDatasetLister
codeHolder.setCode(escapeHtml(codeRecord.code));
}
- private static DataStore createDataStore(DataStoreRecord codeRecord,
- String defaultDataStoreBaseURL)
+ private static DataStore createDataStore(DataStoreRecord codeRecord)
{
DataStore result = new DataStore();
setCode(result, codeRecord);
- String downloadUrl =
- DataStoreTranslator.translateDownloadUrl(defaultDataStoreBaseURL,
- codeRecord.download_url);
+ String downloadUrl = DataStoreTranslator.translateDownloadUrl(codeRecord.download_url);
result.setDownloadUrl(downloadUrl);
return result;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IDataStoreBaseURLProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IDataStoreBaseURLProvider.java
index 29519840c08..2621dd78d14 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IDataStoreBaseURLProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IDataStoreBaseURLProvider.java
@@ -1,6 +1,5 @@
package ch.systemsx.cisd.openbis.generic.shared.basic;
-
/**
* Implementation of this interface provides a way to expose the data store base URL.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataStoreTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataStoreTranslator.java
index 2f947e9cfd6..ef2e49fdfb3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataStoreTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataStoreTranslator.java
@@ -19,34 +19,27 @@ package ch.systemsx.cisd.openbis.generic.shared.translator;
import static ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants.DATA_STORE_SERVER_WEB_APPLICATION_NAME;
import org.apache.commons.lang.StringEscapeUtils;
-import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStore;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
/**
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public class DataStoreTranslator
{
- public static DataStore translate(DataStorePE dataStorePE, String defaultDataStoreBaseURL)
+ public static DataStore translate(DataStorePE dataStorePE)
{
DataStore dataStore = new DataStore();
String downloadUrl = dataStorePE.getDownloadUrl();
- downloadUrl = translateDownloadUrl(defaultDataStoreBaseURL, downloadUrl);
+ downloadUrl = translateDownloadUrl(downloadUrl);
dataStore.setDownloadUrl(downloadUrl);
dataStore.setCode(StringEscapeUtils.escapeHtml(dataStorePE.getCode()));
return dataStore;
}
- public static String translateDownloadUrl(String defaultDataStoreBaseURL, String downloadUrl)
+ public static String translateDownloadUrl(String downloadUrl)
{
- if (StringUtils.isBlank(downloadUrl))
- {
- return defaultDataStoreBaseURL;
- } else
- {
- return downloadUrl + "/" + DATA_STORE_SERVER_WEB_APPLICATION_NAME;
- }
+ return downloadUrl + "/" + DATA_STORE_SERVER_WEB_APPLICATION_NAME;
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
index c850000dc90..bcb905e7a62 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
@@ -58,24 +58,21 @@ public class ExternalDataTranslator
for (ExternalDataPE externalDataPE : list)
{
ExternalData data =
- translate(externalDataPE, defaultDataStoreBaseURL, baseIndexURL, true,
+ translate(externalDataPE, baseIndexURL, true,
ExperimentTranslator.LoadableFields.PROPERTIES);
result.add(data);
}
return result;
}
- public static ExternalData translate(ExternalDataPE externalDataPE,
- String defaultDataStoreBaseURL, String baseIndexURL,
+ public static ExternalData translate(ExternalDataPE externalDataPE, String baseIndexURL,
final LoadableFields... withExperimentFields)
{
- return translate(externalDataPE, defaultDataStoreBaseURL, baseIndexURL, true,
- withExperimentFields);
+ return translate(externalDataPE, baseIndexURL, true, withExperimentFields);
}
- public static ExternalData translate(ExternalDataPE externalDataPE,
- String defaultDataStoreBaseURL, String baseIndexURL, boolean loadSampleProperties,
- final LoadableFields... withExperimentFields)
+ public static ExternalData translate(ExternalDataPE externalDataPE, String baseIndexURL,
+ boolean loadSampleProperties, final LoadableFields... withExperimentFields)
{
SamplePE sampleOrNull = externalDataPE.tryGetSample();
ExperimentPE experiment = externalDataPE.getExperiment();
@@ -106,8 +103,7 @@ public class ExternalDataTranslator
externalData.setRegistrationDate(externalDataPE.getRegistrationDate());
externalData.setSample(sampleOrNull == null ? null : fillSample(new Sample(), sampleOrNull,
loadSampleProperties));
- externalData.setDataStore(DataStoreTranslator.translate(externalDataPE.getDataStore(),
- defaultDataStoreBaseURL));
+ externalData.setDataStore(DataStoreTranslator.translate(externalDataPE.getDataStore()));
externalData.setPermlink(PermlinkUtilities.createPermlinkURL(baseIndexURL,
EntityKind.DATA_SET, externalData.getIdentifier()));
setProperties(externalDataPE, externalData);
diff --git a/openbis/source/java/service.properties b/openbis/source/java/service.properties
index ad3172228ff..8d843243f03 100644
--- a/openbis/source/java/service.properties
+++ b/openbis/source/java/service.properties
@@ -15,6 +15,7 @@ database.create-from-scratch = false
# For debugging set this value to true.
database.script-single-step-mode = false
database.url-host-part =
+#database.kind = plasmids_clean2
database.kind = test
#database.kind = system_test
# database.kind = system_test_strict
@@ -32,10 +33,11 @@ crowd.application.password =
# The database instance local unique identifier. Used when the new database is created.
database-instance = CISD
+#database-instance = CSB
-# Base URL of the Data Store Server.
-# Will be used only for data sets registered in an openBIS server version before 14.04.2009 (or revision 10665)
+# Base URL of the default Data Store Server.
+# Will be used only by DSS client trying to register data sets.
data-store-server-base-url = http://localhost:8889/data_store
# The URL of the CIFEX server
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
index 6882b419740..05ab92da90d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
@@ -358,8 +358,7 @@ public final class CommonClientServiceTest extends AbstractClientServiceTest
fileFormatTypePE.setDescription("Portable Network Graphics");
externalDataPE.setFileFormatType(fileFormatTypePE);
final ExternalData externalData =
- ExternalDataTranslator.translate(externalDataPE, "§SHOULDN'T BE USED",
- BASE_INDEX_URL, false);
+ ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL, false);
context.checking(new Expectations()
{
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
index bbca1f360cc..37c046ce024 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
@@ -507,15 +507,13 @@ public final class CommonServerTest extends AbstractServerTestCase
dataStorePE.setCode("DST");
externalDataPE.setDataStore(dataStorePE);
final ExternalData externalData =
- ExternalDataTranslator.translate(externalDataPE, DATA_STORE_BASE_URL,
- BASE_INDEX_URL);
+ ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL);
prepareGetSession();
final boolean showOnlyDirectlyConnected = true;
context.checking(new Expectations()
{
{
- one(commonBusinessObjectFactory).createDatasetLister(SESSION,
- DATA_STORE_BASE_URL);
+ one(commonBusinessObjectFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
one(datasetLister).listBySampleTechId(sampleId, showOnlyDirectlyConnected);
@@ -548,14 +546,12 @@ public final class CommonServerTest extends AbstractServerTestCase
dataStorePE.setCode("DST");
externalDataPE.setDataStore(dataStorePE);
final ExternalData externalData =
- ExternalDataTranslator.translate(externalDataPE, DATA_STORE_BASE_URL,
- BASE_INDEX_URL);
+ ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL);
prepareGetSession();
context.checking(new Expectations()
{
{
- one(commonBusinessObjectFactory).createDatasetLister(SESSION,
- DATA_STORE_BASE_URL);
+ one(commonBusinessObjectFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
one(datasetLister).listByExperimentTechIds(Collections.singleton(experimentId));
will(returnValue(Arrays.asList(externalData)));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
index 323a2d22a8b..e1272f4b422 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
@@ -59,7 +59,7 @@ public class DatasetListerTest extends AbstractDAOTest
DatasetListingQueryTest.createDatasetListerDAO(daoFactory);
SecondaryEntityDAO secondaryEntityDAO =
SecondaryEntityListingQueryTest.createSecondaryEntityDAO(daoFactory);
- lister = DatasetLister.create(datasetListerDAO, secondaryEntityDAO, "url1", "url2");
+ lister = DatasetLister.create(datasetListerDAO, secondaryEntityDAO, "url");
SamplePE sample =
DatasetListingQueryTest.getSample("CISD", "CP-TEST-1", datasetListerDAO
.getDatabaseInstanceId(), daoFactory);
@@ -76,13 +76,13 @@ public class DatasetListerTest extends AbstractDAOTest
assertFalse(externalData.getProperties().isEmpty());
AssertJUnit.assertNotNull(externalData.getExperiment());
}
-
+
@Test
public void testListParents()
{
- Map<Long, Set<Long>> map = lister.listParentIds(Arrays.<Long>asList(2L, 4L, 9L));
+ Map<Long, Set<Long>> map = lister.listParentIds(Arrays.<Long> asList(2L, 4L, 9L));
System.out.println(map);
-
+
assertEquals(null, map.get(2L));
assertEquals("[2]", map.get(4L).toString());
List<Long> list = new ArrayList<Long>(map.get(9L));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslatorTest.java
index 8a1392cace9..33e113972b6 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslatorTest.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.generic.shared.translator;
+import static ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants.DATA_STORE_SERVER_WEB_APPLICATION_NAME;
+
import java.util.Date;
import java.util.HashSet;
import java.util.Set;
@@ -46,7 +48,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
*/
public class ExternalDataTranslatorTest extends AssertJUnit
{
- private static final String BASE_URL = "url";
+ private static final String DOWNLOAD_URL = "url";
private static final String BASE_INDEX_URL = "index.html";
@@ -54,9 +56,9 @@ public class ExternalDataTranslatorTest extends AssertJUnit
public void testTranslationOfEmptyExternalDataPE()
{
ExternalDataPE externalDataPE = new ExternalDataPE();
- externalDataPE.setDataStore(new DataStorePE());
+ externalDataPE.setDataStore(createStore());
ExternalData externalData =
- ExternalDataTranslator.translate(externalDataPE, BASE_URL, BASE_INDEX_URL);
+ ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL);
assertEquals(null, externalData.getCode());
assertEquals(null, externalData.getExperiment());
@@ -70,7 +72,7 @@ public class ExternalDataTranslatorTest extends AssertJUnit
{
ExternalDataPE externalDataPE = new ExternalDataPE();
externalDataPE.setCode("code");
- externalDataPE.setDataStore(new DataStorePE());
+ externalDataPE.setDataStore(createStore());
externalDataPE.setComplete(BooleanOrUnknown.F);
externalDataPE.setDataProducerCode("dataProducerCode");
DataSetTypePE dataSetTypePE = new DataSetTypePE();
@@ -118,9 +120,10 @@ public class ExternalDataTranslatorTest extends AssertJUnit
externalDataPE.setSampleAcquiredFrom(samplePE);
ExternalData externalData =
- ExternalDataTranslator.translate(externalDataPE, BASE_URL, BASE_INDEX_URL);
+ ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL);
- assertEquals(BASE_URL, externalData.getDataStore().getDownloadUrl());
+ assertEquals(DOWNLOAD_URL + "/" + DATA_STORE_SERVER_WEB_APPLICATION_NAME, externalData
+ .getDataStore().getDownloadUrl());
assertEquals("code", externalData.getCode());
assertEquals(Boolean.FALSE, externalData.getComplete());
assertEquals("dataProducerCode", externalData.getDataProducerCode());
@@ -148,7 +151,7 @@ public class ExternalDataTranslatorTest extends AssertJUnit
public void testTranslationADerivedExternalDataPEWithParents()
{
ExternalDataPE externalDataPE = new ExternalDataPE();
- externalDataPE.setDataStore(new DataStorePE());
+ externalDataPE.setDataStore(createStore());
externalDataPE.setDerived(true);
ExperimentPE experimentPE = new ExperimentPE();
@@ -169,7 +172,7 @@ public class ExternalDataTranslatorTest extends AssertJUnit
externalDataPE.addParent(createParent("parent-2"));
ExternalData externalData =
- ExternalDataTranslator.translate(externalDataPE, BASE_URL, BASE_INDEX_URL);
+ ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL);
assertEquals("my-experiment", externalData.getExperiment().getCode());
assertEquals(2, externalData.getParents().size());
@@ -194,8 +197,15 @@ public class ExternalDataTranslatorTest extends AssertJUnit
{
DataPE parent = new DataPE();
parent.setCode(parentCode);
- parent.setDataStore(new DataStorePE());
+ parent.setDataStore(createStore());
return parent;
}
+ private DataStorePE createStore()
+ {
+ DataStorePE store = new DataStorePE();
+ store.setDownloadUrl(DOWNLOAD_URL);
+ return store;
+ }
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
index 0263f825817..b9e834fbbf1 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
@@ -50,17 +50,19 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validato
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
- *
- *
* @author Franz-Josef Elmer
*/
-public class RawDataServiceInternal extends AbstractServer<IRawDataServiceInternal> implements IRawDataServiceInternal
+public class RawDataServiceInternal extends AbstractServer<IRawDataServiceInternal> implements
+ IRawDataServiceInternal
{
- @Private static final String SPACE_CODE = "MS_DATA";
+ @Private
+ static final String SPACE_CODE = "MS_DATA";
+
+ @Private
+ static final String RAW_DATA_SAMPLE_TYPE = "MS_INJECTION";
- @Private static final String RAW_DATA_SAMPLE_TYPE = "MS_INJECTION";
-
- private static final IValidator<MsInjectionSample> RAW_DATA_SAMPLE_VALIDATOR = new RawDataSampleValidator();
+ private static final IValidator<MsInjectionSample> RAW_DATA_SAMPLE_VALIDATOR =
+ new RawDataSampleValidator();
private ICommonBusinessObjectFactory businessObjectFactory;
@@ -87,12 +89,12 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
{
return new RawDataServiceInternalLogger(getSessionManager(), context);
}
-
+
public List<MsInjectionSample> listRawDataSamples(String sessionToken)
{
return loadAllRawDataSamples(getSession(sessionToken));
}
-
+
public void processRawData(String sessionToken, String dataSetProcessingKey,
long[] rawDataSampleIDs, String dataSetType)
{
@@ -135,7 +137,7 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
ListSampleCriteria criteria = new ListSampleCriteria();
SampleTypePE sampleTypePE =
- getDAOFactory().getSampleTypeDAO().tryFindSampleTypeByCode(RAW_DATA_SAMPLE_TYPE);
+ getDAOFactory().getSampleTypeDAO().tryFindSampleTypeByCode(RAW_DATA_SAMPLE_TYPE);
criteria.setSampleType(SampleTypeTranslator.translate(sampleTypePE, null));
criteria.setIncludeSpace(true);
criteria.setSpaceCode(SPACE_CODE);
@@ -147,10 +149,10 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
{
manager.addSample(sample);
}
- manager.gatherDataSets(businessObjectFactory.createDatasetLister(session, ""));
+ manager.gatherDataSets(businessObjectFactory.createDatasetLister(session));
return manager.getSamples();
}
-
+
private String findDataStoreServer(String dataSetProcessingKey)
{
List<DataStorePE> dataStores = getDAOFactory().getDataStoreDAO().listDataStores();
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
index c1c938ce67e..b99cbae40b3 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
@@ -92,7 +92,7 @@ public class RawDataServiceInternalTest extends AbstractServerTestCase
prepareGetSession();
prepareListRawDataSamples(1L, 2L, 3L, 42L);
final long[] ids = new long[]
- { 2};
+ { 2 };
context.checking(new Expectations()
{
{
@@ -189,7 +189,7 @@ public class RawDataServiceInternalTest extends AbstractServerTestCase
}));
will(returnValue(samples));
- one(boFactory).createDatasetLister(SESSION, "");
+ one(boFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
one(datasetLister).listByExperimentTechIds(experimentIds);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/cli/Login.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/cli/Login.java
index a433b2c64ad..2bf35a46ff5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/cli/Login.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/cli/Login.java
@@ -27,11 +27,11 @@ import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
+import jline.ConsoleReader;
+
import org.apache.log4j.BasicConfigurator;
import org.apache.log4j.varia.NullAppender;
-import jline.ConsoleReader;
-
import ch.systemsx.cisd.args4j.Argument;
import ch.systemsx.cisd.args4j.CmdLineParser;
import ch.systemsx.cisd.args4j.Option;
@@ -118,7 +118,6 @@ public class Login
}
}
- @SuppressWarnings("unused")
public List<String> getArgs()
{
return Collections.unmodifiableList(args);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
index 52f2f2bac3a..b825235d185 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
@@ -51,5 +51,5 @@ public interface IScreeningBusinessObjectFactory
public IExternalDataBO createExternalDataBO(Session session);
- public IDatasetLister createDatasetLister(Session session, String defaultDataStoreBaseURL);
+ public IDatasetLister createDatasetLister(Session session);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
index 2223df0fa4c..e778633e3b2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
@@ -95,10 +95,9 @@ public final class ScreeningBusinessObjectFactory extends AbstractPluginBusiness
return getCommonBusinessObjectFactory().createExternalDataBO(session);
}
- public IDatasetLister createDatasetLister(Session session, String defaultDataStoreBaseURL)
+ public IDatasetLister createDatasetLister(Session session)
{
- return getCommonBusinessObjectFactory().createDatasetLister(session,
- defaultDataStoreBaseURL);
+ return getCommonBusinessObjectFactory().createDatasetLister(session);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 5c247961ada..37421c61e78 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -128,15 +128,14 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
public PlateContent getPlateContent(String sessionToken, TechId plateId)
{
Session session = getSession(sessionToken);
- return PlateContentLoader.loadImagesAndMetadata(session, businessObjectFactory,
- getDataStoreBaseURL(), plateId);
+ return PlateContentLoader.loadImagesAndMetadata(session, businessObjectFactory, plateId);
}
public PlateImages getPlateContentForDataset(String sessionToken, TechId datasetId)
{
Session session = getSession(sessionToken);
return PlateContentLoader.loadImagesAndMetadataForDataset(session, businessObjectFactory,
- getDataStoreBaseURL(), datasetId);
+ datasetId);
}
public List<WellContent> listPlateWells(String sessionToken,
@@ -144,21 +143,21 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
{
Session session = getSession(sessionToken);
return GenePlateLocationsLoader.load(session, businessObjectFactory, getDAOFactory(),
- getDataStoreBaseURL(), materialCriteria, true);
+ materialCriteria, true);
}
public TableModel loadImageAnalysisForExperiment(String sessionToken, TechId experimentId)
{
Session session = getSession(sessionToken);
return PlateContentLoader.loadImageAnalysisForExperiment(session, businessObjectFactory,
- getDataStoreBaseURL(), experimentId);
+ experimentId);
}
public TableModel loadImageAnalysisForPlate(String sessionToken, TechId plateId)
{
Session session = getSession(sessionToken);
- return PlateContentLoader.loadImageAnalysisForPlate(session, businessObjectFactory,
- getDataStoreBaseURL(), plateId);
+ return PlateContentLoader
+ .loadImageAnalysisForPlate(session, businessObjectFactory, plateId);
}
public ExternalData getDataSetInfo(String sessionToken, TechId datasetId)
@@ -232,8 +231,7 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
private ScreeningApiImpl createScreeningApiImpl(String sessionToken)
{
final Session session = getSession(sessionToken);
- return new ScreeningApiImpl(session, businessObjectFactory, getDAOFactory(),
- getDataStoreBaseURL());
+ return new ScreeningApiImpl(session, businessObjectFactory, getDAOFactory());
}
public void logoutScreening(String sessionToken)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
index 572301d1226..169eafcace9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
@@ -48,10 +48,10 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
private List<ExternalData> featureVectorDatasets;
FeatureVectorDatasetLoader(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, String dataStoreBaseURL,
- String homeSpaceOrNull, Collection<? extends PlateIdentifier> plates)
+ IScreeningBusinessObjectFactory businessObjectFactory, String homeSpaceOrNull,
+ Collection<? extends PlateIdentifier> plates)
{
- super(session, businessObjectFactory, dataStoreBaseURL, homeSpaceOrNull, plates,
+ super(session, businessObjectFactory, homeSpaceOrNull, plates,
ScreeningConstants.IMAGE_DATASET_TYPE,
ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE);
featureVectorDatasetTypeCode = ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE;
@@ -69,8 +69,7 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
{
final Long2ObjectSortedMap<ExternalData> featureVectorDatasetSet =
new Long2ObjectLinkedOpenHashMap<ExternalData>();
- IDatasetLister datasetLister =
- businessObjectFactory.createDatasetLister(session, dataStoreBaseURL);
+ IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
for (ExternalData data : getDatasets())
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java
index 67462a95c08..4368104d7b6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java
@@ -65,29 +65,26 @@ public class GenePlateLocationsLoader
{
public static List<WellContent> load(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- String dataStoreBaseURL, TechId geneMaterialId, String experimentPermId,
- boolean enrichWithImages)
+ TechId geneMaterialId, String experimentPermId, boolean enrichWithImages)
{
- return new GenePlateLocationsLoader(session, businessObjectFactory, daoFactory,
- dataStoreBaseURL).getPlateLocations(geneMaterialId, experimentPermId,
- enrichWithImages);
+ return new GenePlateLocationsLoader(session, businessObjectFactory, daoFactory)
+ .getPlateLocations(geneMaterialId, experimentPermId, enrichWithImages);
}
public static List<WellContent> load(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- String dataStoreBaseURL, TechId geneMaterialId)
+ TechId geneMaterialId)
{
- return new GenePlateLocationsLoader(session, businessObjectFactory, daoFactory,
- dataStoreBaseURL).getPlateLocations(geneMaterialId);
+ return new GenePlateLocationsLoader(session, businessObjectFactory, daoFactory)
+ .getPlateLocations(geneMaterialId);
}
public static List<WellContent> load(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- String dataStoreBaseURL, PlateMaterialsSearchCriteria materialCriteria,
- boolean enrichWithImages)
+ PlateMaterialsSearchCriteria materialCriteria, boolean enrichWithImages)
{
- return new GenePlateLocationsLoader(session, businessObjectFactory, daoFactory,
- dataStoreBaseURL).getPlateLocations(materialCriteria, enrichWithImages);
+ return new GenePlateLocationsLoader(session, businessObjectFactory, daoFactory)
+ .getPlateLocations(materialCriteria, enrichWithImages);
}
private final Session session;
@@ -96,16 +93,12 @@ public class GenePlateLocationsLoader
private final IDAOFactory daoFactory;
- private final String dataStoreBaseURL;
-
private GenePlateLocationsLoader(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- String dataStoreBaseURL)
+ IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory)
{
this.session = session;
this.businessObjectFactory = businessObjectFactory;
this.daoFactory = daoFactory;
- this.dataStoreBaseURL = dataStoreBaseURL;
}
private List<WellContent> getPlateLocations(PlateMaterialsSearchCriteria materialCriteria,
@@ -235,8 +228,7 @@ public class GenePlateLocationsLoader
{
Set<Long> plateIds = extractPlateIds(locations);
- IDatasetLister datasetLister =
- businessObjectFactory.createDatasetLister(session, dataStoreBaseURL);
+ IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
List<ExternalData> imageDatasets = datasetLister.listBySampleIds(plateIds);
imageDatasets =
ScreeningUtils.filterExternalDataByType(imageDatasets,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
index cf7c7b92d62..374225ae738 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
@@ -38,10 +38,10 @@ class ImageDatasetLoader extends PlateDatasetLoader
// TODO 2010-05-27, CR : See PlateDatasetLoader todo comment
ImageDatasetLoader(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
- String dataStoreBaseURL, String homeSpaceOrNull,
- Collection<? extends PlateIdentifier> plates, String... datasetTypeCodes)
+ String homeSpaceOrNull, Collection<? extends PlateIdentifier> plates,
+ String... datasetTypeCodes)
{
- super(session, businessObjectFactory, dataStoreBaseURL, homeSpaceOrNull, plates,
+ super(session, businessObjectFactory, homeSpaceOrNull, plates,
(datasetTypeCodes.length == 0) ? new String[]
{ ScreeningConstants.IMAGE_DATASET_TYPE } : datasetTypeCodes);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
index 59febe9802d..f832ef5ecc1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
@@ -58,18 +58,16 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoade
public class PlateContentLoader
{
public static TableModel loadImageAnalysisForPlate(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, String defaultDataStoreBaseURL,
- TechId plateId)
+ IScreeningBusinessObjectFactory businessObjectFactory, TechId plateId)
{
- return new PlateContentLoader(session, businessObjectFactory, defaultDataStoreBaseURL)
+ return new PlateContentLoader(session, businessObjectFactory)
.loadImageAnalysisForPlate(plateId);
}
public static TableModel loadImageAnalysisForExperiment(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, String defaultDataStoreBaseURL,
- TechId experimentId)
+ IScreeningBusinessObjectFactory businessObjectFactory, TechId experimentId)
{
- return new PlateContentLoader(session, businessObjectFactory, defaultDataStoreBaseURL)
+ return new PlateContentLoader(session, businessObjectFactory)
.loadImageAnalysisForExperiment(experimentId);
}
@@ -78,11 +76,9 @@ public class PlateContentLoader
* image analysis only if one dataset with such a data exist.
*/
public static PlateContent loadImagesAndMetadata(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, String defaultDataStoreBaseURL,
- TechId plateId)
+ IScreeningBusinessObjectFactory businessObjectFactory, TechId plateId)
{
- return new PlateContentLoader(session, businessObjectFactory, defaultDataStoreBaseURL)
- .getPlateContent(plateId);
+ return new PlateContentLoader(session, businessObjectFactory).getPlateContent(plateId);
}
/**
@@ -90,10 +86,9 @@ public class PlateContentLoader
* BDS-HCS format.
*/
public static PlateImages loadImagesAndMetadataForDataset(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, String defaultDataStoreBaseURL,
- TechId datasetId)
+ IScreeningBusinessObjectFactory businessObjectFactory, TechId datasetId)
{
- return new PlateContentLoader(session, businessObjectFactory, defaultDataStoreBaseURL)
+ return new PlateContentLoader(session, businessObjectFactory)
.getPlateContentForDataset(datasetId);
}
@@ -101,14 +96,11 @@ public class PlateContentLoader
private final IScreeningBusinessObjectFactory businessObjectFactory;
- private final String defaultDataStoreBaseURL;
-
private PlateContentLoader(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, String defaultDataStoreBaseURL)
+ IScreeningBusinessObjectFactory businessObjectFactory)
{
this.session = session;
this.businessObjectFactory = businessObjectFactory;
- this.defaultDataStoreBaseURL = defaultDataStoreBaseURL;
}
private PlateImages getPlateContentForDataset(TechId datasetId)
@@ -144,8 +136,7 @@ public class PlateContentLoader
private ExternalData translate(ExternalDataPE externalData)
{
- return ExternalDataTranslator.translate(externalData, defaultDataStoreBaseURL, session
- .getBaseIndexURL());
+ return ExternalDataTranslator.translate(externalData, session.getBaseIndexURL());
}
private TableModel loadImageAnalysisForPlate(TechId plateId)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.java
index 768174dea94..31de9e17692 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.java
@@ -50,8 +50,6 @@ class PlateDatasetLoader
protected final IScreeningBusinessObjectFactory businessObjectFactory;
- protected final String dataStoreBaseURL;
-
// Parameter state
private final Collection<? extends PlateIdentifier> plates;
@@ -71,12 +69,11 @@ class PlateDatasetLoader
private boolean loaded = false;
PlateDatasetLoader(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
- String dataStoreBaseURL, String homeSpaceOrNull,
- Collection<? extends PlateIdentifier> plates, String... datasetTypeCodes)
+ String homeSpaceOrNull, Collection<? extends PlateIdentifier> plates,
+ String... datasetTypeCodes)
{
this.session = session;
this.businessObjectFactory = businessObjectFactory;
- this.dataStoreBaseURL = dataStoreBaseURL;
this.homeSpaceOrNull = (homeSpaceOrNull != null) ? ("/" + homeSpaceOrNull + "/") : null;
this.plates = plates;
this.datasetTypeCodes = datasetTypeCodes;
@@ -120,8 +117,7 @@ class PlateDatasetLoader
private void loadDatasets()
{
List<Long> sampleIds = extractSampleIds();
- IDatasetLister datasetLister =
- businessObjectFactory.createDatasetLister(session, dataStoreBaseURL);
+ IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
datasets = datasetLister.listBySampleIds(sampleIds);
datasets = ScreeningUtils.filterExternalDataByType(datasets, datasetTypeCodes);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
index 0b193dc7b7d..68d3e3d45f2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
@@ -90,23 +90,20 @@ public class ScreeningApiImpl
private final IDAOFactory daoFactory;
- private final String dataStoreBaseURL;
-
public ScreeningApiImpl(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
- IDAOFactory daoFactory, String dataStoreBaseURL)
+ IDAOFactory daoFactory)
{
this.session = session;
this.businessObjectFactory = businessObjectFactory;
this.daoFactory = daoFactory;
- this.dataStoreBaseURL = dataStoreBaseURL;
}
public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
List<? extends PlateIdentifier> plates)
{
FeatureVectorDatasetLoader datasetRetriever =
- new FeatureVectorDatasetLoader(session, businessObjectFactory, dataStoreBaseURL,
- session.tryGetHomeGroupCode(), plates);
+ new FeatureVectorDatasetLoader(session, businessObjectFactory, session
+ .tryGetHomeGroupCode(), plates);
List<FeatureVectorDatasetReference> result = datasetRetriever.getFeatureVectorDatasets();
return result;
@@ -114,8 +111,8 @@ public class ScreeningApiImpl
public List<ImageDatasetReference> listImageDatasets(List<? extends PlateIdentifier> plates)
{
- return new ImageDatasetLoader(session, businessObjectFactory, dataStoreBaseURL, session
- .tryGetHomeGroupCode(), plates).getImageDatasets();
+ return new ImageDatasetLoader(session, businessObjectFactory,
+ session.tryGetHomeGroupCode(), plates).getImageDatasets();
}
public List<Plate> listPlates()
@@ -253,8 +250,8 @@ public class ScreeningApiImpl
getExperimentIdentifierFromDB(experimentIdentifier);
wellContent =
GenePlateLocationsLoader.load(session, businessObjectFactory, daoFactory,
- dataStoreBaseURL, new TechId(materialOrNull.getId()),
- fullExperimentIdentifier.getPermId(), false);
+ new TechId(materialOrNull.getId()), fullExperimentIdentifier.getPermId(),
+ false);
if (findDatasets)
{
final Set<Plate> plates = new HashSet<Plate>(wellContent.size());
@@ -263,8 +260,8 @@ public class ScreeningApiImpl
plates.add(asPlate(fullExperimentIdentifier, w));
}
final FeatureVectorDatasetLoader datasetRetriever =
- new FeatureVectorDatasetLoader(session, businessObjectFactory,
- dataStoreBaseURL, session.tryGetHomeGroupCode(), plates);
+ new FeatureVectorDatasetLoader(session, businessObjectFactory, session
+ .tryGetHomeGroupCode(), plates);
final List<ImageDatasetReference> imageDatasets = datasetRetriever.getImageDatasets();
final List<FeatureVectorDatasetReference> featureVectorDatasets =
datasetRetriever.getFeatureVectorDatasets();
@@ -293,7 +290,7 @@ public class ScreeningApiImpl
}
final List<WellContent> wellContent =
GenePlateLocationsLoader.load(session, businessObjectFactory, daoFactory,
- dataStoreBaseURL, new TechId(materialOrNull.getId()));
+ new TechId(materialOrNull.getId()));
if (findDatasets)
{
@@ -303,8 +300,8 @@ public class ScreeningApiImpl
plates.add(asPlate(w));
}
final FeatureVectorDatasetLoader datasetRetriever =
- new FeatureVectorDatasetLoader(session, businessObjectFactory,
- dataStoreBaseURL, session.tryGetHomeGroupCode(), plates);
+ new FeatureVectorDatasetLoader(session, businessObjectFactory, session
+ .tryGetHomeGroupCode(), plates);
final List<ImageDatasetReference> imageDatasets = datasetRetriever.getImageDatasets();
final List<FeatureVectorDatasetReference> featureVectorDatasets =
datasetRetriever.getFeatureVectorDatasets();
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
index 3b69e82472a..c7d94e81902 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
@@ -52,8 +52,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConst
*/
public class ScreeningApiImplTest extends AbstractServerTestCase
{
- private static final String DSS_URL = "http://localhost:8889/";
-
private static final String SERVER_URL = "server-url";
private IScreeningBusinessObjectFactory screeningBOFactory;
@@ -64,7 +62,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
public void beforeMethod()
{
screeningBOFactory = context.mock(IScreeningBusinessObjectFactory.class);
- screeningApi = new ScreeningApiImpl(SESSION, screeningBOFactory, daoFactory, DSS_URL);
+ screeningApi = new ScreeningApiImpl(SESSION, screeningBOFactory, daoFactory);
}
@Test
@@ -80,7 +78,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
Sample p1 = plateSample(pi1, "384_WELLS_16X24");
will(returnValue(Arrays.asList(p1)));
- one(screeningBOFactory).createDatasetLister(SESSION, DSS_URL);
+ one(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1), imageAnalysisDataSet(
@@ -118,7 +116,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
Sample p1 = plateSample(pi1, null);
will(returnValue(Arrays.asList(p1)));
- one(screeningBOFactory).createDatasetLister(SESSION, DSS_URL);
+ one(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1))));
@@ -178,7 +176,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
Sample p1 = plateSample(pi1, "384_WELLS_16X24");
will(returnValue(Arrays.asList(p1)));
- exactly(2).of(screeningBOFactory).createDatasetLister(SESSION, DSS_URL);
+ exactly(2).of(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1), imageAnalysisDataSet(
@@ -222,7 +220,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
Sample p1 = plateSample(pi1, plateGeometry);
will(returnValue(Arrays.asList(p1)));
- one(screeningBOFactory).createDatasetLister(SESSION, DSS_URL);
+ one(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1))));
--
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