From d0774ce28028112e8e03a50ce8666ac39d927113 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 29 Sep 2014 10:22:33 +0000
Subject: [PATCH] SSDM-949: Rename sequence database on DSS to
SearchDomainService.
SVN: 32513
---
.../dss/generic/server/DataStoreService.java | 36 +++++++++----------
.../server/DataStoreServiceLogger.java | 2 +-
....java => AbstractSearchDomainService.java} | 8 ++---
.../v2/sequencedatabases/BlastDatabase.java | 6 ++--
.../v2/sequencedatabases/EchoDatabase.java | 2 +-
.../tasks/IPluginTaskInfoProvider.java | 4 +--
.../plugins/tasks/PluginTaskFactory.java | 10 +++---
.../plugins/tasks/PluginTaskInfoProvider.java | 8 ++---
...atabase.java => ISearchDomainService.java} | 14 ++++----
.../generic/server/DataStoreServiceTest.java | 18 +++++-----
.../server/business/bo/DataSetTable.java | 2 +-
.../generic/shared/IDataStoreService.java | 6 ++--
12 files changed, 59 insertions(+), 57 deletions(-)
rename datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/{AbstractSequenceDatabase.java => AbstractSearchDomainService.java} (81%)
rename datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/{ISequenceDatabase.java => ISearchDomainService.java} (73%)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
index 24b1b8f9295..abe8fcd4543 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
@@ -61,7 +61,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
import ch.systemsx.cisd.openbis.dss.generic.shared.ProcessingStatus;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.ISessionWorkspaceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISequenceDatabase;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchDomainService;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomain;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
@@ -515,11 +515,11 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
}
@Override
- public List<SearchDomain> listAvailableSequenceDatabases(String sessionToken)
+ public List<SearchDomain> listAvailableSearchDomains(String sessionToken)
{
sessionTokenManager.assertValidSessionToken(sessionToken);
- PluginTaskProvider<ISequenceDatabase> provider = pluginTaskInfoProvider.getSequenceDatabasesProvider();
+ PluginTaskProvider<ISearchDomainService> provider = pluginTaskInfoProvider.getSearchDomainServiceProvider();
List<DatastoreServiceDescription> pluginDescriptions = provider.getPluginDescriptions();
List<SearchDomain> result = new ArrayList<SearchDomain>();
for (DatastoreServiceDescription description : pluginDescriptions)
@@ -543,18 +543,18 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
{
sessionTokenManager.assertValidSessionToken(sessionToken);
- PluginTaskProvider<ISequenceDatabase> provider = pluginTaskInfoProvider.getSequenceDatabasesProvider();
- DatastoreServiceDescription sequenceDatabaseDescription
- = findSequenceDatabase(provider, preferredSequenceDatabaseOrNull);
- if (sequenceDatabaseDescription != null)
+ PluginTaskProvider<ISearchDomainService> provider = pluginTaskInfoProvider.getSearchDomainServiceProvider();
+ DatastoreServiceDescription serviceDescription
+ = findSearchDomainService(provider, preferredSequenceDatabaseOrNull);
+ if (serviceDescription != null)
{
- ISequenceDatabase sequenceDatabase = provider.getPluginInstance(sequenceDatabaseDescription.getKey());
- List<SearchDomainSearchResult> result = sequenceDatabase.search(sequenceSnippet, optionalParametersOrNull);
+ ISearchDomainService service = provider.getPluginInstance(serviceDescription.getKey());
+ List<SearchDomainSearchResult> result = service.search(sequenceSnippet, optionalParametersOrNull);
for (SearchDomainSearchResult sequenceSearchResult : result)
{
SearchDomain searchDomain = new SearchDomain();
- searchDomain.setName(sequenceDatabaseDescription.getKey());
- searchDomain.setLabel(sequenceDatabase.getLabel());
+ searchDomain.setName(serviceDescription.getKey());
+ searchDomain.setLabel(serviceDescription.getLabel());
sequenceSearchResult.setSearchDomain(searchDomain);
}
return result;
@@ -563,27 +563,27 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
return new ArrayList<SearchDomainSearchResult>();
}
- private DatastoreServiceDescription findSequenceDatabase(PluginTaskProvider<ISequenceDatabase> provider,
+ private DatastoreServiceDescription findSearchDomainService(PluginTaskProvider<ISearchDomainService> provider,
String preferredSequenceDatabaseOrNull)
{
List<DatastoreServiceDescription> pluginDescriptions = provider.getPluginDescriptions();
- DatastoreServiceDescription availableDatabase = null;
+ DatastoreServiceDescription availableService = null;
for (DatastoreServiceDescription description : pluginDescriptions)
{
- ISequenceDatabase database = provider.getPluginInstance(description.getKey());
- if (database.isAvailable())
+ ISearchDomainService service = provider.getPluginInstance(description.getKey());
+ if (service.isAvailable())
{
if (description.getKey().equals(preferredSequenceDatabaseOrNull))
{
return description;
}
- if (availableDatabase == null)
+ if (availableService == null)
{
- availableDatabase = description;
+ availableService = description;
}
}
}
- return availableDatabase;
+ return availableService;
}
private PutDataSetService getPutDataSetService()
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
index 34e2061bf73..4d92847e6a2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
@@ -208,7 +208,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
}
@Override
- public List<SearchDomain> listAvailableSequenceDatabases(String sessionToken)
+ public List<SearchDomain> listAvailableSearchDomains(String sessionToken)
{
log("listAvailableSequenceDatabases", "");
return null;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/AbstractSequenceDatabase.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/AbstractSearchDomainService.java
similarity index 81%
rename from datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/AbstractSequenceDatabase.java
rename to datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/AbstractSearchDomainService.java
index 342815c6d35..5569c195759 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/AbstractSequenceDatabase.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/AbstractSearchDomainService.java
@@ -20,20 +20,20 @@ import java.io.File;
import java.util.Properties;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskFactory;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISequenceDatabase;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchDomainService;
/**
- * Abstract super class of all {@link ISequenceDatabase} implementations which get the label from
+ * Abstract super class of all {@link ISearchDomainService} implementations which get the label from
* the property {@link PluginTaskFactory#LABEL_PROPERTY_NAME}.
*
* @author Franz-Josef Elmer
*/
-public abstract class AbstractSequenceDatabase implements ISequenceDatabase
+public abstract class AbstractSearchDomainService implements ISearchDomainService
{
private final String label;
protected String name;
- protected AbstractSequenceDatabase(Properties properties, File storeRoot)
+ protected AbstractSearchDomainService(Properties properties, File storeRoot)
{
label = properties.getProperty(PluginTaskFactory.LABEL_PROPERTY_NAME);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java
index 054980e11e1..150908fc33b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java
@@ -42,13 +42,13 @@ import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.process.ProcessExecutionHelper;
import ch.systemsx.cisd.common.process.ProcessResult;
import ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISequenceDatabase;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchDomainService;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.BlastUtils;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFileSearchResultLocation;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
/**
- * Implementation of {@link ISequenceDatabase} based on <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi">BLAST</a>.
+ * Implementation of {@link ISearchDomainService} based on <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi">BLAST</a>.
* The following configuration parameters are understood:
* <ul>
* <li><tt>blast-tools-directory</tt>: Absolute path to the directory with blastn and blastp command line tools.<br/>
@@ -93,7 +93,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResu
*
* @author Franz-Josef Elmer
*/
-public class BlastDatabase extends AbstractSequenceDatabase
+public class BlastDatabase extends AbstractSearchDomainService
{
public static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, BlastDatabase.class);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/EchoDatabase.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/EchoDatabase.java
index dbc5a1423ad..aa804bb0c63 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/EchoDatabase.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/EchoDatabase.java
@@ -34,7 +34,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResu
*
* @author pkupczyk
*/
-public class EchoDatabase extends AbstractSequenceDatabase
+public class EchoDatabase extends AbstractSearchDomainService
{
public EchoDatabase(Properties properties, File storeRoot)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IPluginTaskInfoProvider.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IPluginTaskInfoProvider.java
index be60e2671af..c445ba5774b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IPluginTaskInfoProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IPluginTaskInfoProvider.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks;
import java.io.File;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISequenceDatabase;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchDomainService;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatastoreServiceDescriptions;
/**
@@ -43,7 +43,7 @@ public interface IPluginTaskInfoProvider
public PluginTaskProvider<IProcessingPluginTask> getProcessingPluginsProvider();
- public PluginTaskProvider<ISequenceDatabase> getSequenceDatabasesProvider();
+ public PluginTaskProvider<ISearchDomainService> getSearchDomainServiceProvider();
public ArchiverPluginFactory getArchiverPluginFactory();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskFactory.java
index eca811cb3aa..52973327b8e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskFactory.java
@@ -40,8 +40,8 @@ import ch.systemsx.cisd.common.properties.PropertyUtils;
import ch.systemsx.cisd.common.properties.PropertyParametersUtil.SectionProperties;
import ch.systemsx.cisd.common.reflection.ClassUtils;
import ch.systemsx.cisd.openbis.dss.generic.server.IServletPropertiesManager;
-import ch.systemsx.cisd.openbis.dss.generic.server.api.v2.sequencedatabases.AbstractSequenceDatabase;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISequenceDatabase;
+import ch.systemsx.cisd.openbis.dss.generic.server.api.v2.sequencedatabases.AbstractSearchDomainService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchDomainService;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ReportingPluginType;
@@ -129,14 +129,14 @@ public class PluginTaskFactory<T>
this.description =
DatastoreServiceDescription.reporting(pluginKey, label, datasetCodes,
datastoreCode, type);
- } else if (pluginInstance instanceof ISequenceDatabase)
+ } else if (pluginInstance instanceof ISearchDomainService)
{
this.description =
DatastoreServiceDescription.processing(pluginKey, label, new String[0],
datastoreCode);
- if (this.pluginInstance instanceof AbstractSequenceDatabase)
+ if (this.pluginInstance instanceof AbstractSearchDomainService)
{
- ((AbstractSequenceDatabase) this.pluginInstance).setName(pluginKey);
+ ((AbstractSearchDomainService) this.pluginInstance).setName(pluginKey);
}
} else
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskInfoProvider.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskInfoProvider.java
index 0a926633da7..2243f6c3d64 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskInfoProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskInfoProvider.java
@@ -27,7 +27,7 @@ import ch.systemsx.cisd.common.properties.PropertyParametersUtil.SectionProperti
import ch.systemsx.cisd.openbis.dss.generic.server.DataStoreServer;
import ch.systemsx.cisd.openbis.dss.generic.server.IServletPropertiesManager;
import ch.systemsx.cisd.openbis.dss.generic.shared.Constants;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISequenceDatabase;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchDomainService;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.SessionWorkspaceUtil;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatastoreServiceDescriptions;
@@ -49,7 +49,7 @@ public class PluginTaskInfoProvider implements IPluginTaskInfoProvider
private final PluginTaskProvider<IProcessingPluginTask> processingPlugins;
- private final PluginTaskProvider<ISequenceDatabase> sequenceDatabasePlugins;
+ private final PluginTaskProvider<ISearchDomainService> sequenceDatabasePlugins;
private final ArchiverPluginFactory archiverTaskFactory;
@@ -90,7 +90,7 @@ public class PluginTaskInfoProvider implements IPluginTaskInfoProvider
createProcessingPluginsFactories(serviceProperties, servletPropertiesManager,
datastoreCode, storeRoot);
sequenceDatabasePlugins = createPluginsFactories(serviceProperties, servletPropertiesManager,
- datastoreCode, storeRoot, ISequenceDatabase.class, "Sequence database",
+ datastoreCode, storeRoot, ISearchDomainService.class, "Sequence database",
Constants.SEQUENCE_DATABASES_NAMES);
this.archiverTaskFactory = createArchiverTaskFactory(serviceProperties, datastoreCode);
}
@@ -126,7 +126,7 @@ public class PluginTaskInfoProvider implements IPluginTaskInfoProvider
}
@Override
- public PluginTaskProvider<ISequenceDatabase> getSequenceDatabasesProvider()
+ public PluginTaskProvider<ISearchDomainService> getSearchDomainServiceProvider()
{
return sequenceDatabasePlugins;
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISequenceDatabase.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISearchDomainService.java
similarity index 73%
rename from datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISequenceDatabase.java
rename to datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISearchDomainService.java
index c93d4c2dc21..a9572eab495 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISequenceDatabase.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISearchDomainService.java
@@ -25,31 +25,31 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomain;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
/**
- * Interface for a database for nucleotid or amonioacid sequences.
+ * Interface for a search domain service.
* Implementing classes should have a public constructor with two arguments: First is an instance of
* {@link Properties} and second is an instance of {@link File} which points to the root of the data set store.
*
* @author Franz-Josef Elmer
*/
-public interface ISequenceDatabase
+public interface ISearchDomainService
{
/**
- * Returns the label of this sequence database instance. It can be used for human readable output.
+ * Returns the label of this search domain service instance. It can be used for human readable output.
* Will be used to populated {@link SearchDomain} instances of the search result..
*/
public String getLabel();
/**
- * Returns <code>true</code> if this sequence database is available. For example, a
- * sequence database is available if the external tools are available.
+ * Returns <code>true</code> if this service is available. For example, a local
+ * BLAST sequence search service is available if the external BLAST tools are available.
*/
public boolean isAvailable();
/**
- * Searches for reference sequences matching the specified sequence snippet.
+ * Searches this service for the specified search string.
*
* @param optionalParametersOrNull Optional parameters which might be used. Can be <code>null</code>.
* @return an empty list if nothing be found.
*/
- public List<SearchDomainSearchResult> search(String sequenceSnippet, Map<String, String> optionalParametersOrNull);
+ public List<SearchDomainSearchResult> search(String searchString, Map<String, String> optionalParametersOrNull);
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
index 477b4d6e70f..8dbc90eccb5 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
@@ -38,12 +38,12 @@ import ch.systemsx.cisd.common.exceptions.InvalidSessionException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.mail.MailClientParameters;
import ch.systemsx.cisd.common.properties.PropertyParametersUtil.SectionProperties;
-import ch.systemsx.cisd.openbis.dss.generic.server.api.v2.sequencedatabases.AbstractSequenceDatabase;
+import ch.systemsx.cisd.openbis.dss.generic.server.api.v2.sequencedatabases.AbstractSearchDomainService;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IPluginTaskInfoProvider;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskFactory;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISequenceDatabase;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchDomainService;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.PluginUtilTest;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.IServiceForDataStoreServer;
@@ -96,7 +96,7 @@ public class DataStoreServiceTest extends AssertJUnit
}
}
- public static final class MockSequenceDatabase extends AbstractSequenceDatabase
+ public static final class MockSequenceDatabase extends AbstractSearchDomainService
{
private static final String DATA_SET_KEY = "data-set";
private static final String AVAILABLE_KEY = "available";
@@ -409,8 +409,8 @@ public class DataStoreServiceTest extends AssertJUnit
allowing(pluginTaskParameters).getStoreRoot();
will(returnValue(TEST_STORE));
- List<PluginTaskFactory<ISequenceDatabase>> factories
- = new ArrayList<PluginTaskFactory<ISequenceDatabase>>();
+ List<PluginTaskFactory<ISearchDomainService>> factories
+ = new ArrayList<PluginTaskFactory<ISearchDomainService>>();
for (String database : databases)
{
boolean available = database.startsWith("-") == false;
@@ -423,12 +423,12 @@ public class DataStoreServiceTest extends AssertJUnit
sectionProperties.setProperty(PluginTaskFactory.CLASS_PROPERTY_NAME, MockSequenceDatabase.class.getName());
sectionProperties.setProperty(MockSequenceDatabase.AVAILABLE_KEY, Boolean.toString(available));
sectionProperties.setProperty(MockSequenceDatabase.DATA_SET_KEY, "DS-" + database.toUpperCase());
- factories.add(new PluginTaskFactory<ISequenceDatabase>(null,
+ factories.add(new PluginTaskFactory<ISearchDomainService>(null,
new SectionProperties("db-" + database, sectionProperties), "DSS",
- ISequenceDatabase.class, "Test-db-" + database, TEST_STORE));
+ ISearchDomainService.class, "Test-db-" + database, TEST_STORE));
}
- allowing(pluginTaskParameters).getSequenceDatabasesProvider();
- will(returnValue(new PluginTaskProvider<ISequenceDatabase>(factories)));
+ allowing(pluginTaskParameters).getSearchDomainServiceProvider();
+ will(returnValue(new PluginTaskProvider<ISearchDomainService>(factories)));
}
});
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
index b5bcff52c48..a4459e54be7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
@@ -298,7 +298,7 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
IDataStoreService service = tryGetDataStoreService(dataStore);
if (service != null)
{
- result.addAll(service.listAvailableSequenceDatabases(dataStore.getSessionToken()));
+ result.addAll(service.listAvailableSearchDomains(dataStore.getSessionToken()));
}
}
return result;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
index 20da4976828..e941a8963f8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
@@ -181,9 +181,11 @@ public interface IDataStoreService
Map<String, String> optionalParametersOrNull);
/**
- * Lists all available sequence databases.
+ * Lists all available search domains.
+ *
+ * @since 10
*/
@Conversational(progress = Progress.AUTOMATIC)
- public List<SearchDomain> listAvailableSequenceDatabases(String sessionToken);
+ public List<SearchDomain> listAvailableSearchDomains(String sessionToken);
}
--
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