diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
new file mode 100644
index 0000000000000000000000000000000000000000..77c354c491fc142cf005efc0c22db3c817bd162d
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
@@ -0,0 +1,109 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.server.api.v1;
+
+import java.util.Collections;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import javax.annotation.Resource;
+
+import org.springframework.stereotype.Component;
+
+import ch.systemsx.cisd.authentication.ISessionManager;
+import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
+import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
+import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
+import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@Component(ResourceNames.GENERAL_INFORMATION_CHANGING_SERVICE_SERVER)
+public class GeneralInformationChangingService extends
+ AbstractServer<IGeneralInformationChangingService> implements
+ IGeneralInformationChangingService
+{
+ @Resource(name = ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames.GENERIC_PLUGIN_SERVER)
+ private IGenericServer genericServer;
+
+ // Default constructor needed by Spring
+ public GeneralInformationChangingService()
+ {
+ }
+
+ GeneralInformationChangingService(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager, IGenericServer genericServer)
+ {
+ super(sessionManager, daoFactory, propertiesBatchManager);
+ this.genericServer = genericServer;
+ }
+
+ public IGeneralInformationChangingService createLogger(IInvocationLoggerContext context)
+ {
+ return new GeneralInformationChangingServiceLogger(sessionManager, context);
+ }
+
+ public void updateSampleProperties(String sessionToken, long sampleID,
+ Map<String, String> properties)
+ {
+ TechId id = new TechId(sampleID);
+ Sample sample = genericServer.getSampleInfo(sessionToken, id).getParent();
+ for (Entry<String, String> entry : properties.entrySet())
+ {
+ EntityHelper.createOrUpdateProperty(sample, entry.getKey(), entry.getValue());
+ }
+ Experiment experiment = sample.getExperiment();
+ ExperimentIdentifier experimentIdentifier =
+ experiment == null ? null : ExperimentIdentifierFactory.parse(experiment
+ .getIdentifier());
+ SampleIdentifier sampleIdentifier = SampleIdentifierFactory.parse(sample.getIdentifier());
+ Sample container = sample.getContainer();
+ String containerIdentifier = container == null ? null : container.getIdentifier();
+ SampleUpdatesDTO updates =
+ new SampleUpdatesDTO(id, sample.getProperties(), experimentIdentifier,
+ Collections.<NewAttachment> emptySet(), sample.getModificationDate(),
+ sampleIdentifier, containerIdentifier, null);
+ genericServer.updateSample(sessionToken, updates);
+ }
+
+ public int getMajorVersion()
+ {
+ return 1;
+ }
+
+ public int getMinorVersion()
+ {
+ return 0;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
new file mode 100644
index 0000000000000000000000000000000000000000..0beb69b34ff8a167f97fe58a1acc9391045de9bf
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
@@ -0,0 +1,58 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.server.api.v1;
+
+import java.util.Map;
+
+import ch.systemsx.cisd.authentication.ISessionManager;
+import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
+import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class GeneralInformationChangingServiceLogger extends AbstractServerLogger implements
+ IGeneralInformationChangingService
+{
+
+ public GeneralInformationChangingServiceLogger(ISessionManager<Session> sessionManagerNull,
+ IInvocationLoggerContext context)
+ {
+ super(sessionManagerNull, context);
+ }
+
+ public void updateSampleProperties(String sessionToken, long sampleID,
+ Map<String, String> properties)
+ {
+ logTracking(sessionToken, "update-sample-properties", "SAMPLE(%s)", sampleID);
+ }
+
+ public int getMajorVersion()
+ {
+ return 0;
+ }
+
+ public int getMinorVersion()
+ {
+ return 0;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceServer.java
new file mode 100644
index 0000000000000000000000000000000000000000..b5dc8066e9a9e0f74654e4b4e0c07cd06549db13
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceServer.java
@@ -0,0 +1,47 @@
+/*
+ * 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.generic.server.api.v1;
+
+import javax.annotation.Resource;
+
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.RequestMapping;
+
+import ch.systemsx.cisd.common.api.server.AbstractApiServiceExporter;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@Controller
+@RequestMapping(
+ { IGeneralInformationChangingService.SERVICE_URL, "/openbis" + IGeneralInformationChangingService.SERVICE_URL })
+public class GeneralInformationChangingServiceServer extends AbstractApiServiceExporter
+{
+ @Resource(name = ResourceNames.GENERAL_INFORMATION_CHANGING_SERVICE_SERVER)
+ private IGeneralInformationChangingService service;
+
+ @Override
+ public void afterPropertiesSet()
+ {
+ establishService(IGeneralInformationChangingService.class, service,
+ IGeneralInformationChangingService.SERVICE_NAME, IGeneralInformationChangingService.SERVICE_URL);
+ super.afterPropertiesSet();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/ResourceNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/ResourceNames.java
index 5ce924a871e6d191b5eac019f96e16564a68cdcd..1fdb8174c752653d561a0fd847cd27e59c39ee78 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/ResourceNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/ResourceNames.java
@@ -24,5 +24,6 @@ package ch.systemsx.cisd.openbis.generic.server.api.v1;
public class ResourceNames
{
public final static String GENERAL_INFORMATION_SERVICE_SERVER = "general-information-api-server-v1";
+ public final static String GENERAL_INFORMATION_CHANGING_SERVICE_SERVER = "general-information-changing-api-server-v1";
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
index 5b64b638eb98f3720b7b82295035dcf4713990c0..e634f79a7d25794dbd4fb0b182078e9bebb71bc8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
@@ -73,7 +73,7 @@ public class Translator
List<IEntityProperty> properties = privateSample.getProperties();
for (IEntityProperty prop : properties)
{
- initializer.putProperty(prop.getPropertyType().getCode(), prop.getValue());
+ initializer.putProperty(prop.getPropertyType().getCode(), prop.tryGetAsString());
}
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experimentOrNull =
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityPropertiesConverter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityPropertiesConverter.java
index 56566e83e8831ec945db588fe205a9f64bd02d72..6c290f75a73a0af8c2b5d7a1567f1ffe1e81440c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityPropertiesConverter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityPropertiesConverter.java
@@ -413,7 +413,8 @@ public final class EntityPropertiesConverter implements IEntityPropertiesConvert
final Set<T> set = new HashSet<T>();
for (T newProperty : convertedProperties)
{
- T existingProperty = tryFind(oldProperties, newProperty);
+ PropertyTypePE propertyType = newProperty.getEntityTypePropertyType().getPropertyType();
+ T existingProperty = tryFind(oldProperties, propertyType);
if (existingProperty != null)
{
existingProperty.setUntypedValue(newProperty.getValue(),
@@ -478,12 +479,12 @@ public final class EntityPropertiesConverter implements IEntityPropertiesConvert
return set;
}
- private static <T extends EntityPropertyPE> T tryFind(Collection<T> oldProperties, T p)
+ private static <T extends EntityPropertyPE> T tryFind(Collection<T> oldProperties, PropertyTypePE propertyType)
{
for (T oldProperty : oldProperties)
{
if (oldProperty.getEntityTypePropertyType().getPropertyType()
- .equals(p.getEntityTypePropertyType().getPropertyType()))
+ .equals(propertyType))
{
return oldProperty;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java
new file mode 100644
index 0000000000000000000000000000000000000000..ce933733549ea883f8b713650aa44ac2c1577836
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java
@@ -0,0 +1,47 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.api.v1;
+
+import java.util.Map;
+
+import org.springframework.transaction.annotation.Transactional;
+
+import ch.systemsx.cisd.common.api.IRpcService;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
+
+/**
+ * Service for changing general informations.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IGeneralInformationChangingService extends IRpcService
+{
+ /**
+ * Name of this service for which it is registered at the RPC name server.
+ */
+ public static final String SERVICE_NAME = "general-information-changing";
+
+ /**
+ * Application part of the URL to access this service remotely.
+ */
+ public static final String SERVICE_URL = "/rmi-" + SERVICE_NAME + "-v1";
+
+ @Transactional
+ @RolesAllowed(RoleWithHierarchy.SPACE_USER)
+ public void updateSampleProperties(String sessionToken, long sampleID, Map<String, String> properties);
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
index ba17689f1a5e0bf83cc9df00da2250efe0ac7f40..bbbecc87376ea063307d33fcfa2420a1b76dfbd2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
@@ -121,20 +121,25 @@ public class EntityHelper
}
/**
- * Tries to set the value for a given property in an {@link IEntityPropertiesHolder} instance.
- * Creates a new property if no property for the specified code is found.
+ * Creates a property with specified code and value. An already existing property with same
+ * code will be removed.
*/
public static void createOrUpdateProperty(IEntityPropertiesHolder holder, String propertyCode,
String propertyValue)
{
- IEntityProperty property = tryFindProperty(holder.getProperties(), propertyCode);
-
- if (property == null)
+ IEntityProperty newProperty = createNewProperty(propertyCode, propertyValue);
+ List<IEntityProperty> properties = holder.getProperties();
+ for (int i = 0; i < properties.size(); i++)
{
- property = createNewProperty(propertyCode);
- holder.getProperties().add(property);
+ IEntityProperty property = properties.get(i);
+ PropertyType propertyType = property.getPropertyType();
+ if (propertyType.getCode().equalsIgnoreCase(propertyCode))
+ {
+ properties.set(i, newProperty);
+ return;
+ }
}
- property.setValue(propertyValue);
+ properties.add(newProperty);
}
public static IEntityProperty createNewProperty(String propertyCode, String propertyValue)
diff --git a/screening/build/build.xml b/screening/build/build.xml
index 63ad0254d852b86be8742630f5d1ef0e4fb4fc03..51d39cd7777532e62ae30ba34eb17a303b4e0b1e 100644
--- a/screening/build/build.xml
+++ b/screening/build/build.xml
@@ -373,6 +373,79 @@
</zip>
</target>
+
+ <target name="screening-api-eclipse">
+ <mkdir dir="${dist.screening-api.lib}" />
+ <recursive-jar destfile="${dist.screening-api.jar}">
+ <fileset dir="${targets}/www/WEB-INF/classes">
+ <include name="OpenBISScreeningML*.class" />
+ <include name="ch/systemsx/cisd/common/api/**/*.class" />
+ <exclude name="ch/systemsx/cisd/common/api/server/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/dss/client/api/v1/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/dss/generic/shared/api/v1/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/dss/generic/shared/api/authorization/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/dss/screening/shared/api/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/generic/shared/basic/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/generic/shared/api/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/generic/shared/authorization/annotation/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/plugin/screening/shared/api/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/plugin/screening/client/api/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/plugin/screening/client/cli/**/*.class" />
+ </fileset>
+ <manifest>
+ <attribute name="Main-Class" value="ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningClientApiTest" />
+ <attribute name="Class-Path" value="spring-ext.jar" />
+ <attribute name="Version" value="${version.number}" />
+ <attribute name="Build-Number"
+ value="${version.number} (r${revision.number},${clean.flag})" />
+ </manifest>
+ </recursive-jar>
+ <jar update="true" destfile="${dist.screening-api.jar}">
+ <fileset dir="../openbis/targets/www/WEB-INF/classes">
+ <include name="ch/systemsx/cisd/openbis/generic/client/cli/Login*.class" />
+ <include name="ch/systemsx/cisd/openbis/generic/shared/api/v1/**/*.class" />
+ </fileset>
+ <fileset dir="../datastore_server/targets/classes">
+ <include name="ch/systemsx/cisd/openbis/dss/client/api/v1/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/dss/generic/shared/api/v1/**/*.class" />
+ <include name="ch/systemsx/cisd/openbis/dss/generic/shared/api/authorization/**/*.class" />
+ </fileset>
+ <fileset dir="../server-common/targets/classes">
+ <include name="ch/systemsx/cisd/common/spring/HttpInvokerUtils.class" />
+ <include name="ch/systemsx/cisd/common/api/client/**/*.class" />
+ </fileset>
+ <fileset dir="../common/targets/classes">
+ <include name="ch/systemsx/cisd/common/exceptions/**/*.class" />
+ <include name="ch/systemsx/cisd/common/api/*.class" />
+ <include name="ch/systemsx/cisd/common/io/ConcatenatedFileOutputStreamWriter.class" />
+ <include name="ch/systemsx/cisd/common/io/ConcatenatedContentInputStream.class" />
+ <include name="ch/systemsx/cisd/common/io/FileBasedContent.class" />
+ <include name="ch/systemsx/cisd/common/io/IContent.class" />
+ </fileset>
+ </jar>
+ <zip update="true" destfile="${dist.screening-api.jar}">
+ <zipfileset src="${lib}/gwt2.0/gwt-user.jar">
+ <include name="com/google/gwt/user/client/rpc/IsSerializable.class" />
+ <include name="com/google/gwt/user/client/rpc/SerializableException.class" />
+ </zipfileset>
+ </zip>
+ <recursive-jar destfile="${dist.screening-api.lib}/spring-ext.jar">
+ <zipfileset src="${lib}/spring/spring.jar" />
+ <zipfileset src="${lib}/spring/third-party/stream-supporting-httpinvoker.jar" />
+ <zipfileset src="${lib}/commons-logging/commons-logging.jar" />
+ <zipfileset src="${lib}/commons-httpclient/commons-httpclient.jar" />
+ <zipfileset src="${lib}/commons-codec/commons-codec.jar" />
+ <zipfileset src="${lib}/log4j/log4j.jar" />
+ <zipfileset src="${lib}/jline/jline.jar" />
+ <zipfileset src="${lib}/cisd-args4j/cisd-args4j.jar" />
+ <zipfileset src="${lib}/cisd-base/cisd-base.jar" />
+ <zipfileset src="${lib}/jython/standalone/jython.jar" />
+ </recursive-jar>
+ <recursive-jar destfile="${dist.screening-api-batteries-included.jar}">
+ <zipfileset src="${dist.screening-api.lib}/spring-ext.jar" />
+ <zipfileset src="${dist.screening-api.jar}" />
+ </recursive-jar>
+ </target>
<!--
To test the API you can use
diff --git a/screening/source/java/OpenBISScreeningML.java b/screening/source/java/OpenBISScreeningML.java
index b6eb5b299b29a71db2d2fb3d721ee6a5b2e1f0f4..6c00533f8c58042989ff21b51264adf17ee54887 100644
--- a/screening/source/java/OpenBISScreeningML.java
+++ b/screening/source/java/OpenBISScreeningML.java
@@ -28,7 +28,6 @@ import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
-import java.util.Properties;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO;
@@ -49,6 +48,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
/**
@@ -84,6 +84,9 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
*/
public class OpenBISScreeningML
{
+
+ static final String DATASETS_FOLDER = "openbis_datasets";
+
private static interface ITileNumberIterable extends Iterable<Integer>
{
public void setMaximumNumberOfTiles(int numberOfTiles);
@@ -175,6 +178,15 @@ public class OpenBISScreeningML
private static File dataSetsDir;
+ /**
+ * Root temporary directory for data sets and images. By default <code>java.io.tmpdir</code> is
+ * used.
+ */
+ static File tempDir = new File(System.getProperty("java.io.tmpdir"));
+
+ static final String TEMP_DIR_PREFIX = "openbis_";
+ static final String TEMP_DIR_POSTFIX = "_temp_dir";
+
//
// Authentication methods
//
@@ -194,23 +206,23 @@ public class OpenBISScreeningML
*/
public static void login(String user, String password, String url)
{
- openbis = ScreeningOpenbisServiceFacadeFactory.tryCreate(user, password, url);
- if (openbis == null)
+ IScreeningOpenbisServiceFacade facade = ScreeningOpenbisServiceFacadeFactory.tryCreate(user, password, url);
+ if (facade == null)
{
throw new RuntimeException("Login failed.");
}
- init();
+ init(facade);
}
- private static void init()
+ public static void init(IScreeningOpenbisServiceFacade openBisFacade)
{
- File tempDir = new File(System.getProperty("java.io.tmpdir"));
- dataSetsDir = new File(tempDir, "openbis_datasets");
+ openbis = openBisFacade;
+ dataSetsDir = new File(tempDir, DATASETS_FOLDER);
if (dataSetsDir.isDirectory() == false && dataSetsDir.mkdirs() == false)
{
throw new RuntimeException("Couldn't create a data set directory.");
}
- temporarySessionDir = new File(tempDir, "openbis_" + System.currentTimeMillis() / 1000 + "_temp_dir");
+ temporarySessionDir = new File(tempDir, TEMP_DIR_PREFIX + System.currentTimeMillis() / 1000 + TEMP_DIR_POSTFIX);
if (temporarySessionDir.mkdirs() == false)
{
throw new RuntimeException("Couldn't create a temporary directory.");
@@ -260,8 +272,22 @@ public class OpenBISScreeningML
{
Login.OPENBIS_TOKEN_FILE.delete();
}
+ delete(temporarySessionDir);
openbis = null;
}
+
+ private static void delete(File file)
+ {
+ if (file.isDirectory())
+ {
+ File[] files = file.listFiles();
+ for (File child : files)
+ {
+ delete(child);
+ }
+ }
+ file.delete();
+ }
//
// Information methods
@@ -330,21 +356,7 @@ public class OpenBISScreeningML
public static Object[][] listPlates()
{
checkLoggedIn();
- final Object[][] result = new Object[plates.size()][9];
- for (int i = 0; i < plates.size(); ++i)
- {
- final Object[] annotations =
- new Object[]
- { plates.get(i).getAugmentedCode(), plates.get(i).getPermId(),
- plates.get(i).tryGetSpaceCode(), plates.get(i).getPlateCode(),
- plates.get(i).getExperimentIdentifier().getAugmentedCode(),
- plates.get(i).getExperimentIdentifier().getPermId(),
- plates.get(i).getExperimentIdentifier().getSpaceCode(),
- plates.get(i).getExperimentIdentifier().getProjectCode(),
- plates.get(i).getExperimentIdentifier().getExperimentCode(), };
- System.arraycopy(annotations, 0, result[i], 0, annotations.length);
- }
- return result;
+ return listPlates(plates);
}
/**
@@ -378,27 +390,110 @@ public class OpenBISScreeningML
{
throw new RuntimeException("No experiment with that code found.");
}
- final Object[][] result = new Object[experimentPlates.size()][9];
- for (int i = 0; i < experimentPlates.size(); ++i)
+ return listPlates(experimentPlates);
+ }
+
+ private static Object[][] listPlates(final List<Plate> list)
+ {
+ final Object[][] result = new Object[list.size()][9];
+ for (int i = 0; i < list.size(); ++i)
{
final Object[] annotations =
new Object[]
{
- experimentPlates.get(i).getAugmentedCode(),
+ list.get(i).getAugmentedCode(),
plates.get(i).getPermId(),
- experimentPlates.get(i).tryGetSpaceCode(),
+ list.get(i).tryGetSpaceCode(),
plates.get(i).getPlateCode(),
- experimentPlates.get(i).getExperimentIdentifier()
+ list.get(i).getExperimentIdentifier()
.getAugmentedCode(),
- experimentPlates.get(i).getExperimentIdentifier().getPermId(),
- experimentPlates.get(i).getExperimentIdentifier().getSpaceCode(),
- experimentPlates.get(i).getExperimentIdentifier().getProjectCode(),
- experimentPlates.get(i).getExperimentIdentifier()
+ list.get(i).getExperimentIdentifier().getPermId(),
+ list.get(i).getExperimentIdentifier().getSpaceCode(),
+ list.get(i).getExperimentIdentifier().getProjectCode(),
+ list.get(i).getExperimentIdentifier()
.getExperimentCode(), };
System.arraycopy(annotations, 0, result[i], 0, annotations.length);
}
return result;
}
+
+ /**
+ * Returns the properties of specified well for specified plate.
+ * <p>
+ * Matlab example:
+ *
+ * <pre>
+ * % Get properties for well A03 of plate P005 in space SPACE
+ * properties = OpenBISScreeningML.getWellProperties('/SPACE/P005', 1, 3, properties)
+ * % Get property type code of first property
+ * properties(1,1)
+ * % Get property value of first property
+ * properties(1,2)
+ * </pre>
+ *
+ * @param augmentedPlateCode The augmented plate code
+ * @param row The row in the plate to get the well properties for
+ * @param column The column in the plate to get the well properties for
+ * @return A two dimensional array where the first column contains the property
+ * codes and the second column the corresponding property values.
+ */
+ public static Object[][] getWellProperties(String augmentedPlateCode, int row,
+ int column)
+ {
+ checkLoggedIn();
+ WellPosition wellPosition = new WellPosition(row, column);
+ WellIdentifier wellIdentifier = getWell(augmentedPlateCode, wellPosition);
+ List<Map.Entry<String, String>> list =
+ new ArrayList<Map.Entry<String, String>>(openbis.getWellProperties(wellIdentifier)
+ .entrySet());
+ Object[][] result = new Object[list.size()][2];
+ for (int i = 0; i < list.size(); i++)
+ {
+ result[i] = new Object[] {list.get(i).getKey(), list.get(i).getValue()};
+ }
+ return result;
+ }
+
+ /**
+ * Updates properties of specified well for specified plate.
+ * <p>
+ * Matlab example:
+ *
+ * <pre>
+ * % Updates properties DESCRIPTION and NUMBER for well A03 of plate P005 in space SPACE
+ * properties = {'DESCRIPTION' 'hello example'; 'NUMBER' 3.14}
+ * OpenBISScreeningML.updateWellProperties('/SPACE/P005', 1, 3, properties)
+ * </pre>
+ *
+ * @param augmentedPlateCode The augmented plate code
+ * @param row The row in the plate to get the well properties for
+ * @param column The column in the plate to get the well properties for
+ * @param properties A two dimensional array where the first column contains the property
+ * codes and the second column the corresponding property values.
+ */
+ public static void updateWellProperties(String augmentedPlateCode, int row,
+ int column, Object[][] properties)
+ {
+ checkLoggedIn();
+ WellPosition wellPosition = new WellPosition(row, column);
+ WellIdentifier wellIdentifier = getWell(augmentedPlateCode, wellPosition);
+ openbis.updateWellProperties(wellIdentifier, createMap(properties));
+ }
+
+ private static WellIdentifier getWell(String augmentedPlateCode, WellPosition wellPosition)
+ {
+ Plate plate = getPlate(augmentedPlateCode);
+ List<WellIdentifier> wells = openbis.listPlateWells(plate);
+ for (WellIdentifier wellIdentifier : wells)
+ {
+ if (wellIdentifier.getWellPosition().equals(wellPosition))
+ {
+ return wellIdentifier;
+ }
+ }
+ throw new RuntimeException("Plate '" + augmentedPlateCode + "' has now well at "
+ + wellPosition + ".");
+ }
/**
* Lists all channels measured in <var>experiment</var>.
@@ -522,7 +617,7 @@ public class OpenBISScreeningML
*
* <pre>
* % Load all data sets of plate P005 in space SPACE
- * dsinfo = loadDataSets('/SPACE/P005')
+ * dsinfo = OpenBISScreeningML.loadDataSets('/SPACE/P005')
* % Get the data set codes
* dsinfo(:,1)
* % Get root path of first data set (assuming there is at least one)
@@ -545,12 +640,13 @@ public class OpenBISScreeningML
for (int i = 0; i < dataSets.size(); i++)
{
IDataSetDss dataSet = dataSets.get(i);
- File file = new File(dataSetsDir, dataSet.getCode());
+ String code = dataSet.getCode();
+ File file = new File(dataSetsDir, code);
if (file.exists() == false)
{
file = dataSet.getLinkOrCopyOfContents(null, dataSetsDir);
}
- result[i] = new Object[] {dataSet.getCode(), file.getPath()};
+ result[i] = new Object[] {code, file.getPath()};
}
return result;
} catch (Exception ex)
@@ -569,7 +665,7 @@ public class OpenBISScreeningML
* % Upload data set /path/to/my-data-set with properties DESCRIPTION and NUMBER for
* % plate P005 in space SPACE
* properties = {'DESCRIPTION' 'hello example'; 'NUMBER' 3.14}
- * datasetcode = uploadDataSet('/SPACE/P005', '/path/to/my-data-set', 'HCS_IMAGE', properties)
+ * datasetcode = OpenBISScreeningML.uploadDataSet('/SPACE/P005', '/path/to/my-data-set', 'HCS_IMAGE', properties)
* </pre>
*
* @param augmentedPlateCode The augmented plate code.
@@ -590,14 +686,7 @@ public class OpenBISScreeningML
}
try
{
- HashMap<String, String> map = new HashMap<String, String>();
- for (Object[] objects : dataSetProperties)
- {
- if (objects.length == 2)
- {
- map.put(objects[0].toString(), objects[1].toString());
- }
- }
+ Map<String, String> map = createMap(dataSetProperties);
IDataSetDss dataSet =
openbis.putDataSet(plateIdentifier, dataSetFile, new NewDataSetMetadataDTO(
dataSetType, map));
@@ -609,10 +698,20 @@ public class OpenBISScreeningML
}
}
- public static Object testProperties(Properties properties)
+ private static Map<String, String> createMap(Object[][] properties)
{
- return properties.toString();
+ Map<String, String> map = new HashMap<String, String>();
+ for (Object[] objects : properties)
+ {
+ if (objects.length == 2)
+ {
+ Object value = objects[1];
+ map.put(objects[0].toString(), value == null ? null : value.toString());
+ }
+ }
+ return map;
}
+
//
// Images
//
@@ -1502,12 +1601,12 @@ public class OpenBISScreeningML
final String serverUrl = br.readLine();
br.close();
br = null;
- openbis = ScreeningOpenbisServiceFacadeFactory.tryCreate(token, serverUrl);
- if (openbis == null)
+ IScreeningOpenbisServiceFacade facade = ScreeningOpenbisServiceFacadeFactory.tryCreate(token, serverUrl);
+ if (facade == null)
{
throw new RuntimeException("Login failed.");
}
- init();
+ init(facade);
} catch (IOException ex)
{
if (openbis == null)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
index 3337f157e649c43e7db31b290884c5cfe5ea0bb7..130c9cc4e28b9a20378b6115d24ff239bc961df6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.client.api.v1;
import java.io.File;
import java.io.IOException;
import java.util.List;
+import java.util.Map;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
@@ -149,6 +150,16 @@ public interface IScreeningOpenbisServiceFacade
* For the given <var>plateIdentifier</var> find all wells that are connected to it.
*/
public List<WellIdentifier> listPlateWells(PlateIdentifier plateIdentifier);
+
+ /**
+ * Returns all properties of specified well as a map.
+ */
+ public Map<String, String> getWellProperties(WellIdentifier wellIdentifier);
+
+ /**
+ * Updates properties of specified well.
+ */
+ public void updateWellProperties(WellIdentifier wellIdentifier, Map<String, String> properties);
/**
* Get proxies to the data sets owned by specified well.
@@ -555,5 +566,5 @@ public interface IScreeningOpenbisServiceFacade
public List<PlateWellMaterialMapping> listPlateMaterialMapping(
List<? extends PlateIdentifier> plates,
MaterialTypeIdentifier materialTypeIdentifierOrNull);
-
+
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
index de265892d2a30413c53a28a770a90d97fd332328..069dcc63bcad811cb3119ba62fe254b723d96ec6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
@@ -35,6 +35,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetO
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
@@ -92,6 +93,8 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
private final IScreeningApiServer openbisScreeningServer;
private final IGeneralInformationService generalInformationService;
+
+ private final IGeneralInformationChangingService generalInformationChangingService;
private final IDssComponent dssComponent;
@@ -126,18 +129,12 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
String serverUrl)
{
final IScreeningApiServer openbisServer = createScreeningOpenbisServer(serverUrl);
- final IGeneralInformationService generalInformationService =
- createGeneralInformationService(serverUrl);
- final int minorVersion = openbisServer.getMinorVersion();
final String sessionToken = openbisServer.tryLoginScreening(userId, userPassword);
if (sessionToken == null)
{
return null;
}
- final IDssComponent dssComponent =
- DssComponentFactory.tryCreate(sessionToken, serverUrl, SERVER_TIMEOUT_MILLIS);
- return new ScreeningOpenbisServiceFacade(sessionToken, openbisServer, minorVersion,
- DSS_SERVICE_FACTORY, dssComponent, generalInformationService);
+ return tryCreate(sessionToken, serverUrl, openbisServer);
}
/**
@@ -149,14 +146,22 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
*/
public static IScreeningOpenbisServiceFacade tryCreate(String sessionToken, String serverUrl)
{
- final IScreeningApiServer openbisServer = createScreeningOpenbisServer(serverUrl);
+ return tryCreate(sessionToken, serverUrl, createScreeningOpenbisServer(serverUrl));
+ }
+
+ private static IScreeningOpenbisServiceFacade tryCreate(String sessionToken, String serverUrl,
+ final IScreeningApiServer openbisServer)
+ {
final IGeneralInformationService generalInformationService =
createGeneralInformationService(serverUrl);
+ IGeneralInformationChangingService generalInformationChangingService =
+ createGeneralInformationChangingService(serverUrl);
final int minorVersion = openbisServer.getMinorVersion();
final IDssComponent dssComponent =
DssComponentFactory.tryCreate(sessionToken, serverUrl, SERVER_TIMEOUT_MILLIS);
return new ScreeningOpenbisServiceFacade(sessionToken, openbisServer, minorVersion,
- DSS_SERVICE_FACTORY, dssComponent, generalInformationService);
+ DSS_SERVICE_FACTORY, dssComponent, generalInformationService,
+ generalInformationChangingService);
}
private static IScreeningApiServer createScreeningOpenbisServer(String serverUrl)
@@ -175,12 +180,25 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
return service;
}
+ private static IGeneralInformationChangingService createGeneralInformationChangingService(
+ String serverUrl)
+ {
+ ServiceFinder generalInformationServiceFinder =
+ new ServiceFinder("openbis", IGeneralInformationChangingService.SERVICE_URL);
+ IGeneralInformationChangingService service =
+ generalInformationServiceFinder.createService(
+ IGeneralInformationChangingService.class, serverUrl);
+ return service;
+ }
+
ScreeningOpenbisServiceFacade(String sessionToken, IScreeningApiServer screeningServer,
int minorVersion, final IDssServiceFactory dssServiceFactory,
- IDssComponent dssComponent, IGeneralInformationService generalInformationService)
+ IDssComponent dssComponent, IGeneralInformationService generalInformationService,
+ IGeneralInformationChangingService generalInformationChangingService)
{
this.openbisScreeningServer = screeningServer;
this.generalInformationService = generalInformationService;
+ this.generalInformationChangingService = generalInformationChangingService;
this.dssComponent = dssComponent;
this.sessionToken = sessionToken;
this.minorVersionApplicationServer = minorVersion;
@@ -365,6 +383,19 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
checkASMinimalMinorVersion("listPlateWells", PlateIdentifier.class);
return openbisScreeningServer.listPlateWells(sessionToken, plateIdentifier);
}
+
+ public Map<String, String> getWellProperties(WellIdentifier wellIdentifier)
+ {
+ Sample wellSample = openbisScreeningServer.getWellSample(sessionToken, wellIdentifier);
+ Map<String, String> properties = wellSample.getProperties();
+ return properties;
+ }
+
+ public void updateWellProperties(WellIdentifier wellIdentifier, Map<String, String> properties)
+ {
+ Sample wellSample = openbisScreeningServer.getWellSample(sessionToken, wellIdentifier);
+ generalInformationChangingService.updateSampleProperties(sessionToken, wellSample.getId(), properties);
+ }
/**
* Get proxies to the data sets owned by specified well.
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 7213a26b21c9d4c7d967857bd5878a4e32cb3c31..1f22d54c6627caa73f43d2b424970be5c74572d8 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
@@ -375,7 +375,7 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
public Sample getWellSample(String sessionToken, WellIdentifier wellIdentifier)
{
- return createScreeningApiImpl(sessionToken).getWellSample(wellIdentifier);
+ return createScreeningApiImpl(sessionToken).getWellSample(wellIdentifier, true);
}
public Sample getPlateSample(String sessionToken, PlateIdentifier plateIdentifier)
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 63768caeeb1184935c53f62cf6901bed430b4063..8044637a04f1d3ad5117381415f269b64ceca88f 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
@@ -422,7 +422,7 @@ public class ScreeningApiImpl
Sample sample;
if (plateIdentifier.getPermId() != null)
{
- sample = loadSampleByPermId(plateIdentifier.getPermId());
+ sample = loadSampleByPermId(plateIdentifier.getPermId(), false);
} else
{
SampleIdentifier sampleIdentifier = createSampleIdentifier(plateIdentifier);
@@ -434,9 +434,9 @@ public class ScreeningApiImpl
}
public ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample getWellSample(
- WellIdentifier wellIdentifier)
+ WellIdentifier wellIdentifier, boolean enrichWithProperties)
{
- Sample sample = loadSampleByPermId(wellIdentifier.getPermId());
+ Sample sample = loadSampleByPermId(wellIdentifier.getPermId(), enrichWithProperties);
return Translator.translate(sample);
}
@@ -446,10 +446,14 @@ public class ScreeningApiImpl
return Translator.translate(getSample(plateIdentifier));
}
- private Sample loadSampleByPermId(String permId)
+ private Sample loadSampleByPermId(String permId, boolean enrichWithProperties)
{
ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
sampleBO.loadBySamplePermId(permId);
+ if (enrichWithProperties)
+ {
+ sampleBO.enrichWithProperties();
+ }
SamplePE samplePE = sampleBO.getSample();
return translate(samplePE);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
index 62b06910dc1bbb73e5f8382c92fab26762f21028..38f3ef90065d4700bd497d1dcd2059e6651c5a12 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
@@ -231,7 +231,7 @@ public interface IScreeningApiServer extends IRpcService
@AuthorizationGuard(guardClass = PlateIdentifierPredicate.class) PlateIdentifier plateIdentifier);
/**
- * For a given <var>wellIdentifier</var>, return the corresponding {@link Sample}.
+ * For a given <var>wellIdentifier</var>, return the corresponding {@link Sample} including properties.
*
* @since 1.3
*/
diff --git a/screening/sourceTest/java/OpenBISScreeningMLTest.java b/screening/sourceTest/java/OpenBISScreeningMLTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..4fa28e23817b3ceb99c359aaf599f61a7a682cd9
--- /dev/null
+++ b/screening/sourceTest/java/OpenBISScreeningMLTest.java
@@ -0,0 +1,532 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.hamcrest.BaseMatcher;
+import org.hamcrest.Description;
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.jmock.Sequence;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class OpenBISScreeningMLTest extends AbstractFileSystemTestCase
+{
+ private static final FilenameFilter FILTER_TEMP_DIR = new FilenameFilter()
+ {
+ public boolean accept(File dir, String name)
+ {
+ return name.startsWith(OpenBISScreeningML.TEMP_DIR_PREFIX)
+ && name.endsWith(OpenBISScreeningML.TEMP_DIR_POSTFIX);
+ }
+ };
+
+ private Mockery context;
+ private IScreeningOpenbisServiceFacade openbis;
+
+ private File tempDir;
+
+ private ExperimentIdentifier eId1;
+
+ private ExperimentIdentifier eId2;
+
+ private IDataSetDss ds1;
+
+ private IDataSetDss ds2;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ context = new Mockery();
+ openbis = context.mock(IScreeningOpenbisServiceFacade.class);
+ ds1 = context.mock(IDataSetDss.class, "ds1");
+ ds2 = context.mock(IDataSetDss.class, "ds2");
+ FileUtilities.deleteRecursively(workingDirectory);
+ workingDirectory.mkdirs();
+ OpenBISScreeningML.tempDir = workingDirectory;
+ eId1 = new ExperimentIdentifier("E1", "P", "S", "e-1");
+ eId2 = new ExperimentIdentifier("E2", "P", "S", "e-2");
+ context.checking(new Expectations()
+ {
+ {
+ one(openbis).listExperiments();
+ will(returnValue(Arrays.asList(eId1, eId2)));
+
+ one(openbis).listPlates();
+ Plate p1 = new Plate("PLATE-1", "S", "s-1", eId1);
+ Plate p2 = new Plate("PLATE-2", "S", "s-2", eId2);
+ will(returnValue(Arrays.asList(p1, p2)));
+ }
+ });
+ OpenBISScreeningML.init(openbis);
+ tempDir = OpenBISScreeningML.tempDir.listFiles(FILTER_TEMP_DIR)[0];
+ }
+
+ @AfterMethod
+ public void afterMethod()
+ {
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLogout()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(openbis).logout();
+ }
+ });
+ File a = new File(tempDir, "a");
+ a.mkdirs();
+ FileUtilities.writeToFile(new File(a, "1.txt"), "one");
+ FileUtilities.writeToFile(new File(tempDir, "2.txt"), "two");
+
+ OpenBISScreeningML.logout();
+
+ assertEquals(false, tempDir.exists());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testListExperiments()
+ {
+ Object[][] experiments = OpenBISScreeningML.listExperiments();
+
+ sort(experiments);
+ assertEquals("/S/P/E1", experiments[0][0]);
+ assertEquals("e-1", experiments[0][1]);
+ assertEquals("S", experiments[0][2]);
+ assertEquals("P", experiments[0][3]);
+ assertEquals("E1", experiments[0][4]);
+ assertEquals("/S/P/E2", experiments[1][0]);
+ assertEquals("e-2", experiments[1][1]);
+ assertEquals("S", experiments[1][2]);
+ assertEquals("P", experiments[1][3]);
+ assertEquals("E2", experiments[1][4]);
+ assertEquals(2, experiments.length);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testListPlates()
+ {
+ Object[][] plates = OpenBISScreeningML.listPlates();
+
+ sort(plates);
+ assertEquals("/S/PLATE-1", plates[0][0]);
+ assertEquals("s-1", plates[0][1]);
+ assertEquals("S", plates[0][2]);
+ assertEquals("PLATE-1", plates[0][3]);
+ assertEquals("/S/P/E1", plates[0][4]);
+ assertEquals("e-1", plates[0][5]);
+ assertEquals("S", plates[0][6]);
+ assertEquals("P", plates[0][7]);
+ assertEquals("E1", plates[0][8]);
+ assertEquals("/S/PLATE-2", plates[1][0]);
+ assertEquals("s-2", plates[1][1]);
+ assertEquals("S", plates[1][2]);
+ assertEquals("PLATE-2", plates[1][3]);
+ assertEquals("/S/P/E2", plates[1][4]);
+ assertEquals("e-2", plates[1][5]);
+ assertEquals("S", plates[1][6]);
+ assertEquals("P", plates[1][7]);
+ assertEquals("E2", plates[1][8]);
+ assertEquals(2, plates.length);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testListPlatesByExperiment()
+ {
+ try
+ {
+ OpenBISScreeningML.listPlates("/S/P/E3");
+ fail("RuntimeException expected");
+ } catch (RuntimeException ex)
+ {
+ assertEquals("No experiment with that code found.", ex.getMessage());
+ }
+
+ Object[][] plates = OpenBISScreeningML.listPlates("/S/P/E1");
+
+ sort(plates);
+ assertEquals("/S/PLATE-1", plates[0][0]);
+ assertEquals("s-1", plates[0][1]);
+ assertEquals("S", plates[0][2]);
+ assertEquals("PLATE-1", plates[0][3]);
+ assertEquals("/S/P/E1", plates[0][4]);
+ assertEquals("e-1", plates[0][5]);
+ assertEquals("S", plates[0][6]);
+ assertEquals("P", plates[0][7]);
+ assertEquals("E1", plates[0][8]);
+ assertEquals(1, plates.length);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testGetWellProperties()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ Plate plate1 = new Plate("PLATE-1", "S", "s-1", eId1);
+ one(openbis).listPlateWells(plate1);
+ WellIdentifier w1 = new WellIdentifier(plate1, new WellPosition(1, 1), "w1");
+ WellIdentifier w2 = new WellIdentifier(plate1, new WellPosition(1, 2), "w2");
+ WellIdentifier w3 = new WellIdentifier(plate1, new WellPosition(2, 1), "w3");
+ will(returnValue(Arrays.asList(w1, w2, w3)));
+
+ one(openbis).getWellProperties(w2);
+ Map<String, String> properties = new LinkedHashMap<String, String>();
+ properties.put("answer", "42");
+ properties.put("name", "Albert");
+ will(returnValue(properties));
+ }
+ });
+
+ Object[][] wellProperties = OpenBISScreeningML.getWellProperties("/S/PLATE-1", 1, 2);
+
+ assertEquals("answer", wellProperties[0][0]);
+ assertEquals("42", wellProperties[0][1]);
+ assertEquals("name", wellProperties[1][0]);
+ assertEquals("Albert", wellProperties[1][1]);
+ assertEquals(2, wellProperties.length);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testUpdateWellProperties()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ Plate plate1 = new Plate("PLATE-1", "S", "s-1", eId1);
+ one(openbis).listPlateWells(plate1);
+ WellIdentifier w1 = new WellIdentifier(plate1, new WellPosition(1, 1), "w1");
+ WellIdentifier w2 = new WellIdentifier(plate1, new WellPosition(1, 2), "w2");
+ WellIdentifier w3 = new WellIdentifier(plate1, new WellPosition(2, 1), "w3");
+ will(returnValue(Arrays.asList(w1, w2, w3)));
+
+ Map<String, String> properties = new LinkedHashMap<String, String>();
+ properties.put("A", "42");
+ properties.put("B", "43");
+ one(openbis).updateWellProperties(w2, properties);
+ }
+ });
+
+ OpenBISScreeningML.updateWellProperties("/S/PLATE-1", 1, 2, new Object[][] {{"A", "42"}, {"B", "43"}});
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoadDataSets()
+ {
+ final File dataSetFolder = new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
+ final File ds1Folder = new File(dataSetFolder, "ds-1");
+ File ds2Folder = new File(dataSetFolder, "ds-2");
+ ds2Folder.mkdirs();
+ context.checking(new Expectations()
+ {
+ {
+ one(openbis).getDataSets(new Plate("PLATE-1", "S", "s-1", eId1));
+ will(returnValue(Arrays.asList(ds1, ds2)));
+
+ one(ds1).getCode();
+ will(returnValue("ds-1"));
+
+ one(ds1).getLinkOrCopyOfContents(null, dataSetFolder);
+ will(returnValue(ds1Folder));
+
+ one(ds2).getCode();
+ will(returnValue("ds-2"));
+ }
+ });
+
+ Object[][] result = OpenBISScreeningML.loadDataSets("/S/PLATE-1");
+
+ assertEquals("ds-1", result[0][0]);
+ assertEquals(ds1Folder.getPath(), result[0][1]);
+ assertEquals("ds-2", result[1][0]);
+ assertEquals(ds2Folder.getPath(), result[1][1]);
+ assertEquals(2, result.length);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testUpdateDataSet()
+ {
+ final File dataSetFolder = new File(OpenBISScreeningML.tempDir, OpenBISScreeningML.DATASETS_FOLDER);
+ final File ds1Folder = new File(dataSetFolder, "ds-1");
+ ds1Folder.mkdirs();
+ final RecordingMatcher<NewDataSetMetadataDTO> metaDataMatcher = new RecordingMatcher<NewDataSetMetadataDTO>();
+ context.checking(new Expectations()
+ {
+ {
+ Map<String, String> properties = new LinkedHashMap<String, String>();
+ properties.put("A", "42");
+ properties.put("B", "43");
+ try
+ {
+ one(openbis).putDataSet(with(new Plate("PLATE-1", "S", "s-1", eId1)),
+ with(ds1Folder), with(metaDataMatcher));
+ will(returnValue(ds1));
+ } catch (Exception ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+
+ one(ds1).getCode();
+ will(returnValue("DS-1"));
+ }
+ });
+
+ Object code =
+ OpenBISScreeningML.uploadDataSet("/S/PLATE-1", ds1Folder.getPath(), "my-type",
+ new Object[][] {{"A", "42"}, {"B", "43"}});
+
+ assertEquals("DS-1", code);
+ assertEquals("my-type", metaDataMatcher.recordedObject().tryDataSetType());
+ assertEquals("{A=42, B=43}", metaDataMatcher.recordedObject().getProperties().toString());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoadImages()
+ {
+ final RecordingMatcher<List<PlateImageReference>> imgRefsMatcher1 =
+ new RecordingMatcher<List<PlateImageReference>>();
+ final RecordingMatcher<List<PlateImageReference>> imgRefsMatcher2 =
+ new RecordingMatcher<List<PlateImageReference>>();
+ final Sequence sequence = context.sequence("load");
+ context.checking(new Expectations()
+ {
+ {
+ Plate plate = new Plate("PLATE-1", "S", "s-1", eId1);
+ exactly(2).of(openbis).listRawImageDatasets(Arrays.asList(plate));
+ ImageDatasetReference ds1Ref =
+ new ImageDatasetReference("ds1", "", plate, eId1, null, null, null,
+ null);
+ List<ImageDatasetReference> imageRefs = Arrays.asList(ds1Ref);
+ will(returnValue(imageRefs));
+
+ exactly(2).of(openbis).listImageMetadata(imageRefs);
+ List<String> channelCodes = Arrays.asList("R", "G");
+ List<String> channelLabels = Arrays.asList("red", "green");
+ ImageDatasetMetadata metaData1 =
+ new ImageDatasetMetadata(ds1Ref, channelCodes, channelLabels, 1, 2,
+ 100, 60, 10, 6);
+ will(returnValue(Arrays.asList(metaData1)));
+
+ try
+ {
+ one(openbis).loadImages(with(imgRefsMatcher1),
+ with(new BaseMatcher<IImageOutputStreamProvider>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof IImageOutputStreamProvider)
+ {
+ IImageOutputStreamProvider provider =
+ (IImageOutputStreamProvider) item;
+ List<PlateImageReference> recordedObject =
+ imgRefsMatcher1.recordedObject();
+ for (PlateImageReference ref : recordedObject)
+ {
+ try
+ {
+ OutputStream outputStream =
+ provider.getOutputStream(ref);
+ new PrintWriter(outputStream, true)
+ .println(ref.toString() + " (1)");
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel
+ .wrapIfNecessary(ex);
+ }
+ }
+ return true;
+ }
+ return false;
+ }
+
+ public void describeTo(Description description)
+ {
+ }
+ }), with(false));
+ inSequence(sequence);
+ one(openbis).loadImages(with(imgRefsMatcher2),
+ with(new BaseMatcher<IImageOutputStreamProvider>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof IImageOutputStreamProvider)
+ {
+ IImageOutputStreamProvider provider =
+ (IImageOutputStreamProvider) item;
+ List<PlateImageReference> recordedObject =
+ imgRefsMatcher2.recordedObject();
+ for (PlateImageReference ref : recordedObject)
+ {
+ try
+ {
+ OutputStream outputStream =
+ provider.getOutputStream(ref);
+ new PrintWriter(outputStream, true)
+ .println(ref.toString() + " (2)");
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel
+ .wrapIfNecessary(ex);
+ }
+ }
+ return true;
+ }
+ return false;
+ }
+
+ public void describeTo(Description description)
+ {
+ }
+ }), with(false));
+ inSequence(sequence);
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+ });
+
+ Object[][][] result1 = OpenBISScreeningML.loadImages("/S/PLATE-1", 1, 2, 1, new String[] {"G"});
+ List<PlateImageReference> imgRefs1 = imgRefsMatcher1.recordedObject();
+ for (PlateImageReference plateImageReference : imgRefs1)
+ {
+ assertEquals("ds1", plateImageReference.getDatasetCode());
+ assertEquals(1, plateImageReference.getWellPosition().getWellRow());
+ assertEquals(2, plateImageReference.getWellPosition().getWellColumn());
+ }
+ assertEquals("G", imgRefs1.get(0).getChannel());
+ assertEquals(1, imgRefs1.get(0).getTile());
+ assertEquals(1, imgRefs1.size());
+ assertEquals(2, result1.length);
+ assertEquals("/images/img_PLATE-1_ds1_row1_col2_G_tile1.tiff", getImagePath(result1, 0));
+ assertEquals("Image for [dataset ds1, well [1, 2], channel G, tile 1] (1)", FileUtilities
+ .loadToString(new File(result1[0][0][0].toString())).trim());
+ assertEquals(1, result1[0].length);
+ assertEquals(
+ "[G, 1, PLATE-1:A2, /S/PLATE-1, s-1, S, PLATE-1, 1, 2, /S/P/E1, e-1, S, P, E1, ds1]",
+ Arrays.asList(result1[1][0]).toString());
+ assertEquals(1, result1[1].length);
+
+ Object[][][] result2 = OpenBISScreeningML.loadImages("/S/PLATE-1", 1, 2);
+ List<PlateImageReference> imgRefs2 = imgRefsMatcher2.recordedObject();
+ for (PlateImageReference plateImageReference : imgRefs2)
+ {
+ assertEquals("ds1", plateImageReference.getDatasetCode());
+ assertEquals(1, plateImageReference.getWellPosition().getWellRow());
+ assertEquals(2, plateImageReference.getWellPosition().getWellColumn());
+ }
+ assertEquals("R", imgRefs2.get(0).getChannel());
+ assertEquals(0, imgRefs2.get(0).getTile());
+ assertEquals("R", imgRefs2.get(1).getChannel());
+ assertEquals(1, imgRefs2.get(1).getTile());
+ assertEquals("G", imgRefs2.get(2).getChannel());
+ assertEquals(0, imgRefs2.get(2).getTile());
+ assertEquals(3, imgRefs2.size());
+
+ assertEquals(2, result2.length);
+ assertEquals("/images/img_PLATE-1_ds1_row1_col2_R_tile0.tiff", getImagePath(result2, 0));
+ assertEquals("Image for [dataset ds1, well [1, 2], channel R, tile 0] (2)", FileUtilities
+ .loadToString(new File(result2[0][0][0].toString())).trim());
+ assertEquals("/images/img_PLATE-1_ds1_row1_col2_R_tile1.tiff", getImagePath(result2, 1));
+ assertEquals("Image for [dataset ds1, well [1, 2], channel R, tile 1] (2)", FileUtilities
+ .loadToString(new File(result2[0][1][0].toString())).trim());
+ assertEquals("/images/img_PLATE-1_ds1_row1_col2_G_tile0.tiff", getImagePath(result2, 2));
+ assertEquals("Image for [dataset ds1, well [1, 2], channel G, tile 0] (2)", FileUtilities
+ .loadToString(new File(result2[0][2][0].toString())).trim());
+ assertEquals("/images/img_PLATE-1_ds1_row1_col2_G_tile1.tiff", getImagePath(result2, 3));
+ assertEquals("Image for [dataset ds1, well [1, 2], channel G, tile 1] (1)", FileUtilities
+ .loadToString(new File(result2[0][3][0].toString())).trim());
+ assertEquals(4, result2[0].length);
+ assertEquals(
+ "[R, 0, PLATE-1:A2, /S/PLATE-1, s-1, S, PLATE-1, 1, 2, /S/P/E1, e-1, S, P, E1, ds1]",
+ Arrays.asList(result2[1][0]).toString());
+ assertEquals(
+ "[R, 1, PLATE-1:A2, /S/PLATE-1, s-1, S, PLATE-1, 1, 2, /S/P/E1, e-1, S, P, E1, ds1]",
+ Arrays.asList(result2[1][1]).toString());
+ assertEquals(
+ "[G, 0, PLATE-1:A2, /S/PLATE-1, s-1, S, PLATE-1, 1, 2, /S/P/E1, e-1, S, P, E1, ds1]",
+ Arrays.asList(result2[1][2]).toString());
+ assertEquals(
+ "[G, 1, PLATE-1:A2, /S/PLATE-1, s-1, S, PLATE-1, 1, 2, /S/P/E1, e-1, S, P, E1, ds1]",
+ Arrays.asList(result2[1][3]).toString());
+ assertEquals(4, result2[1].length);
+ context.assertIsSatisfied();
+ }
+
+ private String getImagePath(Object[][][] result, int i)
+ {
+ return result[0][i][0].toString()
+ .substring(tempDir.getPath().length());
+ }
+
+ private void sort(Object[][] entities)
+ {
+ Arrays.sort(entities, new Comparator<Object[]>()
+ {
+ public int compare(Object[] o1, Object[] o2)
+ {
+ return o1[0].toString().compareTo(o2[0].toString());
+ }
+ });
+ }
+
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
index a734609c0dfe06c12605529e7ce1e293bff3f13c..e1f185bec004a07be15716e71206937ffec9b783 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
@@ -37,6 +37,7 @@ import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent;
import ch.systemsx.cisd.openbis.dss.screening.server.DssServiceRpcScreening;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
import ch.systemsx.cisd.openbis.plugin.screening.server.ScreeningServer;
@@ -118,12 +119,15 @@ public class ScreeningOpenbisServiceFacadeTest extends AssertJUnit
private IImageTransformerFactory transformerFactory;
+ private IGeneralInformationChangingService generalInformationChangingService;
+
@BeforeMethod
public void beforeMethod()
{
context = new Mockery();
screeningService = context.mock(IScreeningApiServer.class);
generalInformationService = context.mock(IGeneralInformationService.class);
+ generalInformationChangingService = context.mock(IGeneralInformationChangingService.class);
dssComponent = context.mock(IDssComponent.class);
dssServiceFactory = context.mock(IDssServiceFactory.class);
i1id = new ImageDatasetReference(DATA_SET1, URL1, null, null, null, null, null, null);
@@ -170,7 +174,7 @@ public class ScreeningOpenbisServiceFacadeTest extends AssertJUnit
facade =
new ScreeningOpenbisServiceFacade(SESSION_TOKEN, screeningService,
ScreeningServer.MINOR_VERSION, dssServiceFactory, dssComponent,
- generalInformationService);
+ generalInformationService, generalInformationChangingService);
}
@AfterMethod
diff --git a/screening/sourceTest/java/tests.xml b/screening/sourceTest/java/tests.xml
index f94a4e51e6a67b419f812d793786684c87708c5c..a51e0e7f7a657316b2e08f141241ca0a1daa6e52 100644
--- a/screening/sourceTest/java/tests.xml
+++ b/screening/sourceTest/java/tests.xml
@@ -9,5 +9,8 @@
<package name="ch.systemsx.cisd.openbis.plugin.screening.*" />
<package name="ch.systemsx.cisd.openbis.dss.*" />
</packages>
+ <classes>
+ <class name="OpenBISScreeningMLTest"/>
+ </classes>
</test>
</suite>
diff --git a/screening/sourceTest/java/tests_fast.xml b/screening/sourceTest/java/tests_fast.xml
index e85dda9499724b398faca07d2646e9de8d415df9..6a5f4e0060c4026b1c586020cf584722f2c42db2 100644
--- a/screening/sourceTest/java/tests_fast.xml
+++ b/screening/sourceTest/java/tests_fast.xml
@@ -11,6 +11,9 @@
<packages>
<package name="ch.systemsx.cisd.openbis.plugin.screening.*" />
<package name="ch.systemsx.cisd.openbis.dss.*" />
- </packages>
+ </packages>
+ <classes>
+ <class name="OpenBISScreeningMLTest"/>
+ </classes>
</test>
</suite>