diff --git a/rtd_phosphonetx/etc/service.properties b/rtd_phosphonetx/etc/service.properties
index b3ff87fa062ef46397721ad20baa563932d13039..5cb41163842ac67f1dacc71ce0ab41cd83621879 100644
--- a/rtd_phosphonetx/etc/service.properties
+++ b/rtd_phosphonetx/etc/service.properties
@@ -113,6 +113,16 @@ demo-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.D
# The property file. Its content will be passed as a parameter to the plugin.
demo-reporter.properties-file =
+# Comma separated names of processing plugins. Each plugin should have configuration properties prefixed with its name.
+processing-plugins = copy-data-sets
+
+# The configuration of the processing plugin is the same as the reporting plugins configuration.
+copy-data-sets.label = Data Set Copier
+copy-data-sets.dataset-types = UNKNOWN
+copy-data-sets.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopier
+#copy-data-sets.destination = /Volumes/share-1-\$/user/cisd/felmer/phosphonetx/
+copy-data-sets.destination = vesuvio:tmp/LMS-1267
+
data-set-validators = val1
val1.data-set-type = HCS_IMAGE_ANALYSIS_DATA
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataService.java
index 5eb5d23bb1eb17955d596338ba3f3f239d86acf6..3fd32b1a160d8c63a705f4730ab625fea03e96ef 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataService.java
@@ -16,26 +16,17 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
-import java.util.ArrayList;
import java.util.List;
-import javax.annotation.Resource;
-
-import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
-import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.GroupValidator;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Group;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
/**
* Imlementation of {@link IRawDataService}.
@@ -44,22 +35,17 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataService;
*/
public class RawDataService extends AbstractServer<IRawDataService> implements IRawDataService
{
- @Private static final String GROUP_CODE = "MS_DATA";
-
- @Private static final String RAW_DATA_SAMPLE_TYPE = "MS_INJECTION";
-
- @Resource(name = ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER)
- private ICommonServer commonServer;
+ private IRawDataServiceInternal service;
public RawDataService()
{
}
- public RawDataService(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
- ICommonServer commonServer)
+ public RawDataService(final ISessionManager<Session> sessionManager, final IDAOFactory daoFactory,
+ IRawDataServiceInternal service)
{
super(sessionManager, daoFactory);
- this.commonServer = commonServer;
+ this.service = service;
}
public IRawDataService createLogger(boolean invocationSuccessful, long elapsedTime)
@@ -70,34 +56,38 @@ public class RawDataService extends AbstractServer<IRawDataService> implements I
public List<Sample> listRawDataSamples(String sessionToken, String userID)
{
checkSession(sessionToken);
-
- PersonPE person = getDAOFactory().getPersonDAO().tryFindPersonByUserId(userID);
- if (person == null)
+ SessionContextDTO session = login(userID);
+ try
{
- throw new UserFailureException("Unknown user ID: " + userID);
- }
- ListSampleCriteria criteria = new ListSampleCriteria();
- SampleTypePE sampleTypePE =
- getDAOFactory().getSampleTypeDAO().tryFindSampleTypeByCode(RAW_DATA_SAMPLE_TYPE);
- criteria.setSampleType(SampleTypeTranslator.translate(sampleTypePE, null));
- criteria.setIncludeGroup(true);
- criteria.setGroupCode(GROUP_CODE);
- List<Sample> samples = commonServer.listSamples(sessionToken, criteria);
- List<Sample> filteredList = new ArrayList<Sample>();
- GroupValidator validator = new GroupValidator();
- for (Sample sample : samples)
+ return service.listRawDataSamples(session.getSessionToken());
+
+ } finally
{
- Sample parent = sample.getGeneratedFrom();
- if (parent != null)
- {
- Group group = parent.getGroup();
- if (group == null || validator.doValidation(person, group))
- {
- filteredList.add(sample);
- }
- }
+ service.logout(session.getSessionToken());
}
- return filteredList;
}
+ public void copyRawData(String sessionToken, String userID, long[] rawDataSampleIDs)
+ {
+ checkSession(sessionToken);
+ SessionContextDTO session = login(userID);
+ try
+ {
+ service.copyRawData(session.getSessionToken(), rawDataSampleIDs);
+ } finally
+ {
+ service.logout(session.getSessionToken());
+ }
+ }
+
+ private SessionContextDTO login(String userID)
+ {
+ SessionContextDTO session = service.tryToAuthenticate(userID, "dummy-password");
+ if (session == null)
+ {
+ throw new UserFailureException("Unknown user ID: " + userID);
+ }
+ return session;
+ }
+
}
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
new file mode 100644
index 0000000000000000000000000000000000000000..9480b1c67f0b53b01e35bd609665383efd16a5ed
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
@@ -0,0 +1,159 @@
+/*
+ * 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.plugin.phosphonetx.server;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.authentication.ISessionManager;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.IValidator;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validator.RawDataSampleValidator;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class RawDataServiceInternal extends AbstractServer<IRawDataServiceInternal> implements IRawDataServiceInternal
+{
+ @Private static final String COPY_PROCESSING_KEY = "copy-data-sets";
+
+ @Private static final String GROUP_CODE = "MS_DATA";
+
+ @Private static final String RAW_DATA_SAMPLE_TYPE = "MS_INJECTION";
+
+ private static final IValidator<Sample> RAW_DATA_SAMPLE_VALIDATOR = new RawDataSampleValidator();
+
+ private ICommonBusinessObjectFactory businessObjectFactory;
+
+ public RawDataServiceInternal()
+ {
+ }
+
+ public RawDataServiceInternal(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
+ ICommonBusinessObjectFactory businessObjectFactory)
+ {
+ super(sessionManager, daoFactory);
+ this.businessObjectFactory = businessObjectFactory;
+ }
+
+
+ public IRawDataServiceInternal createLogger(boolean invocationSuccessful, long elapsedTime)
+ {
+ return new RawDataServiceInternalLogger(getSessionManager(), invocationSuccessful, elapsedTime);
+ }
+
+ public List<Sample> listRawDataSamples(String sessionToken)
+ {
+ return loadAllRawDataSamples(getSession(sessionToken));
+ }
+
+ public void copyRawData(String sessionToken, long[] rawDataSampleIDs)
+ {
+ Session session = getSession(sessionToken);
+ PersonPE person = session.tryGetPerson();
+
+ List<Sample> samples = loadAllRawDataSamples(session);
+ Set<Long> sampleIDs = new HashSet<Long>();
+ for (Sample sample : samples)
+ {
+ if (RAW_DATA_SAMPLE_VALIDATOR.isValid(person, sample))
+ {
+ sampleIDs.add(sample.getId());
+ }
+ }
+
+ ISampleDAO sampleDAO = getDAOFactory().getSampleDAO();
+ IExternalDataDAO externalDataDAO = getDAOFactory().getExternalDataDAO();
+ List<String> dataSetCodes = new ArrayList<String>();
+ for (long id : rawDataSampleIDs)
+ {
+ if (sampleIDs.contains(id) == false)
+ {
+ throw new UserFailureException("Invalid or unauthorized access on sample with ID: "
+ + id);
+ }
+ SamplePE sample = sampleDAO.getByTechId(new TechId(id));
+ List<ExternalDataPE> dataSets = externalDataDAO.listExternalData(sample);
+ for (ExternalDataPE dataSet : dataSets)
+ {
+ dataSetCodes.add(dataSet.getCode());
+ }
+ }
+ String dataStoreServerCode = findDataStoreServer();
+ IExternalDataTable externalDataTable =
+ businessObjectFactory.createExternalDataTable(session);
+ externalDataTable.processDatasets(COPY_PROCESSING_KEY, dataStoreServerCode, dataSetCodes);
+ }
+
+ private List<Sample> loadAllRawDataSamples(Session session)
+ {
+ ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
+ ListSampleCriteria criteria = new ListSampleCriteria();
+ SampleTypePE sampleTypePE =
+ getDAOFactory().getSampleTypeDAO().tryFindSampleTypeByCode(RAW_DATA_SAMPLE_TYPE);
+ criteria.setSampleType(SampleTypeTranslator.translate(sampleTypePE, null));
+ criteria.setIncludeGroup(true);
+ criteria.setGroupCode(GROUP_CODE);
+ return sampleLister.list(new ListOrSearchSampleCriteria(criteria));
+ }
+
+ private String findDataStoreServer()
+ {
+ List<DataStorePE> dataStores = getDAOFactory().getDataStoreDAO().listDataStores();
+ for (DataStorePE dataStore : dataStores)
+ {
+ Set<DataStoreServicePE> services = dataStore.getServices();
+ for (DataStoreServicePE dataStoreService : services)
+ {
+ if (DataStoreServiceKind.PROCESSING.equals(dataStoreService.getKind())
+ && COPY_PROCESSING_KEY.equals(dataStoreService.getKey()))
+ {
+ return dataStore.getCode();
+ }
+ }
+ }
+ throw new EnvironmentFailureException("No data store processing service with key '"
+ + COPY_PROCESSING_KEY + "' found.");
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalLogger.java
new file mode 100644
index 0000000000000000000000000000000000000000..98fbf7a477259a4542975b59d461cbab124e98f2
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalLogger.java
@@ -0,0 +1,53 @@
+/*
+ * 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.plugin.phosphonetx.server;
+
+import java.util.List;
+
+import ch.systemsx.cisd.authentication.ISessionManager;
+import ch.systemsx.cisd.openbis.generic.server.AbstractServerLogger;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class RawDataServiceInternalLogger extends AbstractServerLogger implements IRawDataServiceInternal
+{
+
+ RawDataServiceInternalLogger(ISessionManager<Session> sessionManager,
+ boolean invocationSuccessful, long elapsedTime)
+ {
+ super(sessionManager, invocationSuccessful, elapsedTime);
+ }
+
+ public List<Sample> listRawDataSamples(String sessionToken)
+ {
+ logAccess(sessionToken, "list_raw_data_samples");
+ return null;
+ }
+
+ public void copyRawData(String sessionToken, long[] rawDataSampleIDs)
+ {
+ int numberOfDataSets = rawDataSampleIDs == null ? 0 : rawDataSampleIDs.length;
+ logAccess(sessionToken, "copy_raw_data", "NUMBER_OF_DATA_SETS(%s)", numberOfDataSets);
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceLogger.java
index 04a028cec3bfef5bbd71f5a6a2c5e8bfe998e81a..32d98dff7e08d92f3c549f3de83f87794d3589e0 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceLogger.java
@@ -29,7 +29,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataService;
*
* @author Franz-Josef Elmer
*/
-public class RawDataServiceLogger extends AbstractServerLogger implements IRawDataService
+class RawDataServiceLogger extends AbstractServerLogger implements IRawDataService
{
RawDataServiceLogger(ISessionManager<Session> sessionManager,
@@ -44,4 +44,11 @@ public class RawDataServiceLogger extends AbstractServerLogger implements IRawDa
return null;
}
+ public void copyRawData(String sessionToken, String userID, long[] rawDataSampleIDs)
+ {
+ int numberOfDataSets = rawDataSampleIDs == null ? 0 : rawDataSampleIDs.length;
+ logAccess(sessionToken, "copy_raw_data", "USER_ID(%s) NUMBER_OF_DATA_SETS(%s)", userID,
+ numberOfDataSets);
+ }
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataService.java
index df2cc2540db8fa4dadf5427090b556e6e61a3dcb..542e60a5b70c42a76f6b2a90f95832a312073afe 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataService.java
@@ -33,10 +33,14 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
public interface IRawDataService extends IServer
{
/**
- * Returns all samples of type MS_INJECTION in group MS_DATA which have a parent sample the
- * specified user is allow to read.
+ * Returns all samples of type MS_INJECTION in group MS_DATA which have a parent sample which
+ * the specified user is allow to read.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.INSTANCE_ADMIN_OBSERVER)
public List<Sample> listRawDataSamples(String sessionToken, String userID);
+
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN_OBSERVER)
+ public void copyRawData(String sessionToken, String userID, long[] rawDataSampleIDs);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataServiceInternal.java
new file mode 100644
index 0000000000000000000000000000000000000000..f0b3483c468d880bcf06393f08ba2fcf71361d55
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataServiceInternal.java
@@ -0,0 +1,49 @@
+/*
+ * 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.plugin.phosphonetx.shared;
+
+import java.util.List;
+
+import org.springframework.transaction.annotation.Transactional;
+
+import ch.systemsx.cisd.openbis.generic.shared.IServer;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.ReturnValueFilter;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validator.RawDataSampleValidator;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IRawDataServiceInternal extends IServer
+{
+ /**
+ * Returns all samples of type MS_INJECTION in group MS_DATA which have a parent sample which
+ * the specified user is allow to read.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.USER)
+ @ReturnValueFilter(validatorClass = RawDataSampleValidator.class)
+ public List<Sample> listRawDataSamples(String sessionToken);
+
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.USER)
+ public void copyRawData(String sessionToken, long[] rawDataSampleIDs);
+}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidator.java
new file mode 100644
index 0000000000000000000000000000000000000000..6918f0fac9eae54c68011dabe5eeff424f89ac28
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidator.java
@@ -0,0 +1,31 @@
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validator;
+
+import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.GroupValidator;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.IValidator;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Group;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public final class RawDataSampleValidator implements IValidator<Sample>
+{
+ private IValidator<Group> validator = new GroupValidator();
+
+ public boolean isValid(PersonPE person, Sample sample)
+ {
+ Sample parent = sample.getGeneratedFrom();
+ if (parent != null)
+ {
+ Group group = parent.getGroup();
+ if (group == null || validator.isValid(person, group))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
index 75d1796c11a7069e0b1b1b0ce05ae161b8aa5dcb..49fe1a591d1ed9507d5d83d34a29244040d303ab 100644
--- a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
+++ b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
@@ -41,7 +41,7 @@
</bean>
<!--
- // Raw Data Server with interceptors for translating results
+ // Raw Data Server
-->
<bean id="phosphonetx-raw-data-service" class="org.springframework.aop.framework.ProxyFactoryBean">
@@ -54,7 +54,7 @@
<bean class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataService">
<constructor-arg ref="session-manager" />
<constructor-arg ref="dao-factory" />
- <constructor-arg ref="common-server" />
+ <constructor-arg ref="phosphonetx-raw-data-service-internal" />
</bean>
</property>
<property name="interceptorNames">
@@ -64,4 +64,28 @@
</property>
</bean>
+ <bean id="phosphonetx-raw-data-service-internal"
+ class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataServiceInternal">
+ <constructor-arg>
+ <bean class="ch.systemsx.cisd.authentication.DefaultSessionManager">
+ <constructor-arg>
+ <bean class="ch.systemsx.cisd.openbis.generic.server.SessionFactory" />
+ </constructor-arg>
+ <constructor-arg>
+ <bean class="ch.systemsx.cisd.openbis.generic.server.LogMessagePrefixGenerator" />
+ </constructor-arg>
+ <constructor-arg ref="dummy-authentication-service" />
+ <constructor-arg>
+ <bean class="ch.systemsx.cisd.common.servlet.RequestContextProviderAdapter">
+ <constructor-arg ref="request-context-provider" />
+ </bean>
+ </constructor-arg>
+ <constructor-arg value="${session-timeout}" />
+ </bean>
+ </constructor-arg>
+ <constructor-arg ref="dao-factory"/>
+ <constructor-arg ref="common-business-object-factory" />
+ </bean>
+
+
</beans>
\ No newline at end of file
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java
index b96531f519a29f7277bca526c3897deec7089d6b..de9cb66793ad26ddd3e5cb252aff36c832e17d6c 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx;
import java.util.List;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
@@ -37,17 +38,35 @@ public class RawDataTestClient
{
IRawDataService service = HttpInvokerUtils.createServiceStub(IRawDataService.class, SERVICE_PATH, 5);
- SessionContextDTO session = service.tryToAuthenticate("test_b", "t");
for (String user : new String[] {"test", "test_a", "test_b", "test_c"})
{
- List<Sample> samples = service.listRawDataSamples(session.getSessionToken(), user);
- System.out.println("User: " + user);
- for (Sample sample : samples)
+ try
+ {
+ System.out.println("User: " + user);
+ SessionContextDTO session = service.tryToAuthenticate("test_b", "t");
+ String sessionToken = session.getSessionToken();
+ List<Sample> samples = service.listRawDataSamples(sessionToken, user);
+ for (Sample sample : samples)
+ {
+ System.out.println(" " + sample.getCode()+" -> "+sample.getGeneratedFrom().getIdentifier());
+ }
+ } catch (UserFailureException ex)
{
- System.out.println(" " + sample.getCode()+" -> "+sample.getGeneratedFrom().getIdentifier());
+ System.out.println(" Exception: " + ex);
}
}
-
+ System.out.println("--------------------");
+ SessionContextDTO session = service.tryToAuthenticate("test_b", "t");
+ String sessionToken = session.getSessionToken();
+
+ List<Sample> samples = service.listRawDataSamples(sessionToken, "test_a");
+ long[] ids = new long[samples.size()];
+ for (int i = 0; i < samples.size(); i++)
+ {
+ Sample sample = samples.get(i);
+ ids[i] = sample.getId();
+ }
+ service.copyRawData(sessionToken, "test_a", ids);
}
}
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
new file mode 100644
index 0000000000000000000000000000000000000000..866bfec3698d73568aa435d204cbc646341b3922
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
@@ -0,0 +1,204 @@
+/*
+ * 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.plugin.phosphonetx.server;
+
+import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind.PROCESSING;
+import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind.QUERIES;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataServiceInternal.COPY_PROCESSING_KEY;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataServiceInternal.GROUP_CODE;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataServiceInternal.RAW_DATA_SAMPLE_TYPE;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedHashSet;
+import java.util.List;
+
+import org.hamcrest.BaseMatcher;
+import org.hamcrest.Description;
+import org.jmock.Expectations;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
+import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@Friend(toClasses=RawDataServiceInternal.class)
+public class RawDataServiceInternalTest extends AbstractServerTestCase
+{
+ private IRawDataServiceInternal service;
+ private ICommonBusinessObjectFactory boFactory;
+ private ISampleLister sampleLister;
+
+ @Override
+ @BeforeMethod
+ public final void setUp()
+ {
+ super.setUp();
+ boFactory = context.mock(ICommonBusinessObjectFactory.class);
+ sampleLister = context.mock(ISampleLister.class);
+ service = new RawDataServiceInternal(sessionManager, daoFactory, boFactory);
+ }
+
+ @Test
+ public void testListRawDataSamples()
+ {
+ prepareGetSession();
+ prepareListRawDataSamples(42L);
+
+ List<Sample> samples = service.listRawDataSamples(SESSION_TOKEN);
+
+ assertEquals(42L, samples.get(0).getId().longValue());
+ assertEquals(1, samples.size());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testCopyRawData()
+ {
+ prepareGetSession();
+ prepareListRawDataSamples(1L, 2L, 3L, 42L);
+ final long[] ids = new long[] {2, 3};
+ context.checking(new Expectations()
+ {
+ {
+ for (long id : ids)
+ {
+ one(sampleDAO).getByTechId(new TechId(id));
+ SamplePE sample = new SamplePE();
+ sample.setId(id);
+ sample.setCode("s" + id);
+ will(returnValue(sample));
+
+ one(externalDataDAO).listExternalData(sample);
+ List<ExternalDataPE> dataSets = new ArrayList<ExternalDataPE>();
+ for (int i = 0; i < (int) (id % 3); i++)
+ {
+ ExternalDataPE dataSet = new ExternalDataPE();
+ dataSet.setCode("ds" + id + "." + i);
+ dataSets.add(dataSet);
+ }
+ will(returnValue(dataSets ));
+ }
+
+ one(dataStoreDAO).listDataStores();
+ DataStorePE s1 = store("s1", service("a", PROCESSING), service(COPY_PROCESSING_KEY, QUERIES));
+ DataStorePE s2 = store("s2", service(COPY_PROCESSING_KEY, PROCESSING));
+ will(returnValue(Arrays.asList(s1, s2)));
+
+ one(boFactory).createExternalDataTable(SESSION);
+ will(returnValue(externalDataTable));
+
+ List<String> dataSetCodes = Arrays.asList("ds2.0", "ds2.1");
+ one(externalDataTable).processDatasets(COPY_PROCESSING_KEY, "s2", dataSetCodes);
+ }
+
+ });
+
+ service.copyRawData(SESSION_TOKEN, ids);
+
+ context.assertIsSatisfied();
+ }
+
+ private void prepareListRawDataSamples(final Long... sampleIDs)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(boFactory).createSampleLister(SESSION);
+ will(returnValue(sampleLister));
+
+ one(sampleTypeDAO).tryFindSampleTypeByCode(RAW_DATA_SAMPLE_TYPE);
+ final SampleTypePE sampleType = new SampleTypePE();
+ sampleType.setCode(RAW_DATA_SAMPLE_TYPE);
+ sampleType.setId(20100104l);
+ sampleType.setListable(Boolean.TRUE);
+ sampleType.setAutoGeneratedCode(Boolean.FALSE);
+ sampleType.setGeneratedFromHierarchyDepth(0);
+ sampleType.setContainerHierarchyDepth(0);
+ will(returnValue(sampleType));
+
+ one(sampleLister).list(with(new BaseMatcher<ListOrSearchSampleCriteria>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof ListOrSearchSampleCriteria)
+ {
+ ListOrSearchSampleCriteria criteria =
+ (ListOrSearchSampleCriteria) item;
+ assertEquals(GROUP_CODE, criteria.getGroupCode());
+ assertEquals(true, criteria.isIncludeGroup());
+ SampleType type = criteria.getSampleType();
+ assertEquals(RAW_DATA_SAMPLE_TYPE, type.getCode());
+ assertEquals(sampleType.getId(), type.getId());
+ return true;
+ }
+ return false;
+ }
+
+ public void describeTo(Description description)
+ {
+ description.appendValue(sampleType);
+ }
+ }));
+ List<Sample> samples = new ArrayList<Sample>();
+ for (Long id : sampleIDs)
+ {
+ Sample sample = new Sample();
+ sample.setId(id);
+ Sample parent = new Sample();
+ sample.setGeneratedFrom(parent);
+ samples.add(sample);
+ }
+ will(returnValue(samples));
+ }
+ });
+ }
+
+ private DataStorePE store(String code, DataStoreServicePE... services)
+ {
+ DataStorePE store = new DataStorePE();
+ store.setCode(code);
+ store.setServices(new LinkedHashSet<DataStoreServicePE>(Arrays.asList(services)));
+ return store;
+ }
+
+ private DataStoreServicePE service(String key, DataStoreServiceKind kind)
+ {
+ DataStoreServicePE dataStoreService = new DataStoreServicePE();
+ dataStoreService.setKey(key);
+ dataStoreService.setKind(kind);
+ return dataStoreService;
+ }
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java
deleted file mode 100644
index 13951e4662c793eded77b0e22d9f86a9d8bef76e..0000000000000000000000000000000000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java
+++ /dev/null
@@ -1,289 +0,0 @@
-/*
- * 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.plugin.phosphonetx.server;
-
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataService.GROUP_CODE;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataService.RAW_DATA_SAMPLE_TYPE;
-
-import java.util.Arrays;
-import java.util.LinkedHashSet;
-import java.util.List;
-
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
-import org.jmock.Expectations;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
-import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Group;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses=RawDataService.class)
-public class RawDataServiceTest extends AbstractServerTestCase
-{
- private static final String USER_ID = "a-user";
- private static final Sample NO_PARENT = create("no-parent", null);
- private static final Sample WITH_INSTANCE_PARENT = create("with-instance-parent", "t:/parent");
- private static final Sample WITH_PARENT_IN_G1 = create("with-parent-in-g1", "t:/g1/parent");
- private static final Sample WITH_PARENT_IN_G2 = create("with-parent-in-g2", "t:/g2/parent");
-
- private static Sample create(String sampleCode, String parentSampleIdentifierOrNull)
- {
- Sample sample = new Sample();
- sample.setCode(sampleCode);
- if (parentSampleIdentifierOrNull != null)
- {
- Sample parent = new Sample();
- parent.setIdentifier(parentSampleIdentifierOrNull);
- SampleIdentifier identifier = SampleIdentifierFactory.parse(parentSampleIdentifierOrNull);
- parent.setCode(identifier.getSampleCode());
- GroupIdentifier groupLevel = identifier.getGroupLevel();
- if (groupLevel != null)
- {
- Group group = new Group();
- group.setCode(groupLevel.getGroupCode());
- group.setInstance(createDatabaseInstance(groupLevel.getDatabaseInstanceCode()));
- parent.setGroup(group);
- }
- DatabaseInstanceIdentifier databaseInstanceLevel = identifier.getDatabaseInstanceLevel();
- if (databaseInstanceLevel != null)
- {
- String code = databaseInstanceLevel.getDatabaseInstanceCode();
- DatabaseInstance databaseInstance = createDatabaseInstance(code);
- parent.setDatabaseInstance(databaseInstance);
- }
- sample.setGeneratedFrom(parent);
- }
- return sample;
- }
-
- private static DatabaseInstance createDatabaseInstance(String code)
- {
- DatabaseInstance databaseInstance = new DatabaseInstance();
- databaseInstance.setCode(code);
- databaseInstance.setUuid(code);
- return databaseInstance;
- }
-
- private ICommonServer commonServer;
- private RawDataService rawDataService;
-
- @Override
- @BeforeMethod
- public final void setUp()
- {
- super.setUp();
- commonServer = context.mock(ICommonServer.class);
- rawDataService = new RawDataService(sessionManager, daoFactory, commonServer);
- }
-
- @Test
- public void testListRawDataSamplesForUnknownUser()
- {
- prepareGetSession();
- context.checking(new Expectations()
- {
- {
- one(personDAO).tryFindPersonByUserId(USER_ID);
- }
- });
-
- try
- {
- rawDataService.listRawDataSamples(SESSION_TOKEN, USER_ID);
- fail("UserFailureException expected.");
- } catch (UserFailureException ex)
- {
- assertEquals("Unknown user ID: " + USER_ID, ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListRawDataSamplesForUserWithNoRoles()
- {
- prepareGetSession();
- prepareListRawDataSamples();
-
- List<Sample> samples = rawDataService.listRawDataSamples(SESSION_TOKEN, USER_ID);
-
- assertSame(WITH_INSTANCE_PARENT, samples.get(0));
- assertEquals(1, samples.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListRawDataSamplesForUserWithRightsForGroupG1()
- {
- prepareGetSession();
- prepareListRawDataSamples(createRole("G1", "T"));
-
- List<Sample> samples = rawDataService.listRawDataSamples(SESSION_TOKEN, USER_ID);
-
- assertSame(WITH_INSTANCE_PARENT, samples.get(0));
- assertSame(WITH_PARENT_IN_G1, samples.get(1));
- assertEquals(2, samples.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListRawDataSamplesForUserWithRightsForGroupG1AndG2()
- {
- prepareGetSession();
- prepareListRawDataSamples(createRole("G1", "T"), createRole("G2", "T"));
-
- List<Sample> samples = rawDataService.listRawDataSamples(SESSION_TOKEN, USER_ID);
-
- assertSame(WITH_INSTANCE_PARENT, samples.get(0));
- assertSame(WITH_PARENT_IN_G1, samples.get(1));
- assertSame(WITH_PARENT_IN_G2, samples.get(2));
- assertEquals(3, samples.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListRawDataSamplesForUserWithRightsForGroupG1ButWrongInstance()
- {
- prepareGetSession();
- prepareListRawDataSamples(createRole("G1", "X"));
-
- List<Sample> samples = rawDataService.listRawDataSamples(SESSION_TOKEN, USER_ID);
-
- assertSame(WITH_INSTANCE_PARENT, samples.get(0));
- assertEquals(1, samples.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListRawDataSamplesForUserWithRightsForInstanceT()
- {
- prepareGetSession();
- prepareListRawDataSamples(createRole(null, "T"));
-
- List<Sample> samples = rawDataService.listRawDataSamples(SESSION_TOKEN, USER_ID);
-
- assertSame(WITH_INSTANCE_PARENT, samples.get(0));
- assertSame(WITH_PARENT_IN_G1, samples.get(1));
- assertSame(WITH_PARENT_IN_G2, samples.get(2));
- assertEquals(3, samples.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testListRawDataSamplesForUserWithRightsForInstanceX()
- {
- prepareGetSession();
- prepareListRawDataSamples(createRole(null, "X"));
-
- List<Sample> samples = rawDataService.listRawDataSamples(SESSION_TOKEN, USER_ID);
-
- assertSame(WITH_INSTANCE_PARENT, samples.get(0));
- assertEquals(1, samples.size());
- context.assertIsSatisfied();
- }
-
- private void prepareListRawDataSamples(final RoleAssignmentPE... roles)
- {
- context.checking(new Expectations()
- {
- {
- one(personDAO).tryFindPersonByUserId(USER_ID);
- PersonPE person = new PersonPE();
- person.setRoleAssignments(new LinkedHashSet<RoleAssignmentPE>(Arrays.asList(roles)));
- will(returnValue(person));
-
- one(sampleTypeDAO).tryFindSampleTypeByCode(RAW_DATA_SAMPLE_TYPE);
- final SampleTypePE sampleType = new SampleTypePE();
- sampleType.setCode(RAW_DATA_SAMPLE_TYPE);
- sampleType.setId(20100104l);
- sampleType.setListable(Boolean.TRUE);
- sampleType.setAutoGeneratedCode(Boolean.FALSE);
- sampleType.setGeneratedFromHierarchyDepth(0);
- sampleType.setContainerHierarchyDepth(0);
- will(returnValue(sampleType));
-
- one(commonServer).listSamples(with(SESSION_TOKEN),
- with(new BaseMatcher<ListSampleCriteria>()
- {
- public boolean matches(Object item)
- {
- if (item instanceof ListSampleCriteria)
- {
- ListSampleCriteria criteria = (ListSampleCriteria) item;
- assertEquals(GROUP_CODE, criteria.getGroupCode());
- assertEquals(true, criteria.isIncludeGroup());
- SampleType type = criteria.getSampleType();
- assertEquals(RAW_DATA_SAMPLE_TYPE, type.getCode());
- assertEquals(sampleType.getId(), type.getId());
- return true;
- }
- return false;
- }
-
- public void describeTo(Description description)
- {
- description.appendValue(sampleType);
- }
- }));
- will(returnValue(Arrays.asList(NO_PARENT, WITH_INSTANCE_PARENT,
- WITH_PARENT_IN_G1, WITH_PARENT_IN_G2)));
- }
- });
- }
-
- private RoleAssignmentPE createRole(String groupCodeOrNull, String dataBaseInstanceUUID)
- {
- RoleAssignmentPE role = new RoleAssignmentPE();
- if (groupCodeOrNull == null)
- {
- DatabaseInstancePE databaseInstance = new DatabaseInstancePE();
- databaseInstance.setUuid(dataBaseInstanceUUID);
- role.setDatabaseInstance(databaseInstance);
- } else
- {
- GroupPE group = new GroupPE();
- group.setCode(groupCodeOrNull);
- DatabaseInstancePE databaseInstance = new DatabaseInstancePE();
- databaseInstance.setUuid(dataBaseInstanceUUID);
- group.setDatabaseInstance(databaseInstance);
- role.setGroup(group);
- }
- return role;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidatorTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidatorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..9cc8266ec6f93a8a031f5ff5efc059c13b9c64d3
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidatorTest.java
@@ -0,0 +1,181 @@
+/*
+ * 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.plugin.phosphonetx.shared.authorization.validator;
+
+import java.util.Arrays;
+import java.util.LinkedHashSet;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Group;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class RawDataSampleValidatorTest extends AssertJUnit
+{
+ private static final Sample NO_PARENT = create("no-parent", null);
+ private static final Sample WITH_INSTANCE_PARENT = create("with-instance-parent", "t:/parent");
+ private static final Sample WITH_PARENT_IN_G1 = create("with-parent-in-g1", "t:/g1/parent");
+ private static final Sample WITH_PARENT_IN_G2 = create("with-parent-in-g2", "t:/g2/parent");
+
+ private RawDataSampleValidator validator = new RawDataSampleValidator();
+
+ private static Sample create(String sampleCode, String parentSampleIdentifierOrNull)
+ {
+ Sample sample = new Sample();
+ sample.setCode(sampleCode);
+ if (parentSampleIdentifierOrNull != null)
+ {
+ Sample parent = new Sample();
+ parent.setIdentifier(parentSampleIdentifierOrNull);
+ SampleIdentifier identifier = SampleIdentifierFactory.parse(parentSampleIdentifierOrNull);
+ parent.setCode(identifier.getSampleCode());
+ GroupIdentifier groupLevel = identifier.getGroupLevel();
+ if (groupLevel != null)
+ {
+ Group group = new Group();
+ group.setCode(groupLevel.getGroupCode());
+ group.setInstance(createDatabaseInstance(groupLevel.getDatabaseInstanceCode()));
+ parent.setGroup(group);
+ }
+ DatabaseInstanceIdentifier databaseInstanceLevel = identifier.getDatabaseInstanceLevel();
+ if (databaseInstanceLevel != null)
+ {
+ String code = databaseInstanceLevel.getDatabaseInstanceCode();
+ DatabaseInstance databaseInstance = createDatabaseInstance(code);
+ parent.setDatabaseInstance(databaseInstance);
+ }
+ sample.setGeneratedFrom(parent);
+ }
+ return sample;
+ }
+
+ private static DatabaseInstance createDatabaseInstance(String code)
+ {
+ DatabaseInstance databaseInstance = new DatabaseInstance();
+ databaseInstance.setCode(code);
+ databaseInstance.setUuid(code);
+ return databaseInstance;
+ }
+
+ @Test
+ public void testUserWithNoRights()
+ {
+ PersonPE person = createPersonWithRoles();
+
+ assertEquals(false, validator.isValid(person, NO_PARENT));
+ assertEquals(true, validator.isValid(person, WITH_INSTANCE_PARENT));
+ assertEquals(false, validator.isValid(person, WITH_PARENT_IN_G1));
+ assertEquals(false, validator.isValid(person, WITH_PARENT_IN_G2));
+ }
+
+ @Test
+ public void testUserWithRightsForGroupG1()
+ {
+ PersonPE person = createPersonWithRoles(createRole("G1", "T"));
+
+ assertEquals(false, validator.isValid(person, NO_PARENT));
+ assertEquals(true, validator.isValid(person, WITH_INSTANCE_PARENT));
+ assertEquals(true, validator.isValid(person, WITH_PARENT_IN_G1));
+ assertEquals(false, validator.isValid(person, WITH_PARENT_IN_G2));
+ }
+
+ @Test
+ public void testUserWithRightsForGroupG1AndG2()
+ {
+ PersonPE person = createPersonWithRoles(createRole("G1", "T"), createRole("G2", "T"));
+
+ assertEquals(false, validator.isValid(person, NO_PARENT));
+ assertEquals(true, validator.isValid(person, WITH_INSTANCE_PARENT));
+ assertEquals(true, validator.isValid(person, WITH_PARENT_IN_G1));
+ assertEquals(true, validator.isValid(person, WITH_PARENT_IN_G2));
+ }
+
+ @Test
+ public void testUserWithRightsForGroupG1ButWrongInstance()
+ {
+ PersonPE person = createPersonWithRoles(createRole("G1", "X"));
+
+ assertEquals(false, validator.isValid(person, NO_PARENT));
+ assertEquals(true, validator.isValid(person, WITH_INSTANCE_PARENT));
+ assertEquals(false, validator.isValid(person, WITH_PARENT_IN_G1));
+ assertEquals(false, validator.isValid(person, WITH_PARENT_IN_G2));
+ }
+
+ @Test
+ public void testUserWithRightsForForInstanceT()
+ {
+ PersonPE person = createPersonWithRoles(createRole(null, "T"));
+
+ assertEquals(false, validator.isValid(person, NO_PARENT));
+ assertEquals(true, validator.isValid(person, WITH_INSTANCE_PARENT));
+ assertEquals(true, validator.isValid(person, WITH_PARENT_IN_G1));
+ assertEquals(true, validator.isValid(person, WITH_PARENT_IN_G2));
+ }
+
+ @Test
+ public void testUserWithRightsForForInstanceX()
+ {
+ PersonPE person = createPersonWithRoles(createRole(null, "X"));
+
+ assertEquals(false, validator.isValid(person, NO_PARENT));
+ assertEquals(true, validator.isValid(person, WITH_INSTANCE_PARENT));
+ assertEquals(false, validator.isValid(person, WITH_PARENT_IN_G1));
+ assertEquals(false, validator.isValid(person, WITH_PARENT_IN_G2));
+ }
+
+ private PersonPE createPersonWithRoles(RoleAssignmentPE... roles)
+ {
+ PersonPE person = new PersonPE();
+ person.setRoleAssignments(new LinkedHashSet<RoleAssignmentPE>(Arrays.asList(roles)));
+ return person;
+ }
+
+ private RoleAssignmentPE createRole(String groupCodeOrNull, String dataBaseInstanceUUID)
+ {
+ RoleAssignmentPE role = new RoleAssignmentPE();
+ if (groupCodeOrNull == null)
+ {
+ DatabaseInstancePE databaseInstance = new DatabaseInstancePE();
+ databaseInstance.setUuid(dataBaseInstanceUUID);
+ role.setDatabaseInstance(databaseInstance);
+ } else
+ {
+ GroupPE group = new GroupPE();
+ group.setCode(groupCodeOrNull);
+ DatabaseInstancePE databaseInstance = new DatabaseInstancePE();
+ databaseInstance.setUuid(dataBaseInstanceUUID);
+ group.setDatabaseInstance(databaseInstance);
+ role.setGroup(group);
+ }
+ return role;
+ }
+}