From a78570d135415f1b601895d3aaff2466a6409be3 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 23 Nov 2010 16:25:14 +0000
Subject: [PATCH] SE-316 extend API with new method and deprecate old ones.
SVN: 18888
---
.../api/v1/IProteomicsDataApiFacade.java | 20 ++++++-
.../api/v1/ProteomicsDataApiFacade.java | 12 +++++
.../server/ProteomicsDataServiceInternal.java | 53 +++++++++----------
.../ProteomicsDataServiceInternalLogger.java | 14 ++---
.../server/api/v1/ProteomicsDataService.java | 22 ++++++--
.../api/v1/ProteomicsDataServiceLogger.java | 16 ++++++
.../IProteomicsDataServiceInternal.java | 6 +--
.../shared/api/v1/IProteomicsDataService.java | 19 +++++++
.../ProteomicsDataServiceInternalTest.java | 37 +++++++------
.../api/v1/ProteomicsDataServiceTest.java | 5 +-
10 files changed, 146 insertions(+), 58 deletions(-)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IProteomicsDataApiFacade.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IProteomicsDataApiFacade.java
index 5b0c46c2cde..c3317ebb5bd 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IProteomicsDataApiFacade.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IProteomicsDataApiFacade.java
@@ -18,7 +18,11 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.api.v1;
import java.util.List;
+import org.springframework.transaction.annotation.Transactional;
+
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
@@ -70,17 +74,31 @@ public interface IProteomicsDataApiFacade
* Returns all experiments of type <tt>MS_SEARCH</tt> which the specified user is allowed to
* read.
*/
+ @Deprecated
public List<Experiment> listSearchExperiments(String userID);
+ /**
+ * Returns all experiments of specified type which the specified user is allowed to read.
+ */
+ public List<Experiment> listSearchExperiments(String sessionToken, String userID, String experimentTypeCode);
+
/**
* Processes the data sets of specified experiments of type <tt>MS_SEARCH</tt> by the DSS
* processing plug-in of specified key for the specified user. It will be checked if the
* experiments are of search experiments and if the user has USER access rights.
*/
+ @Deprecated
public void processSearchData(String userID, String dataSetProcessingKey,
long[] searchExperimentIDs);
-
+ /**
+ * Processes the data sets of specified experiments by the DSS
+ * processing plug-in of specified key for the specified user. It will be checked if the
+ * experiments are of specified type and if the user has USER access rights.
+ */
+ public void processProteinResultDataSets(String sessionToken, String userID,
+ String dataSetProcessingKey, String experimentTypeCode, long[] experimentIDs);
+
/**
* Logs current user out.
*/
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacade.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacade.java
index 0c830ef54e3..f3b2a30ce23 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacade.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacade.java
@@ -110,12 +110,24 @@ class ProteomicsDataApiFacade implements IProteomicsDataApiFacade
return service.listSearchExperiments(sessionToken, userID);
}
+ public List<Experiment> listSearchExperiments(String sessionToken, String userID,
+ String experimentTypeCode)
+ {
+ return service.listSearchExperiments(sessionToken, userID, experimentTypeCode);
+ }
+
public void processSearchData(String userID, String dataSetProcessingKey,
long[] searchExperimentIDs)
{
service.processSearchData(sessionToken, userID, dataSetProcessingKey, searchExperimentIDs);
}
+ public void processProteinResultDataSets(String sessionToken, String userID,
+ String dataSetProcessingKey, String experimentTypeCode, long[] experimentIDs)
+ {
+ service.processProteinResultDataSets(sessionToken, userID, dataSetProcessingKey, experimentTypeCode, experimentIDs);
+ }
+
public void logout()
{
generalInfoService.logout(sessionToken);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
index c35d976d3ea..2627bf740c0 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
@@ -27,6 +27,7 @@ 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.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
@@ -65,8 +66,6 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDataServiceInternal> implements
IProteomicsDataServiceInternal
{
- @Private static final String SEARCH_EXPERIMENT_TYPE = "MS_SEARCH";
-
@Private
static final String SPACE_CODE = "MS_DATA";
@@ -153,31 +152,43 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
processDataSets(session, dataSetProcessingKey, dataSetCodes, new HashMap<String, String>());
}
- public List<Experiment> listSearchExperiments(String sessionToken)
+ public List<Experiment> listSearchExperiments(String sessionToken, String experimentTypeCode)
{
checkSession(sessionToken);
- return listSearchExperiments();
+ IDAOFactory daoFactory = getDAOFactory();
+ IEntityTypeDAO entityTypeDAO = daoFactory.getEntityTypeDAO(EntityKind.EXPERIMENT);
+ ExperimentTypePE type =
+ (ExperimentTypePE) entityTypeDAO.tryToFindEntityTypeByCode(experimentTypeCode);
+ List<ExperimentPE> experiments =
+ daoFactory.getExperimentDAO().listExperimentsWithProperties(type, null);
+ return ExperimentTranslator.translate(experiments, "",
+ ExperimentTranslator.LoadableFields.PROPERTIES);
}
- public void processSearchData(String sessionToken, String dataSetProcessingKey,
- long[] searchExperimentIDs)
+ public void processProteinResultDataSets(String sessionToken, String dataSetProcessingKey,
+ String experimentType, long[] searchExperimentIDs)
{
Session session = getSession(sessionToken);
PersonPE person = session.tryGetPerson();
-
- Set<Long> ids = asSet(searchExperimentIDs);
+
List<String> dataSetCodes = new ArrayList<String>();
- List<Experiment> experiments = listSearchExperiments();
- IExternalDataDAO dataSetDAO = getDAOFactory().getExternalDataDAO();
IExperimentDAO experimentDAO = getDAOFactory().getExperimentDAO();
- for (Experiment experiment : experiments)
+ IExternalDataDAO dataSetDAO = getDAOFactory().getExternalDataDAO();
+ for (long experimentID : searchExperimentIDs)
{
- if (EXPERIMENT_VALIDATOR.isValid(person, experiment)
- && ids.contains(experiment.getId()))
+ ExperimentPE experiment = experimentDAO.tryGetByTechId(new TechId(experimentID));
+ String actualExperimentTypeCode = experiment.getExperimentType().getCode();
+ if (actualExperimentTypeCode.equals(experimentType) == false)
{
- ExperimentPE exp = experimentDAO.tryGetByTechId(new TechId(experiment.getId()));
- List<ExternalDataPE> dataSets = dataSetDAO.listExternalData(exp);
+ throw new UserFailureException("Experiment with technical id " + experimentID
+ + " [" + experiment.getIdentifier() + "] is not of type " + experimentType
+ + " but of type " + actualExperimentTypeCode + ".");
+ }
+ Experiment translatedExperiment = ExperimentTranslator.translate(experiment, "");
+ if (EXPERIMENT_VALIDATOR.isValid(person, translatedExperiment))
+ {
+ List<ExternalDataPE> dataSets = dataSetDAO.listExternalData(experiment);
for (ExternalDataPE dataSet : dataSets)
{
dataSetCodes.add(dataSet.getCode());
@@ -188,18 +199,6 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
processDataSets(session, dataSetProcessingKey, dataSetCodes, new HashMap<String, String>());
}
- private List<Experiment> listSearchExperiments()
- {
- IDAOFactory daoFactory = getDAOFactory();
- IEntityTypeDAO entityTypeDAO = daoFactory.getEntityTypeDAO(EntityKind.EXPERIMENT);
- ExperimentTypePE type =
- (ExperimentTypePE) entityTypeDAO.tryToFindEntityTypeByCode(SEARCH_EXPERIMENT_TYPE);
- List<ExperimentPE> experiments =
- daoFactory.getExperimentDAO().listExperimentsWithProperties(type, null);
- return ExperimentTranslator.translate(experiments, "",
- ExperimentTranslator.LoadableFields.PROPERTIES);
- }
-
private List<MsInjectionSample> loadAllRawDataSamples(Session session)
{
List<Sample> samples = loadAccessableSamples(session);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalLogger.java
index 914157c4985..80fcc8c6c32 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalLogger.java
@@ -63,17 +63,19 @@ class ProteomicsDataServiceInternalLogger extends AbstractServerLogger implement
dataSetCodes.size());
}
- public List<Experiment> listSearchExperiments(String sessionToken)
+ public List<Experiment> listSearchExperiments(String sessionToken, String experimentTypeCode)
{
- logAccess(sessionToken, "list_search_experiments");
+ logAccess(sessionToken, "list_search_experiments", "EXPERIMENT_TYPE(%s)", experimentTypeCode);
return null;
}
- public void processSearchData(String sessionToken, String dataSetProcessingKey,
- long[] searchExperimentIDs)
+ public void processProteinResultDataSets(String sessionToken, String dataSetProcessingKey,
+ String experimentTypeCode, long[] searchExperimentIDs)
{
- int numberOfDataSets = searchExperimentIDs == null ? 0 : searchExperimentIDs.length;
- logAccess(sessionToken, "copy_search_data", "NUMBER_OF_DATA_SETS(%s)", numberOfDataSets);
+ int experimentCount = searchExperimentIDs == null ? 0 : searchExperimentIDs.length;
+ logAccess(sessionToken, "process_protein_result_data_sets",
+ "DSS_PROCESSING_PLUGIN(%s) EXPERIMENT_TYPE(%s) NUMBER_OF_EXPERIMENTS(%s)",
+ dataSetProcessingKey, experimentTypeCode, experimentCount);
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
index ada3557605b..e01051d6a90 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
@@ -23,8 +23,8 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import java.util.Map.Entry;
+import java.util.Set;
import javax.annotation.Resource;
@@ -64,6 +64,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
@Component(Constants.PROTEOMICS_DATA_SERVICE)
public class ProteomicsDataService extends AbstractServer<IProteomicsDataService> implements IProteomicsDataService
{
+ private static final String MS_SEARCH = "MS_SEARCH";
@Resource(name = Constants.PROTEOMICS_DATA_SERVICE_INTERNAL)
private IProteomicsDataServiceInternal service;
@@ -228,12 +229,18 @@ public class ProteomicsDataService extends AbstractServer<IProteomicsDataService
public List<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment> listSearchExperiments(
String sessionToken, String userID)
+ {
+ return listSearchExperiments(sessionToken, userID, MS_SEARCH);
+ }
+
+ public List<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment> listSearchExperiments(
+ String sessionToken, String userID, String experimentTypeCode)
{
checkSession(sessionToken);
SessionContextDTO session = login(userID);
try
{
- List<Experiment> experiments = service.listSearchExperiments(session.getSessionToken());
+ List<Experiment> experiments = service.listSearchExperiments(session.getSessionToken(), experimentTypeCode);
List<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment> result =
new ArrayList<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment>();
for (Experiment experiment : experiments)
@@ -265,13 +272,20 @@ public class ProteomicsDataService extends AbstractServer<IProteomicsDataService
public void processSearchData(String sessionToken, String userID, String dataSetProcessingKey,
long[] searchExperimentIDs)
+ {
+ processProteinResultDataSets(sessionToken, userID, dataSetProcessingKey, MS_SEARCH,
+ searchExperimentIDs);
+ }
+
+ public void processProteinResultDataSets(String sessionToken, String userID,
+ String dataSetProcessingKey, String experimentTypeCode, long[] experimentIDs)
{
checkSession(sessionToken);
SessionContextDTO session = login(userID);
try
{
- service.processSearchData(session.getSessionToken(), dataSetProcessingKey,
- searchExperimentIDs);
+ service.processProteinResultDataSets(session.getSessionToken(), dataSetProcessingKey, experimentTypeCode,
+ experimentIDs);
} finally
{
service.logout(session.getSessionToken());
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceLogger.java
index eb6ef432557..bb22a28bf97 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceLogger.java
@@ -79,6 +79,13 @@ class ProteomicsDataServiceLogger extends AbstractServerLogger implements IProte
return null;
}
+ public List<Experiment> listSearchExperiments(String sessionToken, String userID,
+ String experimentTypeCode)
+ {
+ logAccess(sessionToken, "list_search_experiments", "EXPERIMENT_TYPE(%s)", experimentTypeCode);
+ return null;
+ }
+
public void processSearchData(String sessionToken, String userID, String dataSetProcessingKey,
long[] searchExperimentIDs)
{
@@ -86,6 +93,15 @@ class ProteomicsDataServiceLogger extends AbstractServerLogger implements IProte
logAccess(sessionToken, "copy_search_data", "NUMBER_OF_DATA_SETS(%s)", numberOfDataSets);
}
+ public void processProteinResultDataSets(String sessionToken, String userID,
+ String dataSetProcessingKey, String experimentTypeCode, long[] experimentIDs)
+ {
+ int experimentCount = experimentIDs == null ? 0 : experimentIDs.length;
+ logAccess(sessionToken, "process_protein_result_data_sets",
+ "DSS_PROCESSING_PLUGIN(%s) EXPERIMENT_TYPE(%s) NUMBER_OF_EXPERIMENTS(%s)",
+ dataSetProcessingKey, experimentTypeCode, experimentCount);
+ }
+
public int getMajorVersion()
{
return 1;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IProteomicsDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IProteomicsDataServiceInternal.java
index 8cf0e0dfd8a..e9917e1a3ba 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IProteomicsDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IProteomicsDataServiceInternal.java
@@ -63,11 +63,11 @@ public interface IProteomicsDataServiceInternal extends IServer
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
@ReturnValueFilter(validatorClass = ExperimentValidator.class)
- public List<Experiment> listSearchExperiments(String sessionToken);
+ public List<Experiment> listSearchExperiments(String sessionToken, String experimentTypeCode);
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
- public void processSearchData(String sessionToken, String dataSetProcessingKey,
- long[] searchExperimentIDs);
+ public void processProteinResultDataSets(String sessionToken, String dataSetProcessingKey,
+ String experimentTypeCode, long[] searchExperimentIDs);
}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IProteomicsDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IProteomicsDataService.java
index 036179253b7..1197b137e3c 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IProteomicsDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IProteomicsDataService.java
@@ -100,18 +100,37 @@ public interface IProteomicsDataService extends IRpcService
* Returns all experiments of type <tt>MS_SEARCH</tt> which the specified user is allowed to
* read.
*/
+ @Deprecated
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
public List<Experiment> listSearchExperiments(String sessionToken, String userID);
+
+ /**
+ * Returns all experiments of specified type which the specified user is allowed to read.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
+ public List<Experiment> listSearchExperiments(String sessionToken, String userID, String experimentTypeCode);
/**
* Processes the data sets of specified experiments of type <tt>MS_SEARCH</tt> by the DSS
* processing plug-in of specified key for the specified user. It will be checked if the
* experiments are of search experiments and if the user is allowed to read them.
*/
+ @Deprecated
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
public void processSearchData(String sessionToken, String userID, String dataSetProcessingKey,
long[] searchExperimentIDs);
+
+ /**
+ * Processes the data sets of specified experiments by the DSS
+ * processing plug-in of specified key for the specified user. It will be checked if the
+ * experiments are of specified type and if the user is allowed to read them.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
+ public void processProteinResultDataSets(String sessionToken, String userID,
+ String dataSetProcessingKey, String experimentTypeCode, long[] experimentIDs);
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
index 3d17dccd4e3..71bec3a662c 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
@@ -19,7 +19,6 @@ 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.ProteomicsDataServiceInternal.RAW_DATA_SAMPLE_TYPE;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.ProteomicsDataServiceInternal.SEARCH_EXPERIMENT_TYPE;
import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.ProteomicsDataServiceInternal.SPACE_CODE;
import java.util.ArrayList;
@@ -74,8 +73,8 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
{
private static final String GROUP_CODE = "g";
-
private static final String COPY_PROCESSING_KEY = "copy-data-sets";
+ private static final String EXPERIMENT_TYPE = "EXPE";
private IProteomicsDataServiceInternal service;
@@ -97,7 +96,7 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
sampleLoader = context.mock(ISampleLoader.class);
service = new ProteomicsDataServiceInternal(sessionManager, daoFactory, commonBoFactory, boFactory);
experimentType = new ExperimentTypePE();
- experimentType.setCode(SEARCH_EXPERIMENT_TYPE);
+ experimentType.setCode(EXPERIMENT_TYPE);
experimentType.setDatabaseInstance(CommonTestUtils.createHomeDatabaseInstance());
PersonPE person = new PersonPE();
RoleAssignmentPE roleAssignment = new RoleAssignmentPE();
@@ -145,7 +144,7 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
final ExperimentPE e2 = experiment(2, "a");
prepareListSearchExperiments(e1, e2);
- List<Experiment> list = service.listSearchExperiments(SESSION_TOKEN);
+ List<Experiment> list = service.listSearchExperiments(SESSION_TOKEN, EXPERIMENT_TYPE);
assertEquals("HOME_DATABASE:/G/P/e1", list.get(0).getIdentifier());
assertEquals(1, list.get(0).getRegistrationDate().getTime());
@@ -165,7 +164,6 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
final Session session = createSessionAndPrepareGetSession(GROUP_CODE);
final ExperimentPE e1 = experiment(1);
final ExperimentPE e2 = experiment(2, "a");
- prepareListSearchExperiments(e1, e2);
context.checking(new Expectations()
{
{
@@ -188,7 +186,8 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
});
prepareProcessDataSets(session, new HashMap<String, String>(), "ds1", "ds2");
- service.processSearchData(SESSION_TOKEN, COPY_PROCESSING_KEY, new long[] {e1.getId(), e2.getId()});
+ service.processProteinResultDataSets(SESSION_TOKEN, COPY_PROCESSING_KEY, EXPERIMENT_TYPE,
+ new long[] { e1.getId(), e2.getId() });
context.assertIsSatisfied();
}
@@ -199,10 +198,20 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
Session session = createSessionAndPrepareGetSession(GROUP_CODE + 2);
final ExperimentPE e1 = experiment(1);
final ExperimentPE e2 = experiment(2, "a");
- prepareListSearchExperiments(e1, e2);
+ context.checking(new Expectations()
+ {
+ {
+ one(experimentDAO).tryGetByTechId(new TechId(e1.getId()));
+ will(returnValue(e1));
+
+ one(experimentDAO).tryGetByTechId(new TechId(e2.getId()));
+ will(returnValue(e2));
+ }
+ });
prepareProcessDataSets(session, new HashMap<String, String>());
- service.processSearchData(SESSION_TOKEN, COPY_PROCESSING_KEY, new long[] {e1.getId(), e2.getId()});
+ service.processProteinResultDataSets(SESSION_TOKEN, COPY_PROCESSING_KEY, EXPERIMENT_TYPE,
+ new long[] {e1.getId(), e2.getId()});
context.assertIsSatisfied();
}
@@ -212,8 +221,6 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
{
Session session = createSessionAndPrepareGetSession(GROUP_CODE);
final ExperimentPE e1 = experiment(1);
- final ExperimentPE e2 = experiment(2, "a");
- prepareListSearchExperiments(e1, e2);
context.checking(new Expectations()
{
{
@@ -228,7 +235,8 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
});
prepareProcessDataSets(session, new HashMap<String, String>(), "ds1");
- service.processSearchData(SESSION_TOKEN, COPY_PROCESSING_KEY, new long[] {e1.getId()});
+ service.processProteinResultDataSets(SESSION_TOKEN, COPY_PROCESSING_KEY, EXPERIMENT_TYPE,
+ new long[] {e1.getId()});
context.assertIsSatisfied();
}
@@ -264,7 +272,7 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
one(daoFactory).getEntityTypeDAO(EntityKind.EXPERIMENT);
will(returnValue(entityTypeDAO));
- one(entityTypeDAO).tryToFindEntityTypeByCode(SEARCH_EXPERIMENT_TYPE);
+ one(entityTypeDAO).tryToFindEntityTypeByCode(EXPERIMENT_TYPE);
will(returnValue(experimentType));
one(experimentDAO).listExperimentsWithProperties(experimentType, null);
@@ -401,9 +409,8 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
LinkedHashSet<EntityPropertyPE> props = new LinkedHashSet<EntityPropertyPE>();
for (String property : properties)
{
- props.add(CommonTestUtils.createExperimentPropertyPE(property,
- ProteomicsDataServiceInternal.SEARCH_EXPERIMENT_TYPE, DataTypeCode.VARCHAR,
- property + "-value"));
+ props.add(CommonTestUtils.createExperimentPropertyPE(property, EXPERIMENT_TYPE,
+ DataTypeCode.VARCHAR, property + "-value"));
}
experiment.setProperties(props);
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
index 6b87f9e1460..7081ab7b7ee 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
@@ -66,6 +66,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
*/
public class ProteomicsDataServiceTest extends AbstractServerTestCase
{
+ private static final String MS_SEARCH = "MS_SEARCH";
private static final String RAW_DATA = "RAW_DATA";
private static final String MZXML_DATA = "MZXML_DATA";
@@ -321,7 +322,7 @@ public class ProteomicsDataServiceTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- one(internalService).listSearchExperiments(session2.getSessionToken());
+ one(internalService).listSearchExperiments(session2.getSessionToken(), MS_SEARCH);
will(returnValue(Arrays.asList(e)));
}
});
@@ -356,7 +357,7 @@ public class ProteomicsDataServiceTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- one(internalService).processSearchData(session2.getSessionToken(), "dsp1", ids);
+ one(internalService).processProteinResultDataSets(session2.getSessionToken(), "dsp1", MS_SEARCH, ids);
}
});
--
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