From c08a0506df10f07c0904d1c515a49a1c5678c2ca Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 6 Sep 2010 13:31:37 +0000
Subject: [PATCH] OBP-37 new API: Proteomics Data API with same methods as Raw
Data API plus two new methods. Raw Data API are removed. Only deprecated
IRawDataApiFacade for backwards compatibility.
SVN: 17728
---
rtd_phosphonetx/etc/service.properties | 2 +-
.../client/api/v1/FacadeFactory.java | 22 ++--
.../api/v1/IProteomicsDataApiFacade.java | 81 +++++++++++++
.../client/api/v1/IRawDataApiFacade.java | 1 +
...cade.java => ProteomicsDataApiFacade.java} | 20 +++-
...piTest.java => ProteomicsDataApiTest.java} | 31 ++++-
.../phosphonetx/client/api/v1/package.html | 2 +-
.../web/server/PhosphoNetXClientService.java | 8 +-
.../web/server/RawDataSampleProvider.java | 6 +-
...ava => ProteomicsDataServiceInternal.java} | 107 +++++++++++++++---
... ProteomicsDataServiceInternalLogger.java} | 21 +++-
.../phosphonetx/server/api/v1/Constants.java | 4 +-
...ervice.java => ProteomicsDataService.java} | 100 +++++++++++-----
....java => ProteomicsDataServiceLogger.java} | 20 +++-
....java => ProteomicsDataServiceServer.java} | 16 +--
...va => IProteomicsDataServiceInternal.java} | 15 ++-
.../phosphonetx/shared/ResourceNames.java | 2 +-
...rvice.java => IProteomicsDataService.java} | 28 ++++-
.../shared/api/v1/dto/Experiment.java | 105 +++++++++++++++++
.../java/phosphonetx-applicationContext.xml | 30 +----
....java => ProteomicsDataApiFacadeTest.java} | 18 +--
.../web/server/RawDataSampleProviderTest.java | 6 +-
...=> ProteomicsDataServiceInternalTest.java} | 14 +--
...st.java => ProteomicsDataServiceTest.java} | 16 +--
24 files changed, 531 insertions(+), 144 deletions(-)
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IProteomicsDataApiFacade.java
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/{RawDataApiFacade.java => ProteomicsDataApiFacade.java} (83%)
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/{RawDataApiTest.java => ProteomicsDataApiTest.java} (67%)
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/{RawDataServiceInternal.java => ProteomicsDataServiceInternal.java} (63%)
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/{RawDataServiceInternalLogger.java => ProteomicsDataServiceInternalLogger.java} (66%)
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/{RawDataService.java => ProteomicsDataService.java} (73%)
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/{RawDataServiceLogger.java => ProteomicsDataServiceLogger.java} (74%)
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/{RawDataServiceServer.java => ProteomicsDataServiceServer.java} (69%)
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/{IRawDataServiceInternal.java => IProteomicsDataServiceInternal.java} (74%)
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/{IRawDataService.java => IProteomicsDataService.java} (73%)
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/Experiment.java
rename rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/{RawDataApiFacadeTest.java => ProteomicsDataApiFacadeTest.java} (90%)
rename rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/{RawDataServiceInternalTest.java => ProteomicsDataServiceInternalTest.java} (94%)
rename rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/{RawDataServiceTest.java => ProteomicsDataServiceTest.java} (95%)
diff --git a/rtd_phosphonetx/etc/service.properties b/rtd_phosphonetx/etc/service.properties
index 93f45ff53f0..909533fa609 100644
--- a/rtd_phosphonetx/etc/service.properties
+++ b/rtd_phosphonetx/etc/service.properties
@@ -125,7 +125,7 @@ processing-plugins = copy-data-sets, ms-inj-copy
# The configuration of the processing plugin is the same as the reporting plugins configuration.
copy-data-sets.label = Data Set Copier to User Location
-copy-data-sets.dataset-types = UNKNOWN
+copy-data-sets.dataset-types = UNKNOWN, PROT_RESULT
copy-data-sets.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopierForUsers
#copy-data-sets.destination = /Volumes/share-1-\$/user/cisd/felmer/phosphonetx/
copy-data-sets.destination = vesuvio:tmp/${user}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/FacadeFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/FacadeFactory.java
index 0f119a3f0cd..719a53f1028 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/FacadeFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/FacadeFactory.java
@@ -18,17 +18,17 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.api.v1;
import ch.systemsx.cisd.common.api.client.ServiceFinder;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IProteomicsDataService;
/**
- * Factory of {@link IRawDataApiFacade}.
+ * Factory of {@link IProteomicsDataApiFacade}.
*
* @author Franz-Josef Elmer
*/
public class FacadeFactory
{
private static final ServiceFinder SERVICE_FINDER =
- new ServiceFinder("openbis", IRawDataService.SERVER_URL);
+ new ServiceFinder("openbis", IProteomicsDataService.SERVER_URL);
private static final ServiceFinder GENERIC_INFO_SERVICE_FINDER =
new ServiceFinder("openbis", IGeneralInformationService.SERVICE_URL);
@@ -36,31 +36,31 @@ public class FacadeFactory
/**
* Creates a facade for specified server URL, user Id, and password.
*/
- public static IRawDataApiFacade create(String serverURL, String userID, String password)
+ public static IProteomicsDataApiFacade create(String serverURL, String userID, String password)
{
IGeneralInformationService infoService = createGenericInfoService(serverURL);
- IRawDataService service = createService(serverURL);
+ IProteomicsDataService service = createService(serverURL);
String sessionToken = infoService.tryToAuthenticateForAllServices(userID, password);
if (sessionToken == null)
{
throw new IllegalArgumentException("User " + userID + " couldn't be authenticated");
}
- return new RawDataApiFacade(service, infoService, sessionToken);
+ return new ProteomicsDataApiFacade(service, infoService, sessionToken);
}
/**
* Creates a facade for specified url and sessionToken.
*/
- public static IRawDataApiFacade create(String serverURL, String sessionToken)
+ public static IProteomicsDataApiFacade create(String serverURL, String sessionToken)
{
- IRawDataService service = createService(serverURL);
+ IProteomicsDataService service = createService(serverURL);
IGeneralInformationService infoService = createGenericInfoService(serverURL);
- return new RawDataApiFacade(service, infoService, sessionToken);
+ return new ProteomicsDataApiFacade(service, infoService, sessionToken);
}
- private static IRawDataService createService(String serverURL)
+ private static IProteomicsDataService createService(String serverURL)
{
- return SERVICE_FINDER.createService(IRawDataService.class, serverURL);
+ return SERVICE_FINDER.createService(IProteomicsDataService.class, serverURL);
}
private static IGeneralInformationService createGenericInfoService(String serverURL)
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
new file mode 100644
index 00000000000..f076af4e4ba
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IProteomicsDataApiFacade.java
@@ -0,0 +1,81 @@
+/*
+ * 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.client.api.v1;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
+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;
+
+
+/**
+ * Facade for openBIS proteomics data service.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IProteomicsDataApiFacade extends IRawDataApiFacade
+{
+ /**
+ * Return the session token for the logged-in user.
+ */
+ public String getSessionToken();
+
+ /**
+ * Returns all samples of type MS_INJECTION in space MS_DATA which have a parent sample which
+ * the specified user is allow to read.
+ */
+ public List<MsInjectionDataInfo> listRawDataSamples(String userID);
+
+ /**
+ * Lists all processing plugins on DSS.
+ */
+ public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos();
+
+ /**
+ * Processes the data sets of specified samples by the DSS processing plug-in of specified key
+ * for the specified user. Only the most recent data sets of specified type are processed.
+ */
+ public void processingRawData(String userID, String dataSetProcessingKey,
+ long[] rawDataSampleIDs, String dataSetType);
+
+ /**
+ * Returns all projects where the specified user has USER access rights.
+ */
+ public List<Project> listProjects(String userID);
+
+ /**
+ * Returns all experiments of type <tt>MS_SEARCH</tt> which the specified user is allowed to
+ * read.
+ */
+ public List<Experiment> listSearchExperiments(String userID);
+
+ /**
+ * 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.
+ */
+ public void processSearchData(String userID, String dataSetProcessingKey,
+ long[] searchExperimentIDs);
+
+ /**
+ * Logs current user out.
+ */
+ public void logout();
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IRawDataApiFacade.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IRawDataApiFacade.java
index b47e523e82a..866613a3f18 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IRawDataApiFacade.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IRawDataApiFacade.java
@@ -28,6 +28,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjection
*
* @author Franz-Josef Elmer
*/
+@Deprecated
public interface IRawDataApiFacade
{
/**
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiFacade.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacade.java
similarity index 83%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiFacade.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacade.java
index 6840abef472..a416d909f2e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiFacade.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacade.java
@@ -25,8 +25,9 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IProteomicsDataService;
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;
/**
@@ -34,14 +35,14 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjection
*
* @author Franz-Josef Elmer
*/
-class RawDataApiFacade implements IRawDataApiFacade
+class ProteomicsDataApiFacade implements IProteomicsDataApiFacade
{
private static final String USER_ROLE_SET = "SPACE_USER";
- private final IRawDataService service;
+ private final IProteomicsDataService service;
private final IGeneralInformationService generalInfoService;
private final String sessionToken;
- RawDataApiFacade(IRawDataService service, IGeneralInformationService generalInfoService, String sessionToken)
+ ProteomicsDataApiFacade(IProteomicsDataService service, IGeneralInformationService generalInfoService, String sessionToken)
{
this.service = service;
this.generalInfoService = generalInfoService;
@@ -98,6 +99,17 @@ class RawDataApiFacade implements IRawDataApiFacade
return projects;
}
+ public List<Experiment> listSearchExperiments(String userID)
+ {
+ return service.listSearchExperiments(sessionToken, userID);
+ }
+
+ public void processSearchData(String userID, String dataSetProcessingKey,
+ long[] searchExperimentIDs)
+ {
+ service.processSearchData(sessionToken, userID, dataSetProcessingKey, searchExperimentIDs);
+ }
+
public void logout()
{
generalInfoService.logout(sessionToken);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiTest.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiTest.java
similarity index 67%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiTest.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiTest.java
index 81ccf122bcc..f42913c27a1 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiTest.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiTest.java
@@ -22,14 +22,15 @@ import java.util.Map;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
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;
/**
- * Example of usage of Raw Data API.
+ * Example of usage of Proteomics Data API.
*
* @author Franz-Josef Elmer
*/
-public class RawDataApiTest
+public class ProteomicsDataApiTest
{
public static void main(String[] args)
{
@@ -43,7 +44,7 @@ public class RawDataApiTest
String loginID = args[1];
String password = args[2];
String userID = args[3];
- IRawDataApiFacade facade = FacadeFactory.create(serverURL, loginID, password);
+ IProteomicsDataApiFacade facade = FacadeFactory.create(serverURL, loginID, password);
System.out.println("MS_INJECTION samples:");
List<MsInjectionDataInfo> rawDataSamples = facade.listRawDataSamples(userID);
@@ -61,10 +62,15 @@ public class RawDataApiTest
System.out.println("DSS processing plugins:");
List<DataStoreServerProcessingPluginInfo> infos = facade.listDataStoreServerProcessingPluginInfos();
+ String dataSetProcessingKey = null;
for (DataStoreServerProcessingPluginInfo info : infos)
{
System.out.println(" key:" + info.getKey() + ", label:'" + info.getLabel()
+ "', data set types:" + info.getDatasetTypeCodes());
+ if (info.getDatasetTypeCodes().contains("PROT_RESULT"))
+ {
+ dataSetProcessingKey = info.getKey();
+ }
}
System.out.println("Projects:");
@@ -73,6 +79,25 @@ public class RawDataApiTest
{
System.out.println(project);
}
+
+ System.out.println("Search Experiments:");
+ List<Experiment> experiments = facade.listSearchExperiments(userID);
+ long[] ids = new long[experiments.size()];
+ for (int i = 0; i < experiments.size(); i++)
+ {
+ Experiment experiment = experiments.get(i);
+ System.out.println(experiment.getSpaceCode() + "/" + experiment.getProjectCode() + "/"
+ + experiment.getCode() + " [" + experiment.getId() + ", "
+ + experiment.getRegistrationDate() + "] " + experiment.getProperties());
+ ids[i] = experiment.getId();
+ }
+
+ if (dataSetProcessingKey != null)
+ {
+ System.out.println("Process search data of " + ids.length + " experiments");
+ facade.processSearchData(userID, dataSetProcessingKey , ids);
+ }
+
facade.logout();
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/package.html b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/package.html
index 2a39158eb3a..4dd85ccc624 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/package.html
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/package.html
@@ -1,5 +1,5 @@
<html>
<body>
-API Facade
+Proteomics Data API Facade
</body>
</html>
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
index 20c3d34ae4f..cdfa2ac7cc0 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
@@ -43,7 +43,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListPro
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListSampleAbundanceByProteinCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
@@ -65,7 +65,7 @@ public class PhosphoNetXClientService extends AbstractClientService implements
private IPhosphoNetXServer server;
@Resource(name = ResourceNames.PHOSPHONETX_RAW_DATA_SERVICE_WEB)
- private IRawDataServiceInternal rawDataService;
+ private IProteomicsDataServiceInternal proteomicsDataService;
public PhosphoNetXClientService()
{
@@ -224,7 +224,7 @@ public class PhosphoNetXClientService extends AbstractClientService implements
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
{
final String sessionToken = getSessionToken();
- RawDataSampleProvider rawDataSampleProvider = new RawDataSampleProvider(rawDataService, sessionToken);
+ RawDataSampleProvider rawDataSampleProvider = new RawDataSampleProvider(proteomicsDataService, sessionToken);
ResultSet<GenericTableRow> resultSet = listEntities(criteria, rawDataSampleProvider);
return new GenericTableResultSet(resultSet, rawDataSampleProvider.getHeaders());
}
@@ -238,7 +238,7 @@ public class PhosphoNetXClientService extends AbstractClientService implements
public void processRawData(String dataSetProcessingKey, long[] rawDataSampleIDs, String dataSetType)
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
{
- rawDataService.processRawData(getSessionToken(), dataSetProcessingKey, rawDataSampleIDs, dataSetType);
+ proteomicsDataService.processRawData(getSessionToken(), dataSetProcessingKey, rawDataSampleIDs, dataSetType);
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java
index 91d4ab80268..b87ac048022 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java
@@ -31,7 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
@@ -52,11 +52,11 @@ class RawDataSampleProvider implements IOriginalDataProvider<GenericTableRow>
@Private
static final String CODE = "CODE";
- private final IRawDataServiceInternal service;
+ private final IProteomicsDataServiceInternal service;
private final String sessionToken;
- RawDataSampleProvider(IRawDataServiceInternal service, String sessionToken)
+ RawDataSampleProvider(IProteomicsDataServiceInternal service, String sessionToken)
{
this.service = service;
this.sessionToken = sessionToken;
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/ProteomicsDataServiceInternal.java
similarity index 63%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
index b9e834fbbf1..10e322eb180 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
@@ -32,28 +32,39 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObject
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.IEntityTypeDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.ExperimentValidator;
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.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
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.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
+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.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.DataSetManager;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validator.RawDataSampleValidator;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
* @author Franz-Josef Elmer
*/
-public class RawDataServiceInternal extends AbstractServer<IRawDataServiceInternal> implements
- IRawDataServiceInternal
+public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDataServiceInternal> implements
+ IProteomicsDataServiceInternal
{
@Private
static final String SPACE_CODE = "MS_DATA";
@@ -63,16 +74,18 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
private static final IValidator<MsInjectionSample> RAW_DATA_SAMPLE_VALIDATOR =
new RawDataSampleValidator();
+
+ private static final IValidator<Experiment> EXPERIMENT_VALIDATOR = new ExperimentValidator();
private ICommonBusinessObjectFactory businessObjectFactory;
private ISessionManager<Session> sessionManagerFromConstructor;
- public RawDataServiceInternal()
+ public ProteomicsDataServiceInternal()
{
}
- public RawDataServiceInternal(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
+ public ProteomicsDataServiceInternal(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
ICommonBusinessObjectFactory businessObjectFactory)
{
super(sessionManager, daoFactory);
@@ -85,9 +98,9 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
sessionManager = sessionManagerFromConstructor;
}
- public IRawDataServiceInternal createLogger(IInvocationLoggerContext context)
+ public IProteomicsDataServiceInternal createLogger(IInvocationLoggerContext context)
{
- return new RawDataServiceInternalLogger(getSessionManager(), context);
+ return new ProteomicsDataServiceInternalLogger(getSessionManager(), context);
}
public List<MsInjectionSample> listRawDataSamples(String sessionToken)
@@ -102,11 +115,7 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
PersonPE person = session.tryGetPerson();
List<MsInjectionSample> samples = loadAllRawDataSamples(session);
- Set<Long> sampleIDs = new HashSet<Long>();
- for (long id : rawDataSampleIDs)
- {
- sampleIDs.add(id);
- }
+ Set<Long> sampleIDs = asSet(rawDataSampleIDs);
List<String> dataSetCodes = new ArrayList<String>();
Map<String, String> parameterBindings = new HashMap<String, String>();
for (MsInjectionSample sample : samples)
@@ -125,11 +134,54 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
}
}
- String dataStoreServerCode = findDataStoreServer(dataSetProcessingKey);
- IExternalDataTable externalDataTable =
- businessObjectFactory.createExternalDataTable(session);
- externalDataTable.processDatasets(dataSetProcessingKey, dataStoreServerCode, dataSetCodes,
- parameterBindings);
+ processDataSets(session, dataSetProcessingKey, dataSetCodes, parameterBindings);
+ }
+
+ public List<Experiment> listSearchExperiments(String sessionToken)
+ {
+ checkSession(sessionToken);
+
+ return listSearchExperiments();
+ }
+
+ public void processSearchData(String sessionToken, String dataSetProcessingKey,
+ 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)
+ {
+ if (EXPERIMENT_VALIDATOR.isValid(person, experiment)
+ && ids.contains(experiment.getId()))
+ {
+ ExperimentPE exp = experimentDAO.tryGetByTechId(new TechId(experiment.getId()));
+ List<ExternalDataPE> dataSets = dataSetDAO.listExternalData(exp);
+ for (ExternalDataPE dataSet : dataSets)
+ {
+ dataSetCodes.add(dataSet.getCode());
+ }
+ }
+ }
+
+ 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("MS_SEARCH");
+ List<ExperimentPE> experiments =
+ daoFactory.getExperimentDAO().listExperimentsWithProperties(type, null);
+ return ExperimentTranslator.translate(experiments, "",
+ ExperimentTranslator.LoadableFields.PROPERTIES);
}
private List<MsInjectionSample> loadAllRawDataSamples(Session session)
@@ -153,6 +205,16 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
return manager.getSamples();
}
+ private void processDataSets(Session session, String dataSetProcessingKey,
+ List<String> dataSetCodes, Map<String, String> parameterBindings)
+ {
+ String dataStoreServerCode = findDataStoreServer(dataSetProcessingKey);
+ IExternalDataTable externalDataTable =
+ businessObjectFactory.createExternalDataTable(session);
+ externalDataTable.processDatasets(dataSetProcessingKey, dataStoreServerCode, dataSetCodes,
+ parameterBindings);
+ }
+
private String findDataStoreServer(String dataSetProcessingKey)
{
List<DataStorePE> dataStores = getDAOFactory().getDataStoreDAO().listDataStores();
@@ -171,4 +233,15 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
throw new EnvironmentFailureException("No data store processing service with key '"
+ dataSetProcessingKey + "' found.");
}
+
+ private Set<Long> asSet(long[] ids)
+ {
+ Set<Long> result = new HashSet<Long>();
+ for (long id : ids)
+ {
+ result.add(id);
+ }
+ return result;
+ }
}
+
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/ProteomicsDataServiceInternalLogger.java
similarity index 66%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalLogger.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalLogger.java
index 784e9f04985..62acc184618 100644
--- 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/ProteomicsDataServiceInternalLogger.java
@@ -21,8 +21,9 @@ import java.util.List;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServerLogger;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
@@ -30,10 +31,11 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
*
* @author Franz-Josef Elmer
*/
-class RawDataServiceInternalLogger extends AbstractServerLogger implements IRawDataServiceInternal
+class ProteomicsDataServiceInternalLogger extends AbstractServerLogger implements
+ IProteomicsDataServiceInternal
{
- RawDataServiceInternalLogger(ISessionManager<Session> sessionManager,
+ ProteomicsDataServiceInternalLogger(ISessionManager<Session> sessionManager,
IInvocationLoggerContext context)
{
super(sessionManager, context);
@@ -53,4 +55,17 @@ class RawDataServiceInternalLogger extends AbstractServerLogger implements IRawD
numberOfDataSets, dataSetType);
}
+ public List<Experiment> listSearchExperiments(String sessionToken)
+ {
+ logAccess(sessionToken, "list_search_experiments");
+ return null;
+ }
+
+ public void processSearchData(String sessionToken, String dataSetProcessingKey,
+ long[] searchExperimentIDs)
+ {
+ int numberOfDataSets = searchExperimentIDs == null ? 0 : searchExperimentIDs.length;
+ logAccess(sessionToken, "copy_search_data", "NUMBER_OF_DATA_SETS(%s)", numberOfDataSets);
+ }
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/Constants.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/Constants.java
index 728de9189d9..015689596a3 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/Constants.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/Constants.java
@@ -24,7 +24,7 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.api.v1;
public class Constants
{
// Spring bean IDs
- public final static String PHOSPHONETX_RAW_DATA_SERVICE = "phosphonetx-raw-data-service";
- public final static String PHOSPHONETX_RAW_DATA_SERVICE_INTERNAL = "phosphonetx-raw-data-service-internal";
+ public final static String PROTEOMICS_DATA_SERVICE = "proteomics-data-service";
+ public final static String PROTEOMICS_DATA_SERVICE_INTERNAL = "proteomics-data-service-internal";
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
similarity index 73%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataService.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
index 4600bbe58f4..4f94af701e8 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
@@ -47,30 +47,30 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.util.DataTypeUtils;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IProteomicsDataService;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.PropertyKey;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
- * Implementation of {@link IRawDataService}.
+ * Implementation of {@link IProteomicsDataService}.
*
* @author Franz-Josef Elmer
*/
-@Component(Constants.PHOSPHONETX_RAW_DATA_SERVICE)
-public class RawDataService extends AbstractServer<IRawDataService> implements IRawDataService
+@Component(Constants.PROTEOMICS_DATA_SERVICE)
+public class ProteomicsDataService extends AbstractServer<IProteomicsDataService> implements IProteomicsDataService
{
- @Resource(name = Constants.PHOSPHONETX_RAW_DATA_SERVICE_INTERNAL)
- private IRawDataServiceInternal service;
+ @Resource(name = Constants.PROTEOMICS_DATA_SERVICE_INTERNAL)
+ private IProteomicsDataServiceInternal service;
- public RawDataService()
+ public ProteomicsDataService()
{
}
- public RawDataService(final ISessionManager<Session> sessionManager,
- final IDAOFactory daoFactory, IRawDataServiceInternal service)
+ public ProteomicsDataService(final ISessionManager<Session> sessionManager,
+ final IDAOFactory daoFactory, IProteomicsDataServiceInternal service)
{
super(sessionManager, daoFactory);
this.service = service;
@@ -82,9 +82,9 @@ public class RawDataService extends AbstractServer<IRawDataService> implements I
return session == null ? null : session.getSessionToken();
}
- public IRawDataService createLogger(IInvocationLoggerContext context)
+ public IProteomicsDataService createLogger(IInvocationLoggerContext context)
{
- return new RawDataServiceLogger(getSessionManager(), context);
+ return new ProteomicsDataServiceLogger(getSessionManager(), context);
}
public List<MsInjectionDataInfo> listRawDataSamples(String sessionToken, String userID)
@@ -133,19 +133,6 @@ public class RawDataService extends AbstractServer<IRawDataService> implements I
return info;
}
- private Map<PropertyKey, Serializable> translate(List<IEntityProperty> properties)
- {
- HashMap<PropertyKey, Serializable> map = new HashMap<PropertyKey, Serializable>();
- for (IEntityProperty property : properties)
- {
- PropertyType propertyType = property.getPropertyType();
- PropertyKey key = new PropertyKey(propertyType.getCode(), propertyType.getLabel());
- DataTypeCode dataTypeCode = propertyType.getDataType().getCode();
- map.put(key, DataTypeUtils.convertValueTo(dataTypeCode, property.tryGetAsString()));
- }
- return map;
- }
-
public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos(
String sessionToken)
{
@@ -195,6 +182,67 @@ public class RawDataService extends AbstractServer<IRawDataService> implements I
}
}
+ public List<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment> listSearchExperiments(
+ String sessionToken, String userID)
+ {
+ checkSession(sessionToken);
+ SessionContextDTO session = login(userID);
+ try
+ {
+ List<Experiment> experiments = service.listSearchExperiments(session.getSessionToken());
+ 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)
+ {
+ ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment e =
+ new ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment();
+ e.setId(experiment.getId());
+ e.setCode(experiment.getCode());
+ e.setProjectCode(experiment.getProject().getCode());
+ e.setSpaceCode(experiment.getProject().getSpace().getCode());
+ e.setRegistrationDate(experiment.getRegistrationDate());
+ e.setProperties(translate(experiment.getProperties()));
+ result.add(e);
+ }
+ return result;
+ } finally
+ {
+ service.logout(session.getSessionToken());
+ }
+ }
+
+ public void processSearchData(String sessionToken, String userID, String dataSetProcessingKey,
+ long[] searchExperimentIDs)
+ {
+ checkSession(sessionToken);
+ SessionContextDTO session = login(userID);
+ try
+ {
+ service.processSearchData(session.getSessionToken(), dataSetProcessingKey,
+ searchExperimentIDs);
+ } finally
+ {
+ service.logout(session.getSessionToken());
+ }
+ }
+
+ private Map<PropertyKey, Serializable> translate(List<IEntityProperty> properties)
+ {
+ if (properties == null)
+ {
+ return null;
+ }
+ HashMap<PropertyKey, Serializable> map = new HashMap<PropertyKey, Serializable>();
+ for (IEntityProperty property : properties)
+ {
+ PropertyType propertyType = property.getPropertyType();
+ PropertyKey key = new PropertyKey(propertyType.getCode(), propertyType.getLabel());
+ DataTypeCode dataTypeCode = propertyType.getDataType().getCode();
+ map.put(key, DataTypeUtils.convertValueTo(dataTypeCode, property.tryGetAsString()));
+ }
+ return map;
+ }
+
private SessionContextDTO login(String userID)
{
SessionContextDTO session = service.tryToAuthenticate(userID, "dummy-password");
@@ -212,7 +260,7 @@ public class RawDataService extends AbstractServer<IRawDataService> implements I
public int getMinorVersion()
{
- return 1;
+ return 2;
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceLogger.java
similarity index 74%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceLogger.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceLogger.java
index 98cf6922d7a..aa5c525fea4 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceLogger.java
@@ -22,17 +22,18 @@ import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServerLogger;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IProteomicsDataService;
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;
/**
* @author Franz-Josef Elmer
*/
-class RawDataServiceLogger extends AbstractServerLogger implements IRawDataService
+class ProteomicsDataServiceLogger extends AbstractServerLogger implements IProteomicsDataService
{
- RawDataServiceLogger(ISessionManager<Session> sessionManager, IInvocationLoggerContext context)
+ ProteomicsDataServiceLogger(ISessionManager<Session> sessionManager, IInvocationLoggerContext context)
{
super(sessionManager, context);
}
@@ -64,6 +65,19 @@ class RawDataServiceLogger extends AbstractServerLogger implements IRawDataServi
userID, dataSetProcessingKey, numberOfDataSets, dataSetType);
}
+ public List<Experiment> listSearchExperiments(String sessionToken, String userID)
+ {
+ logAccess(sessionToken, "list_search_experiments");
+ return null;
+ }
+
+ public void processSearchData(String sessionToken, String userID, String dataSetProcessingKey,
+ long[] searchExperimentIDs)
+ {
+ int numberOfDataSets = searchExperimentIDs == null ? 0 : searchExperimentIDs.length;
+ logAccess(sessionToken, "copy_search_data", "NUMBER_OF_DATA_SETS(%s)", numberOfDataSets);
+ }
+
public int getMajorVersion()
{
return 1;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceServer.java
similarity index 69%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceServer.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceServer.java
index 16c6ca3fc3a..1aaf05c81b7 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceServer.java
@@ -22,26 +22,26 @@ 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.plugin.phosphonetx.shared.api.v1.IRawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IProteomicsDataService;
/**
- * Server wrapping {@link IRawDataService}.
+ * Server wrapping {@link IProteomicsDataService}.
*
* @author Franz-Josef Elmer
*/
@Controller
@RequestMapping(
- { IRawDataService.SERVER_URL, "/openbis" + IRawDataService.SERVER_URL })
-public class RawDataServiceServer extends AbstractApiServiceExporter
+ { IProteomicsDataService.SERVER_URL, "/openbis" + IProteomicsDataService.SERVER_URL })
+public class ProteomicsDataServiceServer extends AbstractApiServiceExporter
{
- @Resource(name = Constants.PHOSPHONETX_RAW_DATA_SERVICE)
- private IRawDataService service;
+ @Resource(name = Constants.PROTEOMICS_DATA_SERVICE)
+ private IProteomicsDataService service;
@Override
public void afterPropertiesSet()
{
- establishService(IRawDataService.class, service, IRawDataService.SERVICE_NAME,
- IRawDataService.SERVER_URL);
+ establishService(IProteomicsDataService.class, service, IProteomicsDataService.SERVICE_NAME,
+ IProteomicsDataService.SERVER_URL);
super.afterPropertiesSet();
}
}
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/IProteomicsDataServiceInternal.java
similarity index 74%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataServiceInternal.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IProteomicsDataServiceInternal.java
index a4d819a6e21..b707130cdc5 100644
--- 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/IProteomicsDataServiceInternal.java
@@ -23,6 +23,8 @@ 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.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.ExperimentValidator;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validator.RawDataSampleValidator;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
@@ -32,7 +34,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
*
* @author Franz-Josef Elmer
*/
-public interface IRawDataServiceInternal extends IServer
+public interface IProteomicsDataServiceInternal extends IServer
{
/**
* Returns all samples of type MS_INJECTION in group MS_DATA which have a parent sample which
@@ -47,4 +49,15 @@ public interface IRawDataServiceInternal extends IServer
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
public void processRawData(String sessionToken, String dataSetProcessingKey,
long[] rawDataSampleIDs, String dataSetType);
+
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_USER)
+ @ReturnValueFilter(validatorClass = ExperimentValidator.class)
+ public List<Experiment> listSearchExperiments(String sessionToken);
+
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_USER)
+ public void processSearchData(String sessionToken, String dataSetProcessingKey,
+ long[] searchExperimentIDs);
+
}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java
index f33481e7497..318fc560230 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java
@@ -31,7 +31,7 @@ public class ResourceNames
public final static String PHOSPHONETX_PLUGIN_SERVER = "phosphonetx-plugin-server";
- public final static String PHOSPHONETX_RAW_DATA_SERVICE_WEB = "phosphonetx-raw-data-service-web";
+ public final static String PHOSPHONETX_RAW_DATA_SERVICE_WEB = "proteomics-data-service-web";
public final static String PHOSPHONETX_DAO_FACTORY = "phosphonetx-dao-factory";
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IRawDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IProteomicsDataService.java
similarity index 73%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IRawDataService.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IProteomicsDataService.java
index d9793dedec3..79357b48be4 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IRawDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IProteomicsDataService.java
@@ -24,19 +24,20 @@ 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;
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;
/**
- * Service for querying raw data.
*
+ *
* @author Franz-Josef Elmer
*/
-public interface IRawDataService extends IRpcService
+public interface IProteomicsDataService extends IRpcService
{
/**
* Name of this service for which it is registered at the RPC name server.
*/
- public static final String SERVICE_NAME = "phosphonetx-raw-data";
+ public static final String SERVICE_NAME = "proteomics-data";
/**
* Service part of the URL to access this service remotely.
@@ -59,7 +60,7 @@ public interface IRawDataService extends IRpcService
/**
* Returns all samples of type MS_INJECTION in space MS_DATA which have a parent sample which
- * the specified user is allow to read.
+ * the specified user is allowed to read.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
@@ -82,4 +83,23 @@ public interface IRawDataService extends IRpcService
@RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
public void processingRawData(String sessionToken, String userID, String dataSetProcessingKey,
long[] rawDataSampleIDs, String dataSetType);
+
+ /**
+ * Returns all experiments of type <tt>MS_SEARCH</tt> which the specified user is allowed to
+ * read.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
+ public List<Experiment> listSearchExperiments(String sessionToken, String userID);
+
+ /**
+ * 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.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
+ public void processSearchData(String sessionToken, String userID, String dataSetProcessingKey,
+ long[] searchExperimentIDs);
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/Experiment.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/Experiment.java
new file mode 100644
index 00000000000..a0d5e366092
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/Experiment.java
@@ -0,0 +1,105 @@
+/*
+ * 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.api.v1.dto;
+
+import java.io.Serializable;
+import java.util.Date;
+import java.util.Map;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class Experiment implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private long id;
+
+ private String spaceCode;
+
+ private String projectCode;
+
+ private String code;
+
+ private Date registrationDate;
+
+ private Map<PropertyKey, Serializable> properties;
+
+ public final long getId()
+ {
+ return id;
+ }
+
+ public final void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public final String getSpaceCode()
+ {
+ return spaceCode;
+ }
+
+ public final void setSpaceCode(String spaceCode)
+ {
+ this.spaceCode = spaceCode;
+ }
+
+ public final String getProjectCode()
+ {
+ return projectCode;
+ }
+
+ public final void setProjectCode(String projectCode)
+ {
+ this.projectCode = projectCode;
+ }
+
+ public final String getCode()
+ {
+ return code;
+ }
+
+ public final void setCode(String code)
+ {
+ this.code = code;
+ }
+
+ public final Date getRegistrationDate()
+ {
+ return registrationDate;
+ }
+
+ public final void setRegistrationDate(Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ public final Map<PropertyKey, Serializable> getProperties()
+ {
+ return properties;
+ }
+
+ public final void setProperties(Map<PropertyKey, Serializable> properties)
+ {
+ this.properties = properties;
+ }
+
+
+}
diff --git a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
index 0c7bfcc2844..5bec6ae66f6 100644
--- a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
+++ b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
@@ -41,31 +41,11 @@
</bean>
<!--
- // Raw Data Server
+ // Proteomics Data Server
-->
- <!--bean id="phosphonetx-raw-data-service" class="org.springframework.aop.framework.ProxyFactoryBean">
- <property name="proxyInterfaces">
- <list>
- <value>ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService</value>
- </list>
- </property>
- <property name="target">
- <bean class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.api.v1.RawDataService">
- <constructor-arg ref="session-manager" />
- <constructor-arg ref="dao-factory" />
- <constructor-arg ref="phosphonetx-raw-data-service-internal" />
- </bean>
- </property>
- <property name="interceptorNames">
- <list>
- <value>exception-translator</value>
- </list>
- </property>
- </bean-->
-
- <bean id="phosphonetx-raw-data-service-internal"
- class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataServiceInternal"
+ <bean id="proteomics-data-service-internal"
+ class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.ProteomicsDataServiceInternal"
init-method="replaceAutoWiredSesseionManagerByConstructorSessionManager">
<constructor-arg>
<bean class="ch.systemsx.cisd.authentication.DefaultSessionManager">
@@ -88,8 +68,8 @@
<constructor-arg ref="common-business-object-factory" />
</bean>
- <bean id="phosphonetx-raw-data-service-web"
- class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataServiceInternal">
+ <bean id="proteomics-data-service-web"
+ class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.ProteomicsDataServiceInternal">
<constructor-arg ref="session-manager" />
<constructor-arg ref="dao-factory"/>
<constructor-arg ref="common-business-object-factory" />
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiFacadeTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacadeTest.java
similarity index 90%
rename from rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiFacadeTest.java
rename to rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacadeTest.java
index c396731b465..331053b5ece 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiFacadeTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacadeTest.java
@@ -34,7 +34,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IProteomicsDataService;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
@@ -43,22 +43,22 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjection
*
* @author Franz-Josef Elmer
*/
-public class RawDataApiFacadeTest extends AssertJUnit
+public class ProteomicsDataApiFacadeTest extends AssertJUnit
{
private static final String SESSION_TOKEN = "Session-42";
private Mockery context;
- private IRawDataService rawDataService;
+ private IProteomicsDataService proteomicsDataService;
private IGeneralInformationService generalInfoService;
- private IRawDataApiFacade facade;
+ private IProteomicsDataApiFacade facade;
@BeforeMethod
public void beforeMethod()
{
context = new Mockery();
- rawDataService = context.mock(IRawDataService.class);
+ proteomicsDataService = context.mock(IProteomicsDataService.class);
generalInfoService = context.mock(IGeneralInformationService.class);
- facade = new RawDataApiFacade(rawDataService, generalInfoService, SESSION_TOKEN);
+ facade = new ProteomicsDataApiFacade(proteomicsDataService, generalInfoService, SESSION_TOKEN);
}
@AfterMethod
@@ -98,7 +98,7 @@ public class RawDataApiFacadeTest extends AssertJUnit
context.checking(new Expectations()
{
{
- one(rawDataService).listDataStoreServerProcessingPluginInfos(SESSION_TOKEN);
+ one(proteomicsDataService).listDataStoreServerProcessingPluginInfos(SESSION_TOKEN);
will(returnValue(result));
}
});
@@ -114,7 +114,7 @@ public class RawDataApiFacadeTest extends AssertJUnit
context.checking(new Expectations()
{
{
- one(rawDataService).listRawDataSamples(SESSION_TOKEN, "user1");
+ one(proteomicsDataService).listRawDataSamples(SESSION_TOKEN, "user1");
will(returnValue(result));
}
});
@@ -129,7 +129,7 @@ public class RawDataApiFacadeTest extends AssertJUnit
context.checking(new Expectations()
{
{
- one(rawDataService).processingRawData(SESSION_TOKEN, "user1", "key",
+ one(proteomicsDataService).processingRawData(SESSION_TOKEN, "user1", "key",
new long[42], "type");
}
});
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
index 3607d05d025..ff4a334e871 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
@@ -39,7 +39,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericValueEntityPrope
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
@@ -50,7 +50,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
@Friend(toClasses=RawDataSampleProvider.class)
public class RawDataSampleProviderTest extends AbstractServerTestCase
{
- private IRawDataServiceInternal service;
+ private IProteomicsDataServiceInternal service;
private RawDataSampleProvider provider;
@Override
@@ -58,7 +58,7 @@ public class RawDataSampleProviderTest extends AbstractServerTestCase
public final void setUp()
{
super.setUp();
- service = context.mock(IRawDataServiceInternal.class);
+ service = context.mock(IProteomicsDataServiceInternal.class);
provider = new RawDataSampleProvider(service, SESSION_TOKEN);
}
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/ProteomicsDataServiceInternalTest.java
similarity index 94%
rename from rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
rename to rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
index b99cbae40b3..a34d1c2e83a 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
@@ -18,8 +18,8 @@ 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.RAW_DATA_SAMPLE_TYPE;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataServiceInternal.SPACE_CODE;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.ProteomicsDataServiceInternal.RAW_DATA_SAMPLE_TYPE;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.ProteomicsDataServiceInternal.SPACE_CODE;
import java.util.ArrayList;
import java.util.Arrays;
@@ -49,18 +49,18 @@ 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.SampleTypePE;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
* @author Franz-Josef Elmer
*/
-@Friend(toClasses = RawDataServiceInternal.class)
-public class RawDataServiceInternalTest extends AbstractServerTestCase
+@Friend(toClasses = ProteomicsDataServiceInternal.class)
+public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
{
private static final String COPY_PROCESSING_KEY = "copy-data-sets";
- private IRawDataServiceInternal service;
+ private IProteomicsDataServiceInternal service;
private ICommonBusinessObjectFactory boFactory;
@@ -70,7 +70,7 @@ public class RawDataServiceInternalTest extends AbstractServerTestCase
{
super.setUp();
boFactory = context.mock(ICommonBusinessObjectFactory.class);
- service = new RawDataServiceInternal(sessionManager, daoFactory, boFactory);
+ service = new ProteomicsDataServiceInternal(sessionManager, daoFactory, boFactory);
}
@Test
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/ProteomicsDataServiceTest.java
similarity index 95%
rename from rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java
rename to rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceTest.java
index c80fdc3802b..f5f07086470 100644
--- 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/ProteomicsDataServiceTest.java
@@ -43,9 +43,9 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
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.SessionContextDTO;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.api.v1.RawDataService;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.api.v1.ProteomicsDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IProteomicsDataService;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.PropertyKey;
@@ -56,13 +56,13 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
*
* @author Franz-Josef Elmer
*/
-public class RawDataServiceTest extends AbstractServerTestCase
+public class ProteomicsDataServiceTest extends AbstractServerTestCase
{
private static final String RAW_DATA = "RAW_DATA";
private static final String MZXML_DATA = "MZXML_DATA";
- private IRawDataServiceInternal internalService;
- private IRawDataService service;
+ private IProteomicsDataServiceInternal internalService;
+ private IProteomicsDataService service;
private SessionContextDTO session2;
@Override
@@ -70,8 +70,8 @@ public class RawDataServiceTest extends AbstractServerTestCase
public final void setUp()
{
super.setUp();
- internalService = context.mock(IRawDataServiceInternal.class);
- service = new RawDataService(sessionManager, daoFactory, internalService);
+ internalService = context.mock(IProteomicsDataServiceInternal.class);
+ service = new ProteomicsDataService(sessionManager, daoFactory, internalService);
session2 = new SessionContextDTO();
session2.setSessionToken(SESSION_TOKEN + "2");
}
--
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