From 740a8ca6938744acdb43bd5bda99b893af24abe7 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 15 Nov 2010 08:21:11 +0000
Subject: [PATCH] SE-312 introducing processDataSets in Proteomics Data API.
Changes in MsInjectionCopier: target file name is just data set code
SVN: 18676
---
.../server/plugins/MsInjectionCopier.java | 16 ++--------------
.../client/api/v1/IProteomicsDataApiFacade.java | 9 +++++----
.../client/api/v1/ProteomicsDataApiFacade.java | 6 ++++++
.../server/ProteomicsDataServiceInternal.java | 7 +++++++
.../ProteomicsDataServiceInternalLogger.java | 8 ++++++++
.../server/api/v1/ProteomicsDataService.java | 14 ++++++++++++++
.../api/v1/ProteomicsDataServiceLogger.java | 8 ++++++++
.../shared/IProteomicsDataServiceInternal.java | 10 ++++++++++
.../shared/api/v1/IProteomicsDataService.java | 11 +++++++++++
.../server/plugins/MsInjectionCopierTest.java | 5 ++---
.../api/v1/ProteomicsDataApiFacadeTest.java | 14 +++++++-------
.../ProteomicsDataServiceInternalTest.java | 10 +++-------
.../{ => api/v1}/ProteomicsDataServiceTest.java | 13 ++++++-------
13 files changed, 89 insertions(+), 42 deletions(-)
rename rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/{ => api/v1}/ProteomicsDataServiceTest.java (97%)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionCopier.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionCopier.java
index a99b0f51f6c..5d369568c3e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionCopier.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionCopier.java
@@ -279,9 +279,7 @@ class MsInjectionCopier implements Serializable, IPostRegistrationDatasetHandler
/**
* Copies specified data file/folder to destination specified in constructor. The name of the
- * file/folder at the destination is defined as
- * <code><sample code>_<data set type code></code> where sample code is provided by
- * the parameter bindings (key: data set code).
+ * file/folder at the destination is defined by the data set code.
*/
public Status handle(File originalData, DataSetInformation dataSetInformation,
Map<String, String> parameterBindings)
@@ -292,7 +290,7 @@ class MsInjectionCopier implements Serializable, IPostRegistrationDatasetHandler
}
try
{
- String target = createTargetFolderName(dataSetInformation, parameterBindings);
+ String target = dataSetInformation.getDataSetCode();
File targetFolder = new File(destination, target);
deleteTargetFolder(targetFolder);
executor.copyDataSet(originalData, destination);
@@ -305,16 +303,6 @@ class MsInjectionCopier implements Serializable, IPostRegistrationDatasetHandler
}
}
- private String createTargetFolderName(DataSetInformation dataSetInformation,
- Map<String, String> parameterBindings)
- {
- String dataSetTypeCode = dataSetInformation.getDataSetType().getCode();
- String dataSetCode = dataSetInformation.getDataSetCode();
- String sampleCode = parameterBindings.get(dataSetCode);
- return (sampleCode == null ? SAMPLE_UNKNOWN : sampleCode) + "_" + dataSetCode + "_"
- + dataSetTypeCode;
- }
-
private void deleteTargetFolder(File targetFolder)
{
BooleanStatus targetExists = executor.exists(targetFolder);
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 000e372ca7c..54f85e6c406 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
@@ -28,10 +28,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjection
*
* @author Franz-Josef Elmer
*/
-
-// This interfaces replaces the IRawDataApiFacade.
-@SuppressWarnings("deprecation")
-public interface IProteomicsDataApiFacade extends IRawDataApiFacade
+public interface IProteomicsDataApiFacade
{
/**
* Return the session token for the logged-in user.
@@ -53,8 +50,11 @@ public interface IProteomicsDataApiFacade extends IRawDataApiFacade
* 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.
*/
+ @Deprecated
public void processingRawData(String userID, String dataSetProcessingKey,
long[] rawDataSampleIDs, String dataSetType);
+
+ public void processDataSets(String userID, String dataSetProcessingKey, List<String> dataSetCodes);
/**
* Returns all projects where the specified user has USER access rights.
@@ -74,6 +74,7 @@ public interface IProteomicsDataApiFacade extends IRawDataApiFacade
*/
public void processSearchData(String userID, String dataSetProcessingKey,
long[] searchExperimentIDs);
+
/**
* 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 a416d909f2e..0c830ef54e3 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
@@ -71,6 +71,12 @@ class ProteomicsDataApiFacade implements IProteomicsDataApiFacade
dataSetType);
}
+ public void processDataSets(String userID, String dataSetProcessingKey,
+ List<String> dataSetCodes)
+ {
+ service.processDataSets(sessionToken, userID, dataSetProcessingKey, dataSetCodes);
+ }
+
public List<Project> listProjects(String userID)
{
Map<String, Set<Role>> namedRoleSets = generalInfoService.listNamedRoleSets(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 588908834ee..c35d976d3ea 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
@@ -146,6 +146,13 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
processDataSets(session, dataSetProcessingKey, dataSetCodes, parameterBindings);
}
+ public void processDataSets(String sessionToken, String dataSetProcessingKey,
+ List<String> dataSetCodes)
+ {
+ Session session = getSession(sessionToken);
+ processDataSets(session, dataSetProcessingKey, dataSetCodes, new HashMap<String, String>());
+ }
+
public List<Experiment> listSearchExperiments(String sessionToken)
{
checkSession(sessionToken);
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 62acc184618..e3461beb8e7 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
@@ -55,6 +55,14 @@ class ProteomicsDataServiceInternalLogger extends AbstractServerLogger implement
numberOfDataSets, dataSetType);
}
+ public void processDataSets(String sessionToken, String dataSetProcessingKey,
+ List<String> dataSetCodes)
+ {
+ logAccess(sessionToken, "process_data_sets",
+ "DSS_PROCESSING_PLUGIN(%s) NUMBER_OF_DATA_SETS(%s)", dataSetProcessingKey,
+ dataSetCodes.size());
+ }
+
public List<Experiment> listSearchExperiments(String sessionToken)
{
logAccess(sessionToken, "list_search_experiments");
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 3f9451803c2..ada3557605b 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
@@ -212,6 +212,20 @@ public class ProteomicsDataService extends AbstractServer<IProteomicsDataService
}
}
+ public void processDataSets(String sessionToken, String userID, String dataSetProcessingKey,
+ List<String> dataSetCodes)
+ {
+ checkSession(sessionToken);
+ SessionContextDTO session = login(userID);
+ try
+ {
+ service.processDataSets(session.getSessionToken(), dataSetProcessingKey, dataSetCodes);
+ } finally
+ {
+ service.logout(session.getSessionToken());
+ }
+ }
+
public List<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment> listSearchExperiments(
String sessionToken, String userID)
{
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 aa5c525fea4..9233d86fae9 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
@@ -65,6 +65,14 @@ class ProteomicsDataServiceLogger extends AbstractServerLogger implements IProte
userID, dataSetProcessingKey, numberOfDataSets, dataSetType);
}
+ public void processDataSets(String sessionToken, String userID, String dataSetProcessingKey,
+ List<String> dataSetCodes)
+ {
+ logAccess(sessionToken, "process_data_sets",
+ "USER_ID(%s) DSS_PROCESSING_PLUGIN(%s) DATA_SETS(%s)", userID,
+ dataSetProcessingKey, dataSetCodes);
+ }
+
public List<Experiment> listSearchExperiments(String sessionToken, String userID)
{
logAccess(sessionToken, "list_search_experiments");
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 b707130cdc5..8cf0e0dfd8a 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
@@ -21,8 +21,10 @@ import java.util.List;
import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
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.predicate.DataSetCodeCollectionPredicate;
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;
@@ -45,11 +47,19 @@ public interface IProteomicsDataServiceInternal extends IServer
@ReturnValueFilter(validatorClass = RawDataSampleValidator.class)
public List<MsInjectionSample> listRawDataSamples(String sessionToken);
+ @Deprecated
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
public void processRawData(String sessionToken, String dataSetProcessingKey,
long[] rawDataSampleIDs, String dataSetType);
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_USER)
+ public void processDataSets(
+ String sessionToken,
+ String dataSetProcessingKey,
+ @AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> dataSetCodes);
+
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
@ReturnValueFilter(validatorClass = ExperimentValidator.class)
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 65442c24b7e..036179253b7 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
@@ -80,10 +80,21 @@ public interface IProteomicsDataService extends IRpcService
* for the specified user. Implementations should check that the specified user is allowed to
* read specified samples.
*/
+ @Deprecated
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
public void processingRawData(String sessionToken, String userID, String dataSetProcessingKey,
long[] rawDataSampleIDs, String dataSetType);
+
+ /**
+ * Processes the specified data sets by the DSS processing plug-in of specified key for the
+ * specified user. Implementations should check that the specified user is allowed to read
+ * specified data sets.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
+ public void processDataSets(String sessionToken, String userID, String dataSetProcessingKey,
+ List<String> dataSetCodes);
/**
* Returns all experiments of type <tt>MS_SEARCH</tt> which the specified user is allowed to
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionCopierTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionCopierTest.java
index f2e977f2f66..b61e31f853c 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionCopierTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/MsInjectionCopierTest.java
@@ -56,7 +56,7 @@ public class MsInjectionCopierTest extends AbstractFileSystemTestCase
private static final String SAMPLE_CODE = "my-sample";
private static final DataSetType DATA_SET_TYPE = new DataSetType("MY");
private static final String DATA_SET_CODE = "my-dataset-123";
- private static final String FOLDER_NAME = SAMPLE_CODE + "_" + DATA_SET_CODE + "_" + DATA_SET_TYPE.getCode();
+ private static final String FOLDER_NAME = DATA_SET_CODE;
private static final String DATA = "hello test";
private Mockery context;
@@ -139,8 +139,7 @@ public class MsInjectionCopierTest extends AbstractFileSystemTestCase
assertEquals(Status.OK, status);
File copiedDataSet =
- new File(destination, MsInjectionCopier.SAMPLE_UNKNOWN + "_" + DATA_SET_CODE + "_"
- + DATA_SET_TYPE.getCode());
+ new File(destination, DATA_SET_CODE);
assertEquals(true, copiedDataSet.isDirectory());
context.assertIsSatisfied();
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacadeTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacadeTest.java
index 331053b5ece..bdfb5fd6551 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacadeTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacadeTest.java
@@ -122,23 +122,23 @@ public class ProteomicsDataApiFacadeTest extends AssertJUnit
assertSame(result, facade.listRawDataSamples("user1"));
context.assertIsSatisfied();
}
-
+
@Test
- public void testProcessingRawData()
+ public void testProcessDataSets()
{
context.checking(new Expectations()
{
{
- one(proteomicsDataService).processingRawData(SESSION_TOKEN, "user1", "key",
- new long[42], "type");
+ one(proteomicsDataService).processDataSets(SESSION_TOKEN, "user1", "key",
+ Arrays.asList("ds1", "ds2"));
}
});
- facade.processingRawData("user1", "key", new long[42], "type");
-
+ facade.processDataSets("user1", "key", Arrays.asList("ds1", "ds2"));
+
context.assertIsSatisfied();
}
-
+
@Test
public void testListProjectsButNoUserRoles()
{
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 56c4dae0fc6..3d17dccd4e3 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
@@ -126,17 +126,13 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
}
@Test
- public void testCopyRawData()
+ public void testProcessDataSets()
{
prepareGetSession();
- prepareListRawDataSamples(1L, 2L, 3L, 42L);
- final long[] ids = new long[]
- { 2 };
HashMap<String, String> parameterBindings = new HashMap<String, String>();
- parameterBindings.put("ds-21-child", "s-2");
- prepareProcessDataSets(SESSION, parameterBindings, "ds-21-child");
+ prepareProcessDataSets(SESSION, parameterBindings, "ds1", "ds2");
- service.processRawData(SESSION_TOKEN, COPY_PROCESSING_KEY, ids, "dt-0");
+ service.processDataSets(SESSION_TOKEN, COPY_PROCESSING_KEY, Arrays.asList("ds1", "ds2"));
context.assertIsSatisfied();
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
similarity index 97%
rename from rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceTest.java
rename to rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
index be6e67f4404..6b87f9e1460 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.api.v1;
import java.io.Serializable;
import java.util.ArrayList;
@@ -261,14 +261,14 @@ public class ProteomicsDataServiceTest extends AbstractServerTestCase
}
@Test
- public void testCopyRawDataForUnknownUser()
+ public void testProcessDataSetsForUnknownUser()
{
prepareGetSession();
prepareLoginLogout(null);
try
{
- service.processingRawData(SESSION_TOKEN, "abc", null, new long[0], null);
+ service.processDataSets(SESSION_TOKEN, "abc", null, Arrays.asList("ds1"));
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
@@ -279,19 +279,18 @@ public class ProteomicsDataServiceTest extends AbstractServerTestCase
}
@Test
- public void testCopyRawData()
+ public void testProcessDataSets()
{
prepareGetSession();
prepareLoginLogout(session2);
- final long[] ids = new long[] {42};
context.checking(new Expectations()
{
{
- one(internalService).processRawData(session2.getSessionToken(), "dsp1", ids, "my-type");
+ one(internalService).processDataSets(session2.getSessionToken(), "dsp1", Arrays.asList("ds1"));
}
});
- service.processingRawData(SESSION_TOKEN, "abc", "dsp1", ids, "my-type");
+ service.processDataSets(SESSION_TOKEN, "abc", "dsp1", Arrays.asList("ds1"));
context.assertIsSatisfied();
}
--
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