SE-312 introducing processDataSets in Proteomics Data API. Changes in...

SE-312 introducing processDataSets in Proteomics Data API. Changes in MsInjectionCopier: target file name is just data set code

SVN: 18676

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>&lt;sample code&gt;_&lt;data set type code&gt;</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);

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.

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);

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);

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");

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)
     {

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");

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)

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

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();

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()
     {

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();
     }

rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceTest.java → 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();
     }