LMS-1887 Development of the download replica command.

SVN: 18838

rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplica.java

@@ -88,11 +88,22 @@ public class CommandGetReplica extends
         protected ResultCode doExecute(ICinaUtilities component)
         {
             // Find all datasets connected to this sample
+            for (String sampleCode : arguments.getReplicaIdentifiers())
+            {
+                executeForSampleCode(component, sampleCode);
+            }
+            return ResultCode.OK;
+        }
+
+        protected void executeForSampleCode(ICinaUtilities component, String sampleCode)
+        {
+            // Find all datasets connected to this sample
+            component.listDataSetsForSampleCode(sampleCode);
+            // List<DataSet> dataSets = component.listDataSetsForSampleCode(sampleCode);
             // Download the raw-data dataset
             // Download the ...
             // List<Experiment> results =
             // component.listVisibleExperiments(arguments.getReplicaIdentifier());
-            return ResultCode.OK;
         }
     }
 
@@ -115,6 +126,6 @@ public class CommandGetReplica extends
     @Override
     protected String getRequiredArgumentsString()
     {
-        return "<replica identifier>";
+        return "<replica identifier> [<replica identifier> ...]";
     }
 }

rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java

@@ -19,6 +19,8 @@ package ch.systemsx.cisd.cina.client.util.v1;
 import java.util.List;
 
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
@@ -74,6 +76,20 @@ public interface ICinaUtilities
     public List<Experiment> listVisibleExperiments(String experimentType)
             throws IllegalStateException, EnvironmentFailureException;
 
+    /**
+     * Return a list of data sets for the sample specified by code.
+     * 
+     * @param sampleCode The code of the sample we are interested in. It is assumed that the code is
+     *            unique.
+     * @return The data sets connected to the sample
+     * @throws IllegalStateException Thrown if the user has not yet been authenticated.
+     * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
+     *             the server or if there are multiple samples with the given code.
+     * @throws UserFailureException Thrown if no sample exists with the specified code.
+     */
+    public List<DataSet> listDataSetsForSampleCode(String sampleCode) throws IllegalStateException,
+            EnvironmentFailureException, UserFailureException;
+
     /**
      * Logs the current user out.
      */

rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java

@@ -25,14 +25,18 @@ import ch.systemsx.cisd.cina.client.util.v1.ICinaUtilities;
 import ch.systemsx.cisd.common.api.client.ServiceFinder;
 import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
 import ch.systemsx.cisd.openbis.generic.shared.OpenBisServiceFactory;
 import ch.systemsx.cisd.openbis.generic.shared.ResourceNames;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
 
@@ -187,6 +191,12 @@ public class CinaUtilitiesFacade implements ICinaUtilities
     {
         return state.listVisibleExperiments(experimentType);
     }
+
+    public List<DataSet> listDataSetsForSampleCode(String sampleCode) throws IllegalStateException,
+            EnvironmentFailureException
+    {
+        return state.listDataSetsForSampleCode(sampleCode);
+    }
 }
 
 /**
@@ -229,6 +239,12 @@ abstract class AbstractCinaFacadeState implements ICinaUtilities
         throw new IllegalStateException("Please log in");
     }
 
+    public List<DataSet> listDataSetsForSampleCode(String sampleCode) throws IllegalStateException,
+            EnvironmentFailureException
+    {
+        throw new IllegalStateException("Please log in");
+    }
+
     /**
      * Authenticates the <code>user</code> with given <code>password</code>.
      * 
@@ -301,6 +317,8 @@ class AuthenticatedState extends AbstractCinaFacadeState
 
     private final IETLLIMSService openbisService;
 
+    private final int generalInformationServiceMinorVersion;
+
     /**
      * @param service
      */
@@ -310,6 +328,7 @@ class AuthenticatedState extends AbstractCinaFacadeState
         super(service);
         this.sessionToken = sessionToken;
         this.openbisService = openbisService;
+        this.generalInformationServiceMinorVersion = service.getMinorVersion();
     }
 
     @Override
@@ -328,7 +347,7 @@ class AuthenticatedState extends AbstractCinaFacadeState
             throws IllegalStateException, EnvironmentFailureException
     {
         // This functionality has only been supported since version 1.1
-        int minorVersion = service.getMinorVersion();
+        int minorVersion = generalInformationServiceMinorVersion;
         if (minorVersion < 1)
         {
             throw new EnvironmentFailureException("Server does not support this feature.");
@@ -359,7 +378,7 @@ class AuthenticatedState extends AbstractCinaFacadeState
             throws IllegalStateException, EnvironmentFailureException
     {
         // This functionality has only been supported since version 1.2
-        int minorVersion = service.getMinorVersion();
+        int minorVersion = generalInformationServiceMinorVersion;
         if (minorVersion < 2)
         {
             throw new EnvironmentFailureException("Server does not support this feature.");
@@ -378,4 +397,35 @@ class AuthenticatedState extends AbstractCinaFacadeState
         return service.listExperiments(sessionToken, projects, experimentType);
     }
 
+    @Override
+    public List<DataSet> listDataSetsForSampleCode(String sampleCode) throws IllegalStateException,
+            EnvironmentFailureException
+    {
+        // This functionality has only been supported since version 1.1
+        int minorVersion = generalInformationServiceMinorVersion;
+        if (minorVersion < 1)
+        {
+            throw new EnvironmentFailureException("Server does not support this feature.");
+        }
+
+        // Find the sample that matches the given code (there should only be 1)
+        SearchCriteria searchCriteria = new SearchCriteria();
+        searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
+                sampleCode));
+        List<Sample> samples = service.searchForSamples(sessionToken, searchCriteria);
+        if (samples.size() < 1)
+        {
+            throw new UserFailureException("No sample with specified code.");
+        }
+
+        // There should only be 1
+        if (samples.size() > 1)
+        {
+            throw new EnvironmentFailureException(
+                    "Found multiple matching samples -- this should not happen. Please contact administrator to resolve this problem.");
+        }
+
+        return service.listDataSets(sessionToken, samples);
+    }
+
 }
\ No newline at end of file

rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCodeTest.java

@@ -92,6 +92,9 @@ public class CommandGenerateSampleCodeTest extends AssertJUnit
                     one(service).tryToAuthenticateForAllServices(USER_ID, PASSWORD);
                     will(returnValue(SESSION_TOKEN));
 
+                    one(service).getMinorVersion();
+                    will(returnValue(0));
+
                     one(openbisService).getSampleType(SESSION_TOKEN, sampleTypeCode.toUpperCase());
                     will(returnValue(sampleType));
 

rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java

@@ -16,6 +16,8 @@
 
 package ch.systemsx.cisd.cina.client.util.cli;
 
+import java.util.ArrayList;
+
 import org.jmock.Expectations;
 import org.jmock.Mockery;
 import org.testng.AssertJUnit;
@@ -24,10 +26,17 @@ import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 import ch.systemsx.cisd.cina.client.util.v1.ICinaUtilities;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.openbis.dss.client.api.cli.ICommand;
 import ch.systemsx.cisd.openbis.dss.client.api.cli.ResultCode;
 import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
 
 /**
  * @author Chandrasekhar Ramakrishnan
@@ -83,44 +92,51 @@ public class CommandGetReplicaTest extends AssertJUnit
                 {
                     one(service).tryToAuthenticateForAllServices(USER_ID, PASSWORD);
                     will(returnValue(SESSION_TOKEN));
+
+                    one(service).getMinorVersion();
+                    will(returnValue(1));
+
                     one(service).logout(SESSION_TOKEN);
                 }
             });
-
     }
 
-    @Test
-    public void testCodePath()
+    private void setupListDataSetsExpectations(final String sampleCode)
     {
-        setupAuthenticationExpectations();
         context.checking(new Expectations()
             {
                 {
-                    // final ArrayList<Project> projects = new ArrayList<Project>();
-                    // Project project = new Project("PROJECT-1", "SPACE-1");
-                    // projects.add(project);
-                    //
-                    // final ArrayList<Experiment> experiments = new ArrayList<Experiment>();
-                    //
-                    // final ArrayList<SpaceWithProjectsAndRoleAssignments> spaces =
-                    // new ArrayList<SpaceWithProjectsAndRoleAssignments>();
-                    // SpaceWithProjectsAndRoleAssignments space =
-                    // new SpaceWithProjectsAndRoleAssignments("SPACE-1");
-                    // space.add(project);
-                    // space.add("user", new Role("ADMIN", true));
-                    // spaces.add(space);
-
-                    // one(service).getMinorVersion();
-                    // will(returnValue(2));
-
-                    // one(service).listSpacesWithProjectsAndRoleAssignments(SESSION_TOKEN, null);
-                    // will(returnValue(spaces));
-                    //
-                    // one(service).listExperiments(SESSION_TOKEN, projects, "EXP-TYPE");
-                    // will(returnValue(experiments));
+                    SearchCriteria searchCriteria = new SearchCriteria();
+                    searchCriteria.addMatchClause(MatchClause.createAttributeMatch(
+                            MatchClauseAttribute.CODE, sampleCode));
+
+                    ArrayList<Sample> samples = new ArrayList<Sample>();
+                    SampleInitializer initializer = new SampleInitializer();
+                    initializer.setCode(sampleCode);
+                    initializer.setId((long) 1);
+                    initializer.setIdentifier("SPACE/" + sampleCode);
+                    initializer.setPermId("PERM-ID");
+                    initializer.setSampleTypeCode("SAMPLE-TYPE");
+                    initializer.setSampleTypeId((long) 1);
+                    Sample sample = new Sample(initializer);
+                    samples.add(sample);
+
+                    one(service).searchForSamples(SESSION_TOKEN, searchCriteria);
+                    will(returnValue(samples));
+
+                    ArrayList<DataSet> dataSets = new ArrayList<DataSet>();
+                    one(service).listDataSets(SESSION_TOKEN, samples);
+                    will(returnValue(dataSets));
 
                 }
             });
+    }
+
+    @Test
+    public void testCodePath()
+    {
+        setupAuthenticationExpectations();
+        setupListDataSetsExpectations("REPLICA-ID");
 
         ICommand command = new MockCommandGetReplica();
 
@@ -135,6 +151,7 @@ public class CommandGetReplicaTest extends AssertJUnit
     public void testOutputFolder()
     {
         setupAuthenticationExpectations();
+        setupListDataSetsExpectations("REPLICA-ID");
 
         ICommand command = new MockCommandGetReplica();
 
@@ -149,6 +166,8 @@ public class CommandGetReplicaTest extends AssertJUnit
     public void testMultipleReplicas()
     {
         setupAuthenticationExpectations();
+        setupListDataSetsExpectations("REPLICA-ID1");
+        setupListDataSetsExpectations("REPLICA-ID2");
 
         ICommand command = new MockCommandGetReplica();
 
@@ -158,4 +177,34 @@ public class CommandGetReplicaTest extends AssertJUnit
         assertEquals(ResultCode.OK, exitCode);
         context.assertIsSatisfied();
     }
+
+    @Test
+    public void testOldVersion()
+    {
+        context.checking(new Expectations()
+            {
+                {
+                    one(service).tryToAuthenticateForAllServices(USER_ID, PASSWORD);
+                    will(returnValue(SESSION_TOKEN));
+
+                    // The service used wasn't available in version 0
+                    one(service).getMinorVersion();
+                    will(returnValue(0));
+
+                    one(service).logout(SESSION_TOKEN);
+                }
+            });
+
+        ICommand command = new MockCommandGetReplica();
+
+        try
+        {
+            command.execute(new String[]
+                { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "REPLICA-ID" });
+            fail("Command should throw an exception when run against an older version of the interface.");
+        } catch (EnvironmentFailureException e)
+        {
+            assertEquals("Server does not support this feature.", e.getMessage());
+        }
+    }
 }

rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java

@@ -112,6 +112,9 @@ public class CinaUtilitiesFacadeTest extends AssertJUnit
                     one(service).tryToAuthenticateForAllServices(USER_ID, PASSWORD);
                     will(returnValue(SESSION_TOKEN));
 
+                    one(service).getMinorVersion();
+                    will(returnValue(0));
+
                     one(openbisService).getSampleType(SESSION_TOKEN, sampleTypeCode);
                     will(returnValue(sampleType));