diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplica.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplica.java
index fbf3ad367c55940bfb1ff694ecbcfa2d28e3a3b0..d3574e5f4a59d03986d335500e3c573d47f9d0a8 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplica.java
+++ b/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> ...]";
}
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java
index 12bf80e0066dea6cd05a080478e5fce39eaf71a1..c6ee4323cd4cee12ceb9767c7cd5b7234eb9dcab 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java
+++ b/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.
*/
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java
index 4cb50873a530a4045a6bb42619c949b64232975f..4380dc8921f0f3ec1ef0b32c45da97064ead0922 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java
+++ b/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
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCodeTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCodeTest.java
index fcab38fcba19773cee1a9118aa8d20175fd5e0d2..adf51f82152786cd48e04d612cacfdac479b0805 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGenerateSampleCodeTest.java
+++ b/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));
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java
index f2fb0d7da053e86e335b880b49db92cca2584bf7..0b3cec452a45b1c096d1036508b50323cbf7ae87 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java
+++ b/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());
+ }
+ }
}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java
index 328d4c15a1a861ac303d5c42ddd95c4c41ac5a0a..ff04903c86f9ca1e4eb4828f399cde29c8c35d07 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java
+++ b/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));