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 10e322eb180716a3915cd9d6b88fdcd37c5a24b7..61fc559f258fa2782fdb61070dad760f1fe2d2e6 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
@@ -66,6 +66,8 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDataServiceInternal> implements
IProteomicsDataServiceInternal
{
+ @Private static final String SEARCH_EXPERIMENT_TYPE = "MS_SEARCH";
+
@Private
static final String SPACE_CODE = "MS_DATA";
@@ -177,7 +179,7 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
IDAOFactory daoFactory = getDAOFactory();
IEntityTypeDAO entityTypeDAO = daoFactory.getEntityTypeDAO(EntityKind.EXPERIMENT);
ExperimentTypePE type =
- (ExperimentTypePE) entityTypeDAO.tryToFindEntityTypeByCode("MS_SEARCH");
+ (ExperimentTypePE) entityTypeDAO.tryToFindEntityTypeByCode(SEARCH_EXPERIMENT_TYPE);
List<ExperimentPE> experiments =
daoFactory.getExperimentDAO().listExperimentsWithProperties(type, null);
return ExperimentTranslator.translate(experiments, "",
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 a34d1c2e83a95d8c40355482a8f518cd9e304915..a6fc63ba091a2bf67f8e15210f64d2b498c16656 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
@@ -19,14 +19,18 @@ 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.ProteomicsDataServiceInternal.RAW_DATA_SAMPLE_TYPE;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.ProteomicsDataServiceInternal.SEARCH_EXPERIMENT_TYPE;
import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.ProteomicsDataServiceInternal.SPACE_CODE;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
+import java.util.Date;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import org.hamcrest.BaseMatcher;
@@ -38,9 +42,11 @@ import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
+import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
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;
@@ -48,7 +54,17 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
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.EntityPropertyPE;
+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.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
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.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
@@ -58,12 +74,16 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
@Friend(toClasses = ProteomicsDataServiceInternal.class)
public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
{
+ private static final String GROUP_CODE = "g";
+
private static final String COPY_PROCESSING_KEY = "copy-data-sets";
private IProteomicsDataServiceInternal service;
private ICommonBusinessObjectFactory boFactory;
+ private ExperimentTypePE experimentType;
+
@Override
@BeforeMethod
public final void setUp()
@@ -71,6 +91,9 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
super.setUp();
boFactory = context.mock(ICommonBusinessObjectFactory.class);
service = new ProteomicsDataServiceInternal(sessionManager, daoFactory, boFactory);
+ experimentType = new ExperimentTypePE();
+ experimentType.setCode(SEARCH_EXPERIMENT_TYPE);
+ experimentType.setDatabaseInstance(CommonTestUtils.createHomeDatabaseInstance());
}
@Test
@@ -93,6 +116,154 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
prepareListRawDataSamples(1L, 2L, 3L, 42L);
final long[] ids = new long[]
{ 2 };
+ HashMap<String, String> parameterBindings = new HashMap<String, String>();
+ parameterBindings.put("ds-2", "s-2");
+ prepareProcessDataSets(SESSION, parameterBindings, "ds-2");
+
+ service.processRawData(SESSION_TOKEN, COPY_PROCESSING_KEY, ids, "dt-0");
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testListSearchExperiments()
+ {
+ prepareGetSession();
+ final ExperimentPE e1 = experiment(1);
+ final ExperimentPE e2 = experiment(2, "a");
+ prepareListSearchExperiments(e1, e2);
+
+ List<Experiment> list = service.listSearchExperiments(SESSION_TOKEN);
+
+ assertEquals("HOME_DATABASE:/G/P/e1", list.get(0).getIdentifier());
+ assertEquals(1, list.get(0).getRegistrationDate().getTime());
+ assertEquals(0, list.get(0).getProperties().size());
+ assertEquals("HOME_DATABASE:/G/P/e2", list.get(1).getIdentifier());
+ assertEquals(4, list.get(1).getRegistrationDate().getTime());
+ assertEquals("A", list.get(1).getProperties().get(0).getPropertyType().getCode());
+ assertEquals("a-value", list.get(1).getProperties().get(0).getValue());
+ assertEquals(1, list.get(1).getProperties().size());
+ assertEquals(2, list.size());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testProcessSearchData()
+ {
+ final Session session = createSessionAndPrepareGetSession(GROUP_CODE);
+ final ExperimentPE e1 = experiment(1);
+ final ExperimentPE e2 = experiment(2, "a");
+ prepareListSearchExperiments(e1, e2);
+ context.checking(new Expectations()
+ {
+ {
+ one(experimentDAO).tryGetByTechId(new TechId(e1.getId()));
+ will(returnValue(e1));
+
+ one(externalDataDAO).listExternalData(e1);
+ ExternalDataPE ds1 = new ExternalDataPE();
+ ds1.setCode("ds1");
+ will(returnValue(Arrays.asList(ds1)));
+
+ one(experimentDAO).tryGetByTechId(new TechId(e2.getId()));
+ will(returnValue(e2));
+
+ one(externalDataDAO).listExternalData(e2);
+ ExternalDataPE ds2 = new ExternalDataPE();
+ ds2.setCode("ds2");
+ will(returnValue(Arrays.asList(ds2)));
+ }
+ });
+ prepareProcessDataSets(session, new HashMap<String, String>(), "ds1", "ds2");
+
+ service.processSearchData(SESSION_TOKEN, COPY_PROCESSING_KEY, new long[] {e1.getId(), e2.getId()});
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testProcessSearchDataFilteredByValidator()
+ {
+ Session session = createSessionAndPrepareGetSession(GROUP_CODE + 2);
+ final ExperimentPE e1 = experiment(1);
+ final ExperimentPE e2 = experiment(2, "a");
+ prepareListSearchExperiments(e1, e2);
+ prepareProcessDataSets(session, new HashMap<String, String>());
+
+ service.processSearchData(SESSION_TOKEN, COPY_PROCESSING_KEY, new long[] {e1.getId(), e2.getId()});
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testProcessSearchDataFilteredByIds()
+ {
+ Session session = createSessionAndPrepareGetSession(GROUP_CODE);
+ final ExperimentPE e1 = experiment(1);
+ final ExperimentPE e2 = experiment(2, "a");
+ prepareListSearchExperiments(e1, e2);
+ context.checking(new Expectations()
+ {
+ {
+ one(experimentDAO).tryGetByTechId(new TechId(e1.getId()));
+ will(returnValue(e1));
+
+ one(externalDataDAO).listExternalData(e1);
+ ExternalDataPE ds1 = new ExternalDataPE();
+ ds1.setCode("ds1");
+ will(returnValue(Arrays.asList(ds1)));
+ }
+ });
+ prepareProcessDataSets(session, new HashMap<String, String>(), "ds1");
+
+ service.processSearchData(SESSION_TOKEN, COPY_PROCESSING_KEY, new long[] {e1.getId()});
+
+ context.assertIsSatisfied();
+ }
+
+
+ private Session createSessionAndPrepareGetSession(String spaceCode)
+ {
+ final Session session =
+ new Session(CommonTestUtils.USER_ID, SESSION_TOKEN, PRINCIPAL, "remote-host", 1);
+ PersonPE person = new PersonPE();
+ RoleAssignmentPE roleAssignmentPE = new RoleAssignmentPE();
+ GroupPE group = new GroupPE();
+ group.setCode(spaceCode);
+ group.setDatabaseInstance(CommonTestUtils.createHomeDatabaseInstance());
+ roleAssignmentPE.setGroup(group);
+ person.setRoleAssignments(new HashSet<RoleAssignmentPE>(Arrays.asList(roleAssignmentPE)));
+ session.setPerson(person);
+ context.checking(new Expectations()
+ {
+ {
+ allowing(sessionManager).getSession(SESSION_TOKEN);
+ will(returnValue(session));
+ }
+ });
+ return session;
+ }
+
+ private void prepareListSearchExperiments(final ExperimentPE... experiments)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(daoFactory).getEntityTypeDAO(EntityKind.EXPERIMENT);
+ will(returnValue(entityTypeDAO));
+
+ one(entityTypeDAO).tryToFindEntityTypeByCode(SEARCH_EXPERIMENT_TYPE);
+ will(returnValue(experimentType));
+
+ one(experimentDAO).listExperimentsWithProperties(experimentType, null);
+ will(returnValue(Arrays.asList(experiments)));
+ }
+ });
+ }
+
+ private void prepareProcessDataSets(final Session session,
+ final Map<String, String> parameterBindings, final String... dataSetCodes)
+ {
context.checking(new Expectations()
{
{
@@ -103,23 +274,16 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
DataStorePE s2 = store("s2", service(COPY_PROCESSING_KEY, PROCESSING));
will(returnValue(Arrays.asList(s1, s2)));
- one(boFactory).createExternalDataTable(SESSION);
+ one(boFactory).createExternalDataTable(session);
will(returnValue(externalDataTable));
- List<String> dataSetCodes = Arrays.asList("ds-2");
- HashMap<String, String> parameterBindings = new HashMap<String, String>();
- parameterBindings.put("ds-2", "s-2");
- one(externalDataTable).processDatasets(COPY_PROCESSING_KEY, "s2", dataSetCodes,
- parameterBindings);
+ one(externalDataTable).processDatasets(COPY_PROCESSING_KEY, "s2",
+ Arrays.asList(dataSetCodes), parameterBindings);
}
});
-
- service.processRawData(SESSION_TOKEN, COPY_PROCESSING_KEY, ids, "dt-0");
-
- context.assertIsSatisfied();
}
-
+
private void prepareListRawDataSamples(final Long... sampleIDs)
{
final List<Sample> samples = new ArrayList<Sample>();
@@ -200,6 +364,32 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
}
});
}
+
+ private ExperimentPE experiment(long id, String... properties)
+ {
+ ExperimentPE experiment = new ExperimentPE();
+ experiment.setExperimentType(experimentType);
+ experiment.setId(id);
+ experiment.setCode("e" + id);
+ ProjectPE project = new ProjectPE();
+ project.setCode("p");
+ GroupPE group = CommonTestUtils.createGroup(GROUP_CODE, CommonTestUtils.createHomeDatabaseInstance());
+ project.setGroup(group);
+ experiment.setProject(project);
+ experiment.setRegistrationDate(new Date(id * id));
+ if (properties.length > 0)
+ {
+ LinkedHashSet<EntityPropertyPE> props = new LinkedHashSet<EntityPropertyPE>();
+ for (String property : properties)
+ {
+ props.add(CommonTestUtils.createExperimentPropertyPE(property,
+ ProteomicsDataServiceInternal.SEARCH_EXPERIMENT_TYPE, DataTypeCode.VARCHAR,
+ property + "-value"));
+ }
+ experiment.setProperties(props);
+ }
+ return experiment;
+ }
private DataStorePE store(String code, DataStoreServicePE... services)
{
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/ProteomicsDataServiceTest.java
index f5f070864706c1e356e1d20f9bcd41b94cb4c425..df92f95740861676040455621372484ed7add076 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/ProteomicsDataServiceTest.java
@@ -17,12 +17,15 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
import java.io.Serializable;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
+import java.util.Map.Entry;
import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
@@ -35,10 +38,13 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
+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.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
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.generic.shared.basic.dto.Space;
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;
@@ -205,11 +211,81 @@ public class ProteomicsDataServiceTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- one(internalService).processRawData(session2.getSessionToken(), null, ids, "my-type");
+ one(internalService).processRawData(session2.getSessionToken(), "dsp1", ids, "my-type");
}
});
- service.processingRawData(SESSION_TOKEN, "abc", null, ids, "my-type");
+ service.processingRawData(SESSION_TOKEN, "abc", "dsp1", ids, "my-type");
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testListSearchExperiments()
+ {
+ prepareGetSession();
+ prepareLoginLogout(session2);
+ final Experiment e = new Experiment();
+ e.setId(42L);
+ e.setCode("E42");
+ Project project = new Project();
+ project.setCode("p");
+ Space space = new Space();
+ space.setCode("s");
+ project.setSpace(space);
+ e.setProject(project);
+ e.setRegistrationDate(new Date(4711));
+ EntityProperty p1 = new EntityProperty();
+ PropertyType propertyType = new PropertyType();
+ propertyType.setCode("ANSWER");
+ propertyType.setLabel("answer");
+ propertyType.setDataType(new DataType(DataTypeCode.INTEGER));
+ p1.setPropertyType(propertyType);
+ p1.setValue("42");
+ e.setProperties(Arrays.<IEntityProperty>asList(p1));
+ context.checking(new Expectations()
+ {
+ {
+ one(internalService).listSearchExperiments(session2.getSessionToken());
+ will(returnValue(Arrays.asList(e)));
+ }
+ });
+
+ List<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment> experiments =
+ service.listSearchExperiments(SESSION_TOKEN, "abc");
+
+ assertEquals(e.getId().longValue(), experiments.get(0).getId());
+ assertEquals(e.getCode(), experiments.get(0).getCode());
+ assertEquals(e.getProject().getCode(), experiments.get(0).getProjectCode());
+ assertEquals(e.getProject().getSpace().getCode(), experiments.get(0).getSpaceCode());
+ assertEquals(e.getRegistrationDate(), experiments.get(0).getRegistrationDate());
+ Map<PropertyKey, Serializable> properties = experiments.get(0).getProperties();
+ Set<Entry<PropertyKey, Serializable>> entrySet = properties.entrySet();
+ List<Entry<PropertyKey, Serializable>> list = new ArrayList<Entry<PropertyKey, Serializable>>(entrySet);
+ assertEquals(e.getProperties().get(0).getPropertyType().getCode(), list.get(0).getKey().getId());
+ assertEquals(e.getProperties().get(0).getPropertyType().getLabel(), list.get(0).getKey().getLabel());
+ Serializable value = list.get(0).getValue();
+ assertEquals(Long.class, value.getClass());
+ assertEquals(e.getProperties().get(0).getValue(), value.toString());
+ assertEquals(1, properties.size());
+ assertEquals(1, experiments.size());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testProcessSearchData()
+ {
+ prepareGetSession();
+ prepareLoginLogout(session2);
+ final long[] ids = new long[] {42};
+ context.checking(new Expectations()
+ {
+ {
+ one(internalService).processSearchData(session2.getSessionToken(), "dsp1", ids);
+ }
+ });
+
+ service.processSearchData(SESSION_TOKEN, "abc", "dsp1", ids);
context.assertIsSatisfied();
}