diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/SystemTestCase.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/SystemTestCase.java
index 75ad83ec4b183b7660568f8d4fb3ea9c25115d66..b45475f4ac5effde9c31300be9fbac7a46b2decd 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/SystemTestCase.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/SystemTestCase.java
@@ -52,7 +52,6 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.BeforeSuite;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.collection.IExtendedBlockingQueue;
import ch.systemsx.cisd.common.filesystem.QueueingPathRemoverService;
import ch.systemsx.cisd.common.logging.BufferedAppender;
import ch.systemsx.cisd.common.logging.LogCategory;
@@ -62,9 +61,7 @@ import ch.systemsx.cisd.etlserver.ETLDaemon;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
import ch.systemsx.cisd.openbis.dss.generic.server.DataStoreServer;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.DynamicPropertyEvaluationOperation;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.DynamicPropertyEvaluationScheduler;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search.FullTextIndexUpdater;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.util.UpdateUtils;
import ch.systemsx.cisd.openbis.generic.server.util.TestInitializer;
import ch.systemsx.cisd.openbis.generic.shared.Constants;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
@@ -384,39 +381,7 @@ public abstract class SystemTestCase extends AssertJUnit
protected void waitUntilIndexUpdaterIsIdle()
{
- FullTextIndexUpdater indexUpdater = (FullTextIndexUpdater) applicationContext.getBean("full-text-index-updater");
- DynamicPropertyEvaluationScheduler dynamicPropertyScheduler =
- (DynamicPropertyEvaluationScheduler) applicationContext.getBean("dynamic-property-scheduler");
-
- if (indexUpdater != null)
- {
- while (true)
- {
- IExtendedBlockingQueue<DynamicPropertyEvaluationOperation> dynamicPropertiesQueue = dynamicPropertyScheduler.getEvaluatorQueue();
- int indexingQueueSize = indexUpdater.getQueueSize();
-
- try
- {
- if (dynamicPropertiesQueue != null && dynamicPropertiesQueue.size() > 0)
- {
- operationLog.info("Waiting on dynamic properties updater. Still " + dynamicPropertiesQueue.size()
- + " update operations in the queue.");
- Thread.sleep(1000);
- } else if (indexingQueueSize > 0)
- {
- operationLog.info("Waiting on index updater. Still " + indexingQueueSize + " update operations in the queue.");
- Thread.sleep(1000);
- } else
- {
- return;
- }
- } catch (Exception ex)
- {
- // silently ignore
- return;
- }
- }
- }
+ UpdateUtils.waitUntilIndexUpdaterIsIdle(applicationContext, operationLog);
}
@SuppressWarnings("unchecked")
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/util/UpdateUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/util/UpdateUtils.java
new file mode 100644
index 0000000000000000000000000000000000000000..09f72fc67dbbdd1a739bb3e8f56decbe40cca3b6
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/util/UpdateUtils.java
@@ -0,0 +1,72 @@
+/*
+ * Copyright 2015 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.server.dataaccess.util;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.BeanFactory;
+
+import ch.systemsx.cisd.common.collection.IExtendedBlockingQueue;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.DynamicPropertyEvaluationOperation;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.DynamicPropertyEvaluationScheduler;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search.FullTextIndexUpdater;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class UpdateUtils
+{
+
+ public static void waitUntilIndexUpdaterIsIdle(BeanFactory applicationContext, Logger operationLog)
+ {
+ FullTextIndexUpdater indexUpdater = (FullTextIndexUpdater) applicationContext.getBean("full-text-index-updater");
+ DynamicPropertyEvaluationScheduler dynamicPropertyScheduler =
+ (DynamicPropertyEvaluationScheduler) applicationContext.getBean("dynamic-property-scheduler");
+
+ if (indexUpdater != null)
+ {
+ while (true)
+ {
+ IExtendedBlockingQueue<DynamicPropertyEvaluationOperation> dynamicPropertiesQueue = dynamicPropertyScheduler.getEvaluatorQueue();
+ int indexingQueueSize = indexUpdater.getQueueSize();
+
+ try
+ {
+ if (dynamicPropertiesQueue != null && dynamicPropertiesQueue.size() > 0)
+ {
+ operationLog.info("Waiting on dynamic properties updater. Still " + dynamicPropertiesQueue.size()
+ + " update operations in the queue.");
+ Thread.sleep(1000);
+ } else if (indexingQueueSize > 0)
+ {
+ operationLog.info("Waiting on index updater. Still " + indexingQueueSize + " update operations in the queue.");
+ Thread.sleep(1000);
+ } else
+ {
+ return;
+ }
+ } catch (Exception ex)
+ {
+ // silently ignore
+ return;
+ }
+ }
+ }
+ }
+
+}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/AbstractTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/AbstractTest.java
index 3caefafc445da78892fe1d7e4a9ade17f8370faf..069acb4fdf74ecb0759224954eb44ad92d65c5f2 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/AbstractTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/AbstractTest.java
@@ -630,15 +630,6 @@ public class AbstractTest extends SystemTestCase
}
}
- protected void assertNotOlder(Date actualDate, Date referenceDate)
- {
- SimpleDateFormat format = createTimestampFormat();
- String renderedReferenceDate = format.format(referenceDate.getTime());
- String renderedActualDate = format.format(actualDate);
- assertEquals(renderedReferenceDate.compareTo(renderedActualDate) <= 0, true,
- renderedActualDate + " > " + renderedReferenceDate);
- }
-
protected void assertEqualsDate(Date actualDate, String expectedDate)
{
assertEquals(createTimestampFormat().format(actualDate), expectedDate);
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ProjectSampleTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ProjectSampleTest.java
index 0a8f05a6754429136cff918ade6cca0f97792fdd..d63683d79ce2f4280ec22cf14d911fe33822cf2f 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ProjectSampleTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ProjectSampleTest.java
@@ -16,51 +16,176 @@
package ch.ethz.sis.openbis.systemtest.api.v3;
+import static junit.framework.Assert.fail;
import static org.testng.Assert.assertEquals;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.Map;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.transaction.TransactionConfiguration;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import ch.ethz.sis.openbis.generic.shared.api.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.experiment.ExperimentCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.project.Project;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.project.ProjectCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.Sample;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleUpdate;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.space.SpaceCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.fetchoptions.project.ProjectFetchOptions;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.fetchoptions.sample.SampleFetchOptions;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.EntityTypePermId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentIdentifier;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentPermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.IProjectId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectIdentifier;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectPermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SampleIdentifier;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SamplePermId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.ISpaceId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.SpacePermId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.search.SampleSearchCriteria;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.search.SearchResult;
import ch.systemsx.cisd.common.action.IDelegatedAction;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.util.UpdateUtils;
+import ch.systemsx.cisd.openbis.systemtest.base.BaseTest;
/**
*
*
* @author Franz-Josef Elmer
*/
+@TransactionConfiguration(transactionManager = "transaction-manager", defaultRollback = false)
@Test(groups = "project-samples")
-public class ProjectSampleTest extends AbstractTest
+public class ProjectSampleTest extends BaseTest
{
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, ProjectSampleTest.class);
+ private static final EntityTypePermId ENTITY_TYPE_UNKNOWN = new EntityTypePermId("UNKNOWN");
+ private static final String TEST_USER = "test";
+ private static final String PASSWORD = "password";
+
+ private static final String SYSTEM_USER = "system";
+ private static final String NOT_EXISTING_USER = "notexistinguser";
+ private static final String TEST_SPACE_USER = "test_space";
+ private static final String TEST_POWER_USER_CISD = "test_role";
+ private static final String TEST_GROUP_OBSERVER = "observer";
+
+ @Autowired
+ protected IApplicationServerApi v3api;
+
+ private SpacePermId space1;
+ private SpacePermId space2;
+ private ProjectPermId project1inSpace1;
+ private ProjectPermId project2inSpace1;
+ private ProjectPermId project1InSpace2;
+ private ProjectPermId project2InSpace2;
+ private ExperimentPermId experimentInProject1InSpace1;
+ private SamplePermId sharedSample1;
+ private SamplePermId sharedSample2;
+ private SamplePermId sample1InSpace1;
+ private SamplePermId sample2InSpace1;
+
+ @BeforeClass
+ public void createMasterData()
+ {
+ List<SpacePermId> spaces = createSpaces(systemSessionToken, "SPACE1", "SPACE2");
+ space1 = spaces.get(0);
+ space2 = spaces.get(1);
+ List<ProjectPermId> projects = createProjects(systemSessionToken, space1, "PROJECT1", "PROJECT2");
+ project1inSpace1 = projects.get(0);
+ project2inSpace1 = projects.get(1);
+ project1InSpace2 = createProjects(systemSessionToken, space2, "PROJECT1").get(0);
+ project2InSpace2 = createProjects(systemSessionToken, space2, "PROJECT2").get(0);
+ }
+
+ @BeforeMethod
+ @Test(enabled = false)
+ public void createSomeEntities()
+ {
+ experimentInProject1InSpace1 = createExperiments(systemSessionToken, project1inSpace1, "EXP1").get(0);
+ List<SamplePermId> sharedSamples = createSamples(systemSessionToken, null, null, "SHARED1", "SHARED2");
+ sharedSample1 = sharedSamples.get(0);
+ sharedSample2 = sharedSamples.get(1);
+ List<SamplePermId> spaceSamples = createSamples(systemSessionToken, space1, null, "SAMPLE1", "SAMPLE2");
+ sample1InSpace1 = spaceSamples.get(0);
+ sample2InSpace1 = spaceSamples.get(1);
+ waitAtLeastASecond(); // to allow checks on modification time stamps
+ UpdateUtils.waitUntilIndexUpdaterIsIdle(applicationContext, operationLog);
+ System.err.println("Test data created");
+ }
+
+ private List<SpacePermId> createSpaces(String sessionToken, String...spaceCodes)
+ {
+ List<SpaceCreation> newSpaces = new ArrayList<SpaceCreation>();
+ for (String spaceCode : spaceCodes)
+ {
+ SpaceCreation space = new SpaceCreation();
+ space.setCode(spaceCode);
+ newSpaces.add(space);
+ }
+ return v3api.createSpaces(sessionToken, newSpaces);
+ }
+
+ private List<ProjectPermId> createProjects(String sessionToken, ISpaceId spaceId, String...projectCodes)
+ {
+ List<ProjectCreation> newProjects = new ArrayList<ProjectCreation>();
+ for (String projectCode : projectCodes)
+ {
+ ProjectCreation project = new ProjectCreation();
+ project.setSpaceId(spaceId);
+ project.setCode(projectCode);
+ newProjects.add(project);
+ }
+ return v3api.createProjects(sessionToken, newProjects);
+ }
+
+ private List<ExperimentPermId> createExperiments(String sessionToken, IProjectId projectId, String...experimentCodes)
+ {
+ List<ExperimentCreation> newExperiments = new ArrayList<ExperimentCreation>();
+ for (String code : experimentCodes)
+ {
+ ExperimentCreation experiment = new ExperimentCreation();
+ experiment.setTypeId(ENTITY_TYPE_UNKNOWN);
+ experiment.setProjectId(projectId);
+ experiment.setCode(code);
+ newExperiments.add(experiment);
+ }
+ return v3api.createExperiments(sessionToken, newExperiments);
+ }
+
+ private List<SamplePermId> createSamples(String sessionToken, ISpaceId spaceOrNull, IProjectId projectOrNull, String...codes)
+ {
+ List<SampleCreation> newSamples = new ArrayList<SampleCreation>();
+ for (String code : codes)
+ {
+ SampleCreation sample = new SampleCreation();
+ sample.setTypeId(ENTITY_TYPE_UNKNOWN);
+ sample.setSpaceId(spaceOrNull);
+ sample.setProjectId(projectOrNull);
+ sample.setCode(code);
+ newSamples.add(sample);
+ }
+ return v3api.createSamples(sessionToken, newSamples);
+ }
+
@Test
public void testCreateSampleAndMapSamples()
{
+ String sampleCode = createUniqueCode();
SampleCreation sampleCreation = new SampleCreation();
- sampleCreation.setCode("PROJECT-SAMPLE");
- sampleCreation.setTypeId(new EntityTypePermId("CELL_PLATE"));
- sampleCreation.setSpaceId(new SpacePermId("CISD"));
- ProjectIdentifier projectId = new ProjectIdentifier("/CISD/NEMO");
- sampleCreation.setProjectId(projectId);
+ sampleCreation.setCode(sampleCode);
+ sampleCreation.setTypeId(ENTITY_TYPE_UNKNOWN);
+ sampleCreation.setSpaceId(space1);
+ sampleCreation.setProjectId(project1inSpace1);
List<SamplePermId> ids = v3api.createSamples(systemSessionToken, Arrays.asList(sampleCreation));
@@ -68,48 +193,47 @@ public class ProjectSampleTest extends AbstractTest
fetchOptions.withProject();
Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, ids, fetchOptions);
Sample sample = samples.get(ids.get(0));
- assertProjectIdentifiers(Arrays.asList(sample.getProject()), projectId.getIdentifier());
+ assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/" + sampleCode);
+ assertEquals(sample.getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1");
}
@Test
public void testCreateThreeSamplesWithSameCodeInDifferentProjectOfSameSpace()
{
+ String sampleCode = createUniqueCode();
SampleCreation s1 = new SampleCreation();
- s1.setCode("S1");
- s1.setTypeId(new EntityTypePermId("CELL_PLATE"));
- s1.setSpaceId(new SpacePermId("CISD"));
- ProjectIdentifier projectId1 = new ProjectIdentifier("/CISD/NEMO");
- s1.setProjectId(projectId1);
+ s1.setCode(sampleCode);
+ s1.setTypeId(ENTITY_TYPE_UNKNOWN);
+ s1.setSpaceId(space1);
+ s1.setProjectId(project1inSpace1);
SampleCreation s2 = new SampleCreation();
- s2.setCode("S1");
- s2.setTypeId(new EntityTypePermId("CELL_PLATE"));
- s2.setSpaceId(new SpacePermId("CISD"));
- ProjectIdentifier projectId2 = new ProjectIdentifier("/CISD/NOE");
- s2.setProjectId(projectId2);
+ s2.setCode(sampleCode);
+ s2.setTypeId(ENTITY_TYPE_UNKNOWN);
+ s2.setSpaceId(space1);
+ s2.setProjectId(project2inSpace1);
SampleCreation s3 = new SampleCreation();
- s3.setCode("S1");
- s3.setTypeId(new EntityTypePermId("CELL_PLATE"));
- s3.setSpaceId(new SpacePermId("CISD"));
+ s3.setCode(sampleCode);
+ s3.setTypeId(ENTITY_TYPE_UNKNOWN);
+ s3.setSpaceId(space1);
List<SamplePermId> ids = v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2, s3));
SampleFetchOptions fetchOptions = new SampleFetchOptions();
fetchOptions.withProject();
Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, ids, fetchOptions);
- assertEquals(samples.get(ids.get(0)).getProject().getIdentifier().toString(), "/CISD/NEMO");
- assertEquals(samples.get(ids.get(1)).getProject().getIdentifier().toString(), "/CISD/NOE");
+ assertEquals(samples.get(ids.get(0)).getProject().getIdentifier().toString(), "/SPACE1/PROJECT1");
+ assertEquals(samples.get(ids.get(1)).getProject().getIdentifier().toString(), "/SPACE1/PROJECT2");
assertEquals(samples.get(ids.get(2)).getProject(), null);
-
}
-
+
@Test
public void testAssignSpaceSampleToAProject()
{
+ String sampleCode = createUniqueCode();
+ SamplePermId spaceSample = createSamples(systemSessionToken, space1, null, sampleCode).get(0);
SampleUpdate sampleUpdate = new SampleUpdate();
- SampleIdentifier sampleId = new SampleIdentifier("/CISD/C1");
- sampleUpdate.setSampleId(sampleId);
- ProjectIdentifier projectId = new ProjectIdentifier("/CISD/NEMO");
- sampleUpdate.setProjectId(projectId);
+ sampleUpdate.setSampleId(spaceSample);
+ sampleUpdate.setProjectId(project1inSpace1);
Date now = new Date();
v3api.updateSamples(systemSessionToken, Arrays.asList(sampleUpdate));
@@ -117,25 +241,23 @@ public class ProjectSampleTest extends AbstractTest
SampleFetchOptions fetchOptions = new SampleFetchOptions();
fetchOptions.withSpace();
fetchOptions.withProject();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(sampleId), fetchOptions);
- Sample sample = samples.get(sampleId);
+ Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(spaceSample), fetchOptions);
+ Sample sample = samples.get(spaceSample);
assertNotOlder(sample.getModificationDate(), now);
- assertSpaceCodes(Arrays.asList(sample.getSpace()), "CISD");
+ assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/" + sampleCode);
Project project = sample.getProject();
- assertProjectIdentifiers(Arrays.asList(project), projectId.getIdentifier());
+ assertEquals(project.getIdentifier().getIdentifier(), "/SPACE1/PROJECT1");
assertNotOlder(project.getModificationDate(), now);
}
@Test
public void testAssignProjectSampleToADifferentProjectInTheSameSpace()
{
+ String sampleCode = createUniqueCode();
+ SamplePermId spaceSample = createSamples(systemSessionToken, space1, project1inSpace1, sampleCode).get(0);
SampleUpdate sampleUpdate = new SampleUpdate();
- SampleIdentifier sampleId = new SampleIdentifier("/CISD/C1");
- sampleUpdate.setSampleId(sampleId);
- sampleUpdate.setProjectId(new ProjectIdentifier("/CISD/NEMO"));
- v3api.updateSamples(systemSessionToken, Arrays.asList(sampleUpdate));
- ProjectIdentifier projectId = new ProjectIdentifier("/CISD/NOE");
- sampleUpdate.setProjectId(projectId);
+ sampleUpdate.setSampleId(spaceSample);
+ sampleUpdate.setProjectId(project2inSpace1);
Date now = new Date();
v3api.updateSamples(systemSessionToken, Arrays.asList(sampleUpdate));
@@ -143,28 +265,24 @@ public class ProjectSampleTest extends AbstractTest
SampleFetchOptions fetchOptions = new SampleFetchOptions();
fetchOptions.withSpace();
fetchOptions.withProject();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(sampleId), fetchOptions);
- Sample sample = samples.get(sampleId);
+ Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(spaceSample), fetchOptions);
+ Sample sample = samples.get(spaceSample);
assertNotOlder(sample.getModificationDate(), now);
- assertSpaceCodes(Arrays.asList(sample.getSpace()), "CISD");
+ assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/PROJECT2/" + sampleCode);
Project project = sample.getProject();
- assertProjectIdentifiers(Arrays.asList(project), projectId.getIdentifier());
+ assertEquals(project.getIdentifier().getIdentifier(), "/SPACE1/PROJECT2");
assertNotOlder(project.getModificationDate(), now);
- Map<IProjectId, Project> projects = v3api.mapProjects(systemSessionToken, Arrays.asList(projectId),
- new ProjectFetchOptions());
- assertNotOlder(projects.values().iterator().next().getModificationDate(), now);
}
@Test
- public void testAssignProjectSampleToADifferentProjectInADifferentSpace()
+ public void testAssignProjectSampleToAProjectInADifferentSpace()
{
+ String sampleCode = createUniqueCode();
+ SamplePermId spaceSample = createSamples(systemSessionToken, space1, project1inSpace1, sampleCode).get(0);
SampleUpdate sampleUpdate = new SampleUpdate();
- SampleIdentifier sampleId = new SampleIdentifier("/CISD/C1");
- sampleUpdate.setSampleId(sampleId);
- sampleUpdate.setProjectId(new ProjectIdentifier("/CISD/NEMO"));
- v3api.updateSamples(systemSessionToken, Arrays.asList(sampleUpdate));
- sampleUpdate.setSpaceId(new SpacePermId("TEST-SPACE"));
- sampleUpdate.setProjectId(new ProjectIdentifier("/TEST-SPACE/NOE"));
+ sampleUpdate.setSampleId(spaceSample);
+ sampleUpdate.setSpaceId(space2);
+ sampleUpdate.setProjectId(project1InSpace2);
Date now = new Date();
v3api.updateSamples(systemSessionToken, Arrays.asList(sampleUpdate));
@@ -172,27 +290,22 @@ public class ProjectSampleTest extends AbstractTest
SampleFetchOptions fetchOptions = new SampleFetchOptions();
fetchOptions.withSpace();
fetchOptions.withProject();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken,
- Arrays.asList(new SampleIdentifier("/TEST-SPACE/C1")), fetchOptions);
- Sample sample = samples.values().iterator().next();
+ Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(spaceSample), fetchOptions);
+ Sample sample = samples.get(spaceSample);
assertNotOlder(sample.getModificationDate(), now);
- assertSpaceCodes(Arrays.asList(sample.getSpace()), "TEST-SPACE");
+ assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE2/PROJECT1/" + sampleCode);
Project project = sample.getProject();
- assertProjectIdentifiers(Arrays.asList(project), new ProjectIdentifier("/TEST-SPACE/NOE").getIdentifier());
+ assertEquals(project.getIdentifier().getIdentifier(), "/SPACE2/PROJECT1");
assertNotOlder(project.getModificationDate(), now);
- Map<IProjectId, Project> projects = v3api.mapProjects(systemSessionToken,
- Arrays.asList(new ProjectIdentifier("/CISD/NEMO")), new ProjectFetchOptions());
- assertNotOlder(projects.values().iterator().next().getModificationDate(), now);
}
@Test
public void testUnassignProjectSampleFromProject()
{
+ String sampleCode = createUniqueCode();
+ SamplePermId spaceSample = createSamples(systemSessionToken, space1, project1inSpace1, sampleCode).get(0);
SampleUpdate sampleUpdate = new SampleUpdate();
- SampleIdentifier sampleId = new SampleIdentifier("/CISD/C1");
- sampleUpdate.setSampleId(sampleId);
- sampleUpdate.setProjectId(new ProjectIdentifier("/CISD/NEMO"));
- v3api.updateSamples(systemSessionToken, Arrays.asList(sampleUpdate));
+ sampleUpdate.setSampleId(spaceSample);
sampleUpdate.setProjectId(null);
Date now = new Date();
@@ -201,112 +314,105 @@ public class ProjectSampleTest extends AbstractTest
SampleFetchOptions fetchOptions = new SampleFetchOptions();
fetchOptions.withSpace();
fetchOptions.withProject();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken,
- Arrays.asList(new SampleIdentifier("/CISD/C1")), fetchOptions);
- Sample sample = samples.values().iterator().next();
+ Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(spaceSample), fetchOptions);
+ Sample sample = samples.get(spaceSample);
assertNotOlder(sample.getModificationDate(), now);
- assertSpaceCodes(Arrays.asList(sample.getSpace()), "CISD");
+ assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + sampleCode);
Project project = sample.getProject();
assertEquals(project, null);
Map<IProjectId, Project> projects = v3api.mapProjects(systemSessionToken,
- Arrays.asList(new ProjectIdentifier("/CISD/NEMO")), new ProjectFetchOptions());
+ Arrays.asList(project1inSpace1), new ProjectFetchOptions());
assertNotOlder(projects.values().iterator().next().getModificationDate(), now);
}
@Test
public void testCreateWithProjectAndSpaceInconsistent()
{
- final String sessionToken = v3api.login(TEST_USER, PASSWORD);
-
final SampleCreation creation = new SampleCreation();
creation.setCode("SAMPLE_WITH_INCONSISTENT_PROJECT_AND_SPACE");
- creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
- creation.setSpaceId(new SpacePermId("TEST-SPACE"));
- creation.setProjectId(new ProjectIdentifier("/CISD/NEMO"));
+ creation.setTypeId(ENTITY_TYPE_UNKNOWN);
+ creation.setSpaceId(space1);
+ creation.setProjectId(project1InSpace2);
assertUserFailureException(new IDelegatedAction()
{
@Override
public void execute()
{
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ v3api.createSamples(systemSessionToken, Collections.singletonList(creation));
}
- }, "Sample space must be the same as project space");
+ }, "Sample space must be the same as project space. "
+ + "Sample: /SPACE1/SAMPLE_WITH_INCONSISTENT_PROJECT_AND_SPACE, "
+ + "Project: /SPACE2/PROJECT1 "
+ + "(Context: [verify project for sample SAMPLE_WITH_INCONSISTENT_PROJECT_AND_SPACE])");
}
-
+
@Test
public void testCreateWithProjectAndNoSpaceInconsistent()
{
- final String sessionToken = v3api.login(TEST_USER, PASSWORD);
-
final SampleCreation creation = new SampleCreation();
creation.setCode("SAMPLE_WITH_INCONSISTENT_PROJECT_AND_NOSPACE");
- creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
- creation.setProjectId(new ProjectIdentifier("/CISD/NEMO"));
+ creation.setTypeId(ENTITY_TYPE_UNKNOWN);
+ creation.setProjectId(project1inSpace1);
assertUserFailureException(new IDelegatedAction()
{
@Override
public void execute()
{
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ v3api.createSamples(systemSessionToken, Collections.singletonList(creation));
}
}, "Shared samples cannot be attached to projects. "
- + "Sample: /SAMPLE_WITH_INCONSISTENT_PROJECT_AND_NOSPACE, "
- + "Project: /CISD/NEMO "
- + "(Context: [verify project for sample SAMPLE_WITH_INCONSISTENT_PROJECT_AND_NOSPACE])");
+ + "Sample: /SAMPLE_WITH_INCONSISTENT_PROJECT_AND_NOSPACE, "
+ + "Project: /SPACE1/PROJECT1 "
+ + "(Context: [verify project for sample SAMPLE_WITH_INCONSISTENT_PROJECT_AND_NOSPACE])");
}
@Test
public void testCreateWithProjectAndExperimentInconsistent()
{
- final String sessionToken = v3api.login(TEST_USER, PASSWORD);
-
final SampleCreation creation = new SampleCreation();
creation.setCode("SAMPLE_WITH_INCONSISTENT_PROJECT_AND_EXPERIMENT");
- creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
- creation.setSpaceId(new SpacePermId("CISD"));
- creation.setProjectId(new ProjectIdentifier("/CISD/NOE"));
- creation.setExperimentId(new ExperimentIdentifier("/CISD/NEMO/EXP1"));
+ creation.setTypeId(ENTITY_TYPE_UNKNOWN);
+ creation.setSpaceId(space2);
+ creation.setProjectId(project2inSpace1);
+ creation.setExperimentId(experimentInProject1InSpace1);
assertUserFailureException(new IDelegatedAction()
{
@Override
public void execute()
{
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ v3api.createSamples(systemSessionToken, Collections.singletonList(creation));
}
}, "Sample project must be the same as experiment project. "
- + "Sample: /CISD/SAMPLE_WITH_INCONSISTENT_PROJECT_AND_EXPERIMENT, "
- + "Project: /CISD/NOE, "
- + "Experiment: /CISD/NEMO/EXP1 "
+ + "Sample: /SPACE2/SAMPLE_WITH_INCONSISTENT_PROJECT_AND_EXPERIMENT, "
+ + "Project: /SPACE2/PROJECT1, "
+ + "Experiment: /SPACE1/PROJECT1/EXP1 "
+ "(Context: [verify experiment for sample SAMPLE_WITH_INCONSISTENT_PROJECT_AND_EXPERIMENT])");
}
@Test
public void testAssignSpaceSampleToProjectInDifferentSpace()
{
- final String sessionToken = v3api.login(TEST_USER, PASSWORD);
-
final SampleUpdate sampleUpdate = new SampleUpdate();
- SampleIdentifier sampleId = new SampleIdentifier("/CISD/C1");
- sampleUpdate.setSampleId(sampleId);
- ProjectIdentifier projectId = new ProjectIdentifier("/TEST-SPACE/NOE");
- sampleUpdate.setProjectId(projectId);
+ sampleUpdate.setSampleId(sample1InSpace1);
+ sampleUpdate.setProjectId(project2InSpace2);
assertUserFailureException(new IDelegatedAction()
{
@Override
public void execute()
{
- v3api.updateSamples(sessionToken, Collections.singletonList(sampleUpdate));
+ v3api.updateSamples(systemSessionToken, Collections.singletonList(sampleUpdate));
}
}, "Sample space must be the same as project space. "
- + "Sample: /CISD/C1, "
- + "Project: /TEST-SPACE/NOE "
- + "(Context: [verify project for sample C1])");
+ + "Sample: /SPACE1/SAMPLE1, "
+ + "Project: /SPACE2/PROJECT2 "
+ + "(Context: [verify project for sample SAMPLE1])");
}
+ /*
@Test
public void testAssignSampleOfAnExperimentToProjectDifferentToTheExperimentProject()
{
@@ -434,5 +540,41 @@ public class ProjectSampleTest extends AbstractTest
assertEquals(result.getObjects().get(0).getProject(), null);
assertEquals(result.getTotalCount(), 1);
}
+*/
+ private void assertUserFailureException(IDelegatedAction action, String expectedExceptionMessage)
+ {
+ try
+ {
+ action.execute();
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals(ex.getMessage(), expectedExceptionMessage);
+ }
+ }
+
+ private void assertNotOlder(Date actualDate, Date referenceDate)
+ {
+ SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
+ String renderedReferenceDate = format.format(referenceDate.getTime());
+ String renderedActualDate = format.format(actualDate);
+ assertEquals(renderedReferenceDate.compareTo(renderedActualDate) <= 0, true,
+ renderedActualDate + " > " + renderedReferenceDate);
+ }
+ private String createUniqueCode()
+ {
+ return "S-" + System.currentTimeMillis();
+ }
+
+ private void waitAtLeastASecond()
+ {
+ try
+ {
+ Thread.sleep(1100);
+ } catch (InterruptedException ex)
+ {
+ // silently ignored
+ }
+ }
}