From 06d8f737c7af95bb94f83ae91e76f555a72e23af Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 18 Mar 2015 12:27:44 +0000
Subject: [PATCH] SSDM-1621: AssignDataSetToSampleTest: All tests refactored in
order to use EntityGraphGenerator.
SVN: 33685
---
.../business/bo/entitygraph/DataSetNode.java | 9 +
.../bo/entitygraph/EntityGraphGenerator.java | 1 +
.../systemtest/AssignDataSetToSampleTest.java | 390 ++++++++++++------
.../openbis/systemtest/base/BaseTest.java | 67 ++-
.../base/builder/DataSetUpdateBuilder.java | 10 +-
5 files changed, 330 insertions(+), 147 deletions(-)
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/DataSetNode.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/DataSetNode.java
index a4e25ff5e77..75870c97a87 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/DataSetNode.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/DataSetNode.java
@@ -100,6 +100,15 @@ public final class DataSetNode extends EntityNode
}
}
+ void hasParents(DataSetNode...someParentDataSets)
+ {
+ for (DataSetNode parentDataSet : someParentDataSets)
+ {
+ parents.add(parentDataSet);
+ parentDataSet.children.add(this);
+ }
+ }
+
@Override
public String toString()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityGraphGenerator.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityGraphGenerator.java
index dee614076a8..c837ef4e7a2 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityGraphGenerator.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityGraphGenerator.java
@@ -104,6 +104,7 @@ public final class EntityGraphGenerator
private void handle(DataSetNode dataSet, List<String> parts)
{
dataSet.hasChildren(getDataSets("children", parts));
+ dataSet.hasParents(getDataSets("parents", parts));
dataSet.hasComponents(getDataSets("components", parts));
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToSampleTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToSampleTest.java
index 189dc76ec01..b77b52059c9 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToSampleTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToSampleTest.java
@@ -20,11 +20,11 @@ import static org.hamcrest.CoreMatchers.is;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.fail;
-import org.testng.AssertJUnit;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.business.bo.entitygraph.DataSetNode;
import ch.systemsx.cisd.openbis.generic.server.business.bo.entitygraph.EntityGraphGenerator;
@@ -48,6 +48,7 @@ import ch.systemsx.cisd.openbis.systemtest.base.auth.SpaceDomain;
/**
* @author anttil
+ * @author Franz-Josef Elmer
*/
public class AssignDataSetToSampleTest extends BaseTest
{
@@ -64,30 +65,59 @@ public class AssignDataSetToSampleTest extends BaseTest
Space destinationSpace;
@Test
- public void containerWithAComponentOfWrongTypeReassignedFromExperimentToSampleWithoutExperiment()
+ public void reassignTheTwoOriginalDataSetsOfPublishedDataSetsToDifferentOriginalSampleAndExperiment()
{
- EntityGraphGenerator g = parseAndCreateGraph("E1, data sets: DS1[NECT] DS2\n"
- + "S2, data sets: DS5[NET]\n"
- + "DS1[NECT], components: DS2\n");
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS3 DS4 DS5 DS6\n"
+ + "E2, data sets: DS1 DS2\n"
+ + "E3, samples: S3\n"
+ + "S1, data sets: DS3\n"
+ + "DS1, components: DS3\n"
+ + "DS2, components: DS4\n"
+ + "DS3, components: DS5 DS6\n");
+
+ reassignToSample(g.ds(3), g.s(3));
+ reassignToExperiment(g.ds(4), g.e(3));
+
+ assertEquals("E1, samples: S1\n"
+ + "E2, data sets: DS1 DS2\n"
+ + "E3, samples: S3, data sets: DS3 DS4 DS5 DS6\n"
+ + "S3, data sets: DS3\n"
+ + "DS1, components: DS3\n"
+ + "DS2, components: DS4\n"
+ + "DS3, components: DS5 DS6\n", renderGraph(g));
+ repository.assertModified(g.e(1), g.e(3));
+ repository.assertModified(g.s(1), g.s(3));
+ repository.assertModified(g.ds(3), g.ds(4), g.ds(5), g.ds(6));
+ repository.assertUnmodified(g);
+ }
+
+ @Test
+ public void reassignTwoPublishedDataSetToAnotherPublicExperiment()
+ {
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS3 DS4 DS5 DS6\n"
+ + "E2, data sets: DS1 DS2\n"
+ + "E3\n"
+ + "S1, data sets: DS3\n"
+ + "DS1, components: DS3\n"
+ + "DS2, components: DS4\n"
+ + "DS3, components: DS5 DS6\n");
- try
- {
- reassignToSample(g.ds(1), g.s(2));
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- AbstractExternalData dataSet = repository.getDataSet(g.ds(2));
- assertEquals("The dataset '" + dataSet.getCode()
- + "' cannot be connected to the sample '" + repository.getSample(g.s(2)).getIdentifier()
- + "' because the new sample is not connected to any experiment and the data set type ("
- + dataSet.getDataSetType().getCode()
- + ") doesn't match one of the following regular expressions: NO-EXP-.* , NE.* .",
- ex.getMessage());
- }
+ reassignToExperiment(g.ds(1), g.e(3));
+ reassignToExperiment(g.ds(2), g.e(3));
+
+ assertEquals("E1, samples: S1, data sets: DS3 DS4 DS5 DS6\n"
+ + "E3, data sets: DS1 DS2\n"
+ + "S1, data sets: DS3\n"
+ + "DS1, components: DS3\n"
+ + "DS2, components: DS4\n"
+ + "DS3, components: DS5 DS6\n", renderGraph(g));
+ repository.assertModified(g.e(2), g.e(3));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
}
@Test
- public void containerWithSomeComponentsReassigned()
+ public void containerWithSomeComponentsReassignedFromSampleWithoutExperimentToSampleWithExperiment()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, data sets: DS4\n"
+ "E2, samples: S2\n"
@@ -96,15 +126,38 @@ public class AssignDataSetToSampleTest extends BaseTest
+ "DS1[NECT], components: DS2[NECT] DS3[NET]\n"
+ "DS2[NECT], components: DS4");
- reassignToExperiment(g.ds(1), g.e(2));
+ reassignToSample(g.ds(1), g.s(2));
assertEquals("E1, data sets: DS4\n"
+ "E2, samples: S2, data sets: DS1[NECT] DS2[NECT]\n"
+ + "S2, data sets: DS1[NECT] DS2[NECT]\n"
+ "S3, data sets: DS3[NET]\n"
+ "DS1[NECT], components: DS2[NECT] DS3[NET]\n"
+ "DS2[NECT], components: DS4\n", renderGraph(g));
repository.assertModified(g.e(2));
- repository.assertModified(g.s(1));
+ repository.assertModified(g.s(1), g.s(2));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
+ }
+
+ @Test
+ public void containerWithSomeComponentsReassignedFromSampleWithoutExperimentToSampleWithoutExperiment()
+ {
+ EntityGraphGenerator g = parseAndCreateGraph("E1, data sets: DS4\n"
+ + "S1, data sets: DS1[NECT] DS2[NECT]\n"
+ + "S2\n"
+ + "S3, data sets: DS3[NET]\n"
+ + "DS1[NECT], components: DS2[NECT] DS3[NET]\n"
+ + "DS2[NECT], components: DS4");
+
+ reassignToSample(g.ds(1), g.s(2));
+
+ assertEquals("E1, data sets: DS4\n"
+ + "S2, data sets: DS1[NECT] DS2[NECT]\n"
+ + "S3, data sets: DS3[NET]\n"
+ + "DS1[NECT], components: DS2[NECT] DS3[NET]\n"
+ + "DS2[NECT], components: DS4\n", renderGraph(g));
+ repository.assertModified(g.s(1), g.s(2));
repository.assertModified(g.ds(1), g.ds(2));
repository.assertUnmodified(g);
}
@@ -297,6 +350,7 @@ public class AssignDataSetToSampleTest extends BaseTest
repository.assertUnmodified(g);
}
+ // This is screening test case where one container data set is moved to another plate.
@Test
public void containerWithAllItsComponentsReassignedFromSampleWithExperimentToSampleWithExperiment()
{
@@ -387,145 +441,199 @@ public class AssignDataSetToSampleTest extends BaseTest
repository.assertUnmodified(g);
}
- @Test(expectedExceptions =
- { UserFailureException.class })
- public void dataSetCannotBeAssignedToSpaceSample() throws Exception
- {
- Sample sample = create(aSample().inSpace(destinationSpace));
- AbstractExternalData dataset = create(aDataSet().inSample(sourceSample));
-
- perform(anUpdateOf(dataset).toSample(sample));
- }
-
- @Test(expectedExceptions =
- { UserFailureException.class })
- public void dataSetCannotBeAssignedToSharedSample() throws Exception
- {
- Sample sample = create(aSample());
- AbstractExternalData dataset = create(aDataSet().inSample(sourceSample));
-
- perform(anUpdateOf(dataset).toSample(sample));
- }
-
@Test
- public void childDataSetCanBeAssignedToAnotherSample() throws Exception
+ public void containerWithAComponentOfWrongTypeReassignedFromExperimentToSampleWithoutExperiment()
{
- AbstractExternalData parent = create(aDataSet().inSample(sourceSample));
- AbstractExternalData child = create(aDataSet().inSample(sourceSample).withParent(parent));
-
- perform(anUpdateOf(child).toSample(destinationSample));
-
- assertThat(child, is(inSample(destinationSample)));
+ EntityGraphGenerator g = parseAndCreateGraph("E1, data sets: DS1[NECT] DS2\n"
+ + "S2, data sets: DS5[NET]\n"
+ + "DS1[NECT], components: DS2\n");
+
+ try
+ {
+ reassignToSample(g.ds(1), g.s(2));
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ AbstractExternalData dataSet = repository.getDataSet(g.ds(2));
+ Sample sample = repository.getSample(g.s(2));
+ assertDataSetToSampleExceptionMessage(ex, sample, dataSet);
+ }
}
-
+
@Test
- public void sampleAssignmentOfParentDataSetIsNotChangedWhenChildDataSetIsAssignedToAnotherSample()
- throws Exception
+ public void dataSetCannotBeAssignedToSpaceSample()
{
- AbstractExternalData parent = create(aDataSet().inSample(sourceSample));
- AbstractExternalData child = create(aDataSet().inSample(sourceSample).withParent(parent));
+ EntityGraphGenerator g = parseAndCreateGraph("E1, data sets: DS1\nS2\n");
- perform(anUpdateOf(child).toSample(destinationSample));
-
- assertThat(parent, is(inSample(sourceSample)));
+ try
+ {
+ reassignToSample(g.ds(1), g.s(2));
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ AbstractExternalData dataSet = repository.getDataSet(g.ds(1));
+ Sample sample = repository.getSample(g.s(2));
+ assertDataSetToSampleExceptionMessage(ex, sample, dataSet);
+ }
}
@Test
- public void parentDataSetCanBeAssignedToAnotherSample() throws Exception
+ public void dataSetCannotBeAssignedToSharedSample()
{
- AbstractExternalData parent = create(aDataSet().inSample(sourceSample));
- create(aDataSet().inSample(sourceSample).withParent(parent));
-
- perform(anUpdateOf(parent).toSample(destinationSample));
+ Sample sample = create(aSample());
+ AbstractExternalData dataset = create(aDataSet().inSample(sourceSample));
- assertThat(parent, is(inSample(destinationSample)));
+ try
+ {
+ String user = create(aSession().withInstanceRole(RoleCode.ADMIN));
+ reassignToSample(dataset.getCode(), sample.getPermId(), user);
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertDataSetToSampleExceptionMessage(ex, sample, dataset);
+ }
}
@Test
- public void sampleAssignmentOfChildDataSetIsNotChangedWhenParentDatasetIsAssignedToAnotherSample()
- throws Exception
+ public void sampleAssignmentOfParentDataSetIsNotChangedWhenChildDataSetIsAssignedToAnotherSample()
{
- AbstractExternalData parent = create(aDataSet().inSample(sourceSample));
- AbstractExternalData child = create(aDataSet().inSample(sourceSample).withParent(parent));
-
- perform(anUpdateOf(parent).toSample(destinationSample));
-
- assertThat(child, is(inSample(sourceSample)));
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1 DS2\n"
+ + "E2, samples: S2\n"
+ + "S1, data sets: DS1 DS2\n"
+ + "DS1, parents: DS2\n");
+
+ reassignToSample(g.ds(1), g.s(2));
+
+ assertEquals("E1, samples: S1, data sets: DS2\n"
+ + "E2, samples: S2, data sets: DS1\n"
+ + "S1, data sets: DS2\n"
+ + "S2, data sets: DS1\n"
+ + "DS1, parents: DS2\n", renderGraph(g));
+ repository.assertModified(g.e(1), g.e(2));
+ repository.assertModified(g.s(1), g.s(2));
+ repository.assertModified(g.ds(1));
+ repository.assertUnmodified(g);
}
@Test
- public void componentDataSetCanBeAssignedToAnotherSample() throws Exception
+ public void sampleAssignmentOfChildDataSetIsNotChangedWhenParentDatasetIsAssignedToAnotherSample()
{
- AbstractExternalData component = create(aDataSet().inSample(sourceSample));
- create(aDataSet().inSample(sourceSample).withComponent(component));
-
- perform(anUpdateOf(component).toSample(destinationSample));
-
- assertThat(component, is(inSample(destinationSample)));
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1 DS2\n"
+ + "E2, samples: S2\n"
+ + "S1, data sets: DS1 DS2\n"
+ + "DS1, parents: DS2\n");
+
+ reassignToSample(g.ds(2), g.s(2));
+
+ assertEquals("E1, samples: S1, data sets: DS1\n"
+ + "E2, samples: S2, data sets: DS2\n"
+ + "S1, data sets: DS1\n"
+ + "S2, data sets: DS2\n"
+ + "DS1, parents: DS2\n", renderGraph(g));
+ repository.assertModified(g.e(1), g.e(2));
+ repository.assertModified(g.s(1), g.s(2));
+ repository.assertModified(g.ds(2));
+ repository.assertUnmodified(g);
}
@Test
public void sampleAssignmentOfContainerDataSetIsNotChangedWhenComponentDataSetIsAssignedToAnotherSample()
- throws Exception
{
- AbstractExternalData component = create(aDataSet().inSample(sourceSample));
- AbstractExternalData container = create(aDataSet().inSample(sourceSample).withComponent(component));
-
- perform(anUpdateOf(component).toSample(destinationSample));
-
- assertThat(container, is(inSample(sourceSample)));
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1 DS2\n"
+ + "E2, samples: S2\n"
+ + "S1, data sets: DS1 DS2\n"
+ + "DS1, components: DS2\n");
+
+ reassignToSample(g.ds(2), g.s(2));
+
+ assertEquals("E1, samples: S1, data sets: DS1\n"
+ + "E2, samples: S2, data sets: DS2\n"
+ + "S1, data sets: DS1\n"
+ + "S2, data sets: DS2\n"
+ + "DS1, components: DS2\n", renderGraph(g));
+ repository.assertModified(g.e(1), g.e(2));
+ repository.assertModified(g.s(1), g.s(2));
+ repository.assertModified(g.ds(2));
+ repository.assertUnmodified(g);
}
@Test
- public void containerDataSetCanBeAssignedToAnotherSample() throws Exception
+ public void sampleAssignmentOfComponentDataSetIsChangedWhenContainerDataSetIsAssignedToAnotherSample()
{
- AbstractExternalData component = create(aDataSet().inSample(sourceSample));
- AbstractExternalData container = create(aDataSet().inSample(sourceSample).withComponent(component));
-
- perform(anUpdateOf(container).toSample(destinationSample));
-
- assertThat(container, is(inSample(destinationSample)));
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1 DS2\n"
+ + "E2, samples: S2\n"
+ + "S1, data sets: DS1 DS2\n"
+ + "DS1, components: DS2\n");
+
+ reassignToSample(g.ds(1), g.s(2));
+
+ assertEquals("E1, samples: S1\n"
+ + "E2, samples: S2, data sets: DS1 DS2\n"
+ + "S2, data sets: DS1 DS2\n"
+ + "DS1, components: DS2\n", renderGraph(g));
+ repository.assertModified(g.e(1), g.e(2));
+ repository.assertModified(g.s(1), g.s(2));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
}
@Test
- public void sampleAssignmentOfComponentDataSetIsNotChangedWhenContainerDataSetIsAssignedToAnotherSample()
- throws Exception
+ public void dataSetCanBeUnassignedFromSample()
{
- AbstractExternalData component = create(aDataSet().inSample(sourceSample));
- AbstractExternalData container = create(aDataSet().inSample(sourceSample).withComponent(component));
-
- perform(anUpdateOf(container).toSample(destinationSample));
-
- assertThat(component, is(inSample(sourceSample)));
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1\n"
+ + "S1, data sets: DS1\n");
+
+ reassignToSample(g.ds(1), null);
+
+ assertEquals("E1, samples: S1, data sets: DS1\n", renderGraph(g));
+ repository.assertModified(g.s(1));
+ repository.assertModified(g.ds(1));
+ repository.assertUnmodified(g);
}
- @Test
- public void dataSetCanBeUnassignedFromSample() throws Exception
+ private void assertDataSetToSampleExceptionMessage(UserFailureException ex, Sample sample, AbstractExternalData dataset)
{
- AbstractExternalData data = create(aDataSet().inSample(sourceSample));
-
- perform(anUpdateOf(data).removingSample());
-
- assertThat(data, hasNoSample());
- assertThat(data, is(inExperiment(sourceExperiment)));
+ String postfix = sample.getSpace() == null ? "shared." :
+ "not connected to any experiment and the data set type ("
+ + dataset.getDataSetType().getCode()
+ + ") doesn't match one of the following regular expressions: NO-EXP-.* , NE.* .";
+ assertEquals("The dataset '" + dataset.getCode()
+ + "' cannot be connected to the sample '" + sample.getIdentifier()
+ + "' because the new sample is " + postfix, ex.getMessage());
}
- private void reassignToExperiment(DataSetNode dataSetNode, ExperimentNode experimentNode)
+ private void reassignToExperiment(DataSetNode dataSetNode, ExperimentNode experimentNodeOrNull)
{
AbstractExternalData dataSet = getDataSet(dataSetNode);
- Experiment experiment = repository.getExperiment(experimentNode);
- reassignToExperiment(dataSet.getCode(), experiment.getIdentifier());
+ String experimentIdentifierOrNull = null;
+ if (experimentNodeOrNull != null)
+ {
+ Experiment experiment = repository.getExperiment(experimentNodeOrNull);
+ if (experiment == null)
+ {
+ throw new IllegalArgumentException("Unknown experiment " + experimentNodeOrNull.getCode());
+ }
+ experimentIdentifierOrNull = experiment.getIdentifier();
+ }
+ String user = create(aSession().withInstanceRole(RoleCode.ADMIN));
+ reassignToExperiment(dataSet.getCode(), experimentIdentifierOrNull, user);
}
- private void reassignToSample(DataSetNode dataSetNode, SampleNode sampleNode)
+ private void reassignToSample(DataSetNode dataSetNode, SampleNode sampleNodeOrNull)
{
AbstractExternalData dataSet = getDataSet(dataSetNode);
- Sample sample = repository.getSample(sampleNode);
- if (sample == null)
+ String permIdOrNull = null;
+ if (sampleNodeOrNull != null)
{
- throw new IllegalArgumentException("Unknown sample " + sampleNode.getCode());
+ Sample sample = repository.getSample(sampleNodeOrNull);
+ if (sample == null)
+ {
+ throw new IllegalArgumentException("Unknown sample " + sampleNodeOrNull.getCode());
+ }
+ permIdOrNull = sample.getPermId();
}
- reassignToSample(dataSet.getCode(), sample.getPermId());
+ String user = create(aSession().withInstanceRole(RoleCode.ADMIN));
+ reassignToSample(dataSet.getCode(), permIdOrNull, user);
}
private AbstractExternalData getDataSet(DataSetNode dataSetNode)
@@ -538,22 +646,42 @@ public class AssignDataSetToSampleTest extends BaseTest
return dataSet;
}
- protected void reassignToExperiment(String dataSetCode, String experimentIdentifier)
+ /**
+ * Reassign specified data set to specified experiment for the specified user.
+ * If experiment is not specified unassignment is meant.
+ * Sub class for testing API V3 should override this method.
+ */
+ protected void reassignToExperiment(String dataSetCode, String experimentIdentifierOrNull, String user)
{
AbstractExternalData dataSet = etlService.tryGetDataSet(systemSessionToken, dataSetCode);
- Experiment experiment = etlService.tryGetExperiment(systemSessionToken,
- ExperimentIdentifierFactory.parse(experimentIdentifier));
- String user = create(aSession().withInstanceRole(RoleCode.ADMIN));
- perform(anUpdateOf(dataSet).toExperiment(experiment).as(user));
+ if (experimentIdentifierOrNull != null)
+ {
+ Experiment experiment = etlService.tryGetExperiment(systemSessionToken,
+ ExperimentIdentifierFactory.parse(experimentIdentifierOrNull));
+ perform(anUpdateOf(dataSet).toExperiment(experiment).as(user));
+ } else
+ {
+ perform(anUpdateOf(dataSet).removingExperiment().as(user));
+ }
}
- protected void reassignToSample(String dataSetCode, String samplePermId)
+ /**
+ * Reassign specified data set to specified sample for the specified user.
+ * If sample is not specified unassignment is meant.
+ * Sub class for testing API V3 should override this method.
+ */
+ protected void reassignToSample(String dataSetCode, String samplePermIdOrNull, String user)
{
AbstractExternalData dataSet = etlService.tryGetDataSet(systemSessionToken, dataSetCode);
- SampleIdentifier sampleIdentifier = etlService.tryGetSampleIdentifier(systemSessionToken, samplePermId);
- Sample sample = etlService.tryGetSampleWithExperiment(systemSessionToken, sampleIdentifier);
- String user = create(aSession().withInstanceRole(RoleCode.ADMIN));
- perform(anUpdateOf(dataSet).toSample(sample).as(user));
+ if (samplePermIdOrNull != null)
+ {
+ SampleIdentifier sampleIdentifier = etlService.tryGetSampleIdentifier(systemSessionToken, samplePermIdOrNull);
+ Sample sample = etlService.tryGetSampleWithExperiment(systemSessionToken, sampleIdentifier);
+ perform(anUpdateOf(dataSet).toSample(sample).as(user));
+ } else
+ {
+ perform(anUpdateOf(dataSet).removingSample().as(user));
+ }
}
Space unrelatedAdmin;
@@ -562,7 +690,7 @@ public class AssignDataSetToSampleTest extends BaseTest
Space unrelatedNone;
-// @Test(dataProvider = "rolesAllowedToAssignDataSetToSample", groups = "authorization")
+ @Test(dataProvider = "rolesAllowedToAssignDataSetToSample", groups = "authorization")
public void assigningDataSetToSampleIsAllowedFor(RoleWithHierarchy sourceSpaceRole,
RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
throws Exception
@@ -575,11 +703,11 @@ public class AssignDataSetToSampleTest extends BaseTest
.withSpaceRole(RoleWithHierarchy.SPACE_ADMIN, unrelatedAdmin)
.withSpaceRole(RoleWithHierarchy.SPACE_OBSERVER, unrelatedObserver));
- perform(anUpdateOf(dataset).toSample(destinationSample).as(user));
+ reassignToSample(dataset.getCode(), destinationSample.getPermId(), user);
}
-// @Test(dataProvider = "rolesNotAllowedToAssignDataSetToSample", expectedExceptions =
-// { AuthorizationFailureException.class }, groups = "authorization")
+ @Test(dataProvider = "rolesNotAllowedToAssignDataSetToSample", expectedExceptions =
+ { AuthorizationFailureException.class }, groups = "authorization")
public void assigningDataSetToSampleIsNotAllowedFor(RoleWithHierarchy sourceSpaceRole,
RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
throws Exception
@@ -592,7 +720,7 @@ public class AssignDataSetToSampleTest extends BaseTest
.withSpaceRole(RoleWithHierarchy.SPACE_ADMIN, unrelatedAdmin)
.withSpaceRole(RoleWithHierarchy.SPACE_OBSERVER, unrelatedObserver));
- perform(anUpdateOf(dataset).toSample(destinationSample).as(user));
+ reassignToSample(dataset.getCode(), destinationSample.getPermId(), user);
}
@BeforeClass(dependsOnMethods = "loginAsSystem")
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/BaseTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/BaseTest.java
index 570825d19f5..a000f7cf834 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/BaseTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/BaseTest.java
@@ -538,6 +538,7 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
{
StringBuilder builder2 = new StringBuilder();
render(builder2, "components", repository.getComponentDataSetNodes(dataSetNode));
+ render(builder2, "parents", repository.getParentDataSetNodes(dataSetNode));
appendNodeTo(builder, dataSetNode, builder2);
}
return builder.toString();
@@ -571,20 +572,13 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
repository = new EntityRepository();
Space space = create(aSpace());
Project project = create(aProject().inSpace(space));
- for (ExperimentNode experimentNode : g.getExperiments().values())
- {
- addToRepository(experimentNode, create(anExperiment().inProject(project)));
- }
- for (SampleNode sampleNode : g.getSamples().values())
- {
- SampleBuilder sample = aSample().inSpace(space);
- ExperimentNode experimentNode = sampleNode.getExperiment();
- if (experimentNode != null)
- {
- sample.inExperiment(repository.getExperiment(experimentNode));
- }
- addToRepository(sampleNode, sample);
- }
+ createExperiments(project, g);
+ createSamples(space, g);
+ createDataSets(g);
+ }
+
+ private void createDataSets(EntityGraphGenerator g)
+ {
List<DataSetNode> dataSetNodes = new ArrayList<DataSetNode>(g.getDataSets().values());
Collections.reverse(dataSetNodes);
for (DataSetNode dataSetNode : dataSetNodes)
@@ -613,10 +607,44 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
dataSet.withComponent(componentDataSet);
}
}
+ List<DataSetNode> parents = dataSetNode.getParents();
+ for (DataSetNode parent : parents)
+ {
+ AbstractExternalData parentDataSet = repository.getDataSet(parent);
+ if (parentDataSet == null)
+ {
+ throw new IllegalStateException("Data set " + parent.getCode()
+ + " is specified as parent of " + dataSetNode.getCode()
+ + " but hasn't yet created.");
+ }
+ dataSet.withParent(parentDataSet);
+ }
addToRepository(dataSetNode, dataSet);
}
}
+ private void createSamples(Space space, EntityGraphGenerator g)
+ {
+ for (SampleNode sampleNode : g.getSamples().values())
+ {
+ SampleBuilder sample = aSample().inSpace(space);
+ ExperimentNode experimentNode = sampleNode.getExperiment();
+ if (experimentNode != null)
+ {
+ sample.inExperiment(repository.getExperiment(experimentNode));
+ }
+ addToRepository(sampleNode, sample);
+ }
+ }
+
+ private void createExperiments(Project project, EntityGraphGenerator g)
+ {
+ for (ExperimentNode experimentNode : g.getExperiments().values())
+ {
+ addToRepository(experimentNode, create(anExperiment().inProject(project)));
+ }
+ }
+
private void addToRepository(ExperimentNode experimentNode, Experiment experiment)
{
try
@@ -767,6 +795,7 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
private Map<Long, Set<Long>> experimentDataSetsMap = new HashMap<Long, Set<Long>>();
private Map<Long, Set<Long>> sampleDataSetsMap = new HashMap<Long, Set<Long>>();
private Map<Long, Set<Long>> componentDataSetsMap = new HashMap<Long, Set<Long>>();
+ private Map<Long, Set<Long>> parentsDataSetsMap = new HashMap<Long, Set<Long>>();
public String renderNodeToDtoMapping()
{
@@ -854,6 +883,11 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
{
addToDataSetsMap(componentDataSetsMap, dataSet, containerDataSet);
}
+ Collection<AbstractExternalData> parents = dataSet.getParents();
+ for (AbstractExternalData parentDataSet : parents)
+ {
+ addToDataSetsMap(parentsDataSetsMap, parentDataSet, dataSet);
+ }
}
if (showWhereIAm)
{
@@ -1017,6 +1051,11 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
return getDataSetNodes(componentDataSetsMap, dataSetsNodeToDtoMap.get(containerDataSetNode.getId()));
}
+ Set<DataSetNode> getParentDataSetNodes(DataSetNode childDataSetNode)
+ {
+ return getDataSetNodes(parentsDataSetsMap, dataSetsNodeToDtoMap.get(childDataSetNode.getId()));
+ }
+
private Set<DataSetNode> getDataSetNodes(Map<Long, Set<Long>> idHolderDataSetsMap, IIdHolder experiment)
{
Set<DataSetNode> result = new TreeSet<DataSetNode>();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/DataSetUpdateBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/DataSetUpdateBuilder.java
index 7a8dcb1e589..594788bc804 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/DataSetUpdateBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/DataSetUpdateBuilder.java
@@ -72,7 +72,7 @@ public class DataSetUpdateBuilder extends UpdateBuilder<DataSetUpdatesDTO>
public DataSetUpdateBuilder toSample(Sample sample)
{
-// toExperiment(sample.getExperiment());
+ toExperiment(sample.getExperiment());
this.sampleIdentifier = id(sample);
return this;
}
@@ -105,12 +105,18 @@ public class DataSetUpdateBuilder extends UpdateBuilder<DataSetUpdatesDTO>
return this;
}
+ public DataSetUpdateBuilder removingExperiment()
+ {
+ this.experimentIdentifier = null;
+ return this;
+ }
+
public DataSetUpdateBuilder removingSample()
{
this.sampleIdentifier = null;
return this;
}
-
+
public DataSetUpdateBuilder withContainer(AbstractExternalData dataSet)
{
this.containerCode = dataSet.getCode();
--
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