diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentTest.java
index 23138a572a5fc107b17fd8fe17dd70feb6e1247d..ce02933411fd0e9c8347d7a2ab86d39a54c8c356 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentTest.java
@@ -16,14 +16,15 @@
package ch.systemsx.cisd.openbis.systemtest;
-import static org.hamcrest.CoreMatchers.is;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.fail;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
@@ -31,7 +32,6 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.business.bo.entitygraph.EntityGraphGenerator;
import ch.systemsx.cisd.openbis.generic.server.business.bo.entitygraph.ExperimentNode;
import ch.systemsx.cisd.openbis.generic.server.business.bo.entitygraph.SampleNode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
@@ -45,6 +45,7 @@ import ch.systemsx.cisd.openbis.systemtest.base.BaseTest;
import ch.systemsx.cisd.openbis.systemtest.base.auth.AuthorizationRule;
import ch.systemsx.cisd.openbis.systemtest.base.auth.GuardedDomain;
import ch.systemsx.cisd.openbis.systemtest.base.auth.InstanceDomain;
+import ch.systemsx.cisd.openbis.systemtest.base.auth.RolePermutator;
import ch.systemsx.cisd.openbis.systemtest.base.auth.SpaceDomain;
/**
@@ -175,7 +176,22 @@ public class AssignSampleToExperimentTest extends BaseTest
assertModified(g.s(1));
assertModified(g.ds(1));
assertUnmodified(g);
+ }
+
+ @Test
+ public void registerExperimentWithSampleInDifferentSpace()
+ {
+ EntityGraphGenerator g = parseAndCreateGraph("/S1/S1\n");
+ try
+ {
+ registerExperimentWithSamples(g.e(1), g.s(1));
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Sample '" + entityGraphManager.getSample(g.s(1)).getIdentifier()
+ + "' does not belong to the space 'S0'", ex.getMessage());
+ }
}
@Test
@@ -271,7 +287,7 @@ public class AssignSampleToExperimentTest extends BaseTest
}
@Test
- public void addSampleToAnExperimentFailingBecauseSampleHasAlreadyAnExperiment() throws Exception
+ public void addSampleToAnExperimentFailingBecauseSampleHasAlreadyAnExperiment()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1\n"
+ "E2\n");
@@ -289,7 +305,7 @@ public class AssignSampleToExperimentTest extends BaseTest
}
@Test
- public void assignSampleToAnotherExperiment() throws Exception
+ public void assignSampleToAnotherExperiment()
{
EntityGraphGenerator g = parseAndCreateGraph("/S1/P1/E1, samples: /S1/S1\n"
+ "/S2/P2/E2\n");
@@ -303,7 +319,7 @@ public class AssignSampleToExperimentTest extends BaseTest
}
@Test
- public void dataSetsOfSampleAreAssociatedWithNewExperiment() throws Exception
+ public void dataSetsOfSampleAreAssociatedWithNewExperiment()
{
EntityGraphGenerator g = parseAndCreateGraph("/S1/P1/E1, samples: /S1/S1, data sets: DS1\n"
+ "/S1/S1, data sets: DS1\n"
@@ -320,7 +336,7 @@ public class AssignSampleToExperimentTest extends BaseTest
}
@Test
- public void spaceSampleCanBeAssignedToExperiment() throws Exception
+ public void spaceSampleCanBeAssignedToExperiment()
{
EntityGraphGenerator g = parseAndCreateGraph("/S2/P1/E1\n"
+ "/S1/S1\n");
@@ -334,7 +350,7 @@ public class AssignSampleToExperimentTest extends BaseTest
}
@Test
- public void spaceSampleCanNotBeAddedToExperimentFromAnotherSpace() throws Exception
+ public void spaceSampleCanNotBeAddedToExperimentFromAnotherSpace()
{
EntityGraphGenerator g = parseAndCreateGraph("/S2/P1/E1\n"
+ "/S1/S1\n");
@@ -351,7 +367,7 @@ public class AssignSampleToExperimentTest extends BaseTest
}
@Test
- public void spaceSamplesCanBeAddedToExperimentInSameSpace() throws Exception
+ public void spaceSamplesCanBeAddedToExperimentInSameSpace()
{
EntityGraphGenerator g = parseAndCreateGraph("/S1/P1/E1\n"
+ "/S1/S1\n"
@@ -366,7 +382,7 @@ public class AssignSampleToExperimentTest extends BaseTest
}
@Test
- public void sharedSampleCanBeAssignedToExperiment() throws Exception
+ public void sharedSampleCanBeAssignedToExperiment()
{
EntityGraphGenerator g = parseAndCreateGraph("/S2/P1/E1\n"
+ "/S1\n");
@@ -380,160 +396,106 @@ public class AssignSampleToExperimentTest extends BaseTest
}
@Test
- public void childSampleCanBeAssignedToAnotherExperiment() throws Exception
- {
- Sample parent = create(aSample().inExperiment(sourceExperiment));
- Sample child = create(aSample().withParent(parent).inExperiment(sourceExperiment));
-
- perform(anUpdateOf(child).toExperiment(destinationExperiment));
-
- assertThat(child, is(inExperiment(destinationExperiment)));
- assertThat(child, is(inSpace(destinationSpace)));
- }
-
- @Test
- public void experimentAssignmentOfParentSampleIsNotChangedWhenChildSampleIsAssignedToAnotherExperiment()
- throws Exception
- {
- Sample parent = create(aSample().inExperiment(sourceExperiment));
- Sample child = create(aSample().withParent(parent).inExperiment(sourceExperiment));
-
- perform(anUpdateOf(child).toExperiment(destinationExperiment));
-
- assertThat(parent, is(inExperiment(sourceExperiment)));
- assertThat(parent, is(inSpace(sourceSpace)));
- }
-
- @Test
- public void parentSampleCanBeAssignedToAnotherExperiment() throws Exception
- {
- Sample parent = create(aSample().inExperiment(sourceExperiment));
- create(aSample().withParent(parent).inExperiment(sourceExperiment));
-
- perform(anUpdateOf(parent).toExperiment(destinationExperiment));
-
- assertThat(parent, is(inExperiment(destinationExperiment)));
- assertThat(parent, is(inSpace(destinationSpace)));
- }
-
- @Test
- public void experimentAssignmentOfChildSampleIsNotChangedWhenParentSampleIsAssignmedToAnotherExperiment()
- throws Exception
- {
- Sample parent = create(aSample().inExperiment(sourceExperiment));
- Sample child = create(aSample().withParent(parent).inExperiment(sourceExperiment));
-
- perform(anUpdateOf(parent).toExperiment(destinationExperiment));
-
- assertThat(child, is(inExperiment(sourceExperiment)));
- assertThat(child, is(inSpace(sourceSpace)));
- }
-
- @Test
- public void componentSampleCanBeAssignedToAnotherExperiment() throws Exception
+ public void childSampleCanBeAssignedToAnotherExperiment()
{
- Sample container = create(aSample().inExperiment(sourceExperiment));
- Sample component = create(aSample().inContainer(container).inExperiment(sourceExperiment));
-
- perform(anUpdateOf(component).toExperiment(destinationExperiment));
-
- assertThat(component, is(inExperiment(destinationExperiment)));
- assertThat(component, is(inSpace(destinationSpace)));
+ EntityGraphGenerator g = parseAndCreateGraph("/S1/P1/E1, samples: /S1/S1 /S1/S2\n"
+ + "/S2/P2/E2\n"
+ + "/S1/S1, children: /S1/S2\n");
+
+ reassignSampleToExperiment(g.s(2), g.e(2));
+
+ assertEquals("/S1/P1/E1, samples: /S1/S1\n"
+ + "/S2/P2/E2, samples: /S2/S2\n"
+ + "/S1/S1, children: /S2/S2\n", renderGraph(g));
+ assertModified(g.e(1), g.e(2));
+ assertModified(g.s(2));
+ assertUnmodified(g);
}
@Test
- public void experimentAssignmentOfContainerSampleIsNotChangedWhenComponentSampleIsAssignedToAnotherExperiment()
- throws Exception
+ public void parentSampleCanBeAssignedToAnotherExperiment()
{
- Sample container = create(aSample().inExperiment(sourceExperiment));
- Sample component = create(aSample().inContainer(container).inExperiment(sourceExperiment));
-
- perform(anUpdateOf(component).toExperiment(destinationExperiment));
-
- assertThat(container, is(inExperiment(sourceExperiment)));
- assertThat(container, is(inSpace(sourceSpace)));
+ EntityGraphGenerator g = parseAndCreateGraph("/S1/P1/E1, samples: /S1/S1 /S1/S2\n"
+ + "/S2/P2/E2\n"
+ + "/S1/S1, children: /S1/S2\n");
+
+ reassignSampleToExperiment(g.s(1), g.e(2));
+
+ assertEquals("/S1/P1/E1, samples: /S1/S2\n"
+ + "/S2/P2/E2, samples: /S2/S1\n"
+ + "/S2/S1, children: /S1/S2\n", renderGraph(g));
+ assertModified(g.e(1), g.e(2));
+ assertModified(g.s(1));
+ assertUnmodified(g);
}
@Test
- public void containerSampleCanBeAssignedToAnotherExperiment() throws Exception
+ public void componentSampleCanBeAssignedToAnotherExperiment()
{
- Sample container = create(aSample().inExperiment(sourceExperiment));
- create(aSample().inContainer(container).inExperiment(sourceExperiment));
-
- perform(anUpdateOf(container).toExperiment(destinationExperiment));
-
- assertThat(container, is(inExperiment(destinationExperiment)));
- assertThat(container, is(inSpace(destinationSpace)));
+ EntityGraphGenerator g = parseAndCreateGraph("/S1/P1/E1, samples: /S1/S1 /S1/S2\n"
+ + "/S2/P2/E2\n"
+ + "/S1/S1, components: /S1/S2\n");
+
+ reassignSampleToExperiment(g.s(2), g.e(2));
+
+ assertEquals("/S1/P1/E1, samples: /S1/S1\n"
+ + "/S2/P2/E2, samples: /S2/S2\n"
+ + "/S1/S1, components: /S2/S2\n", renderGraph(g));
+ assertModified(g.e(1), g.e(2));
+ assertModified(g.s(2));
+ assertUnmodified(g);
}
@Test
- public void experimentAssignmentOfComponentSampleIsNotChangedWhenContainerSampleIsAssignedToAnotherExperiment()
- throws Exception
+ public void containerSampleCanBeAssignedToAnotherExperiment()
{
- Sample container = create(aSample().inExperiment(sourceExperiment));
- Sample component = create(aSample().inContainer(container).inExperiment(sourceExperiment));
-
- perform(anUpdateOf(container).toExperiment(destinationExperiment));
-
- assertThat(component, is(inExperiment(sourceExperiment)));
- assertThat(component, is(inSpace(sourceSpace)));
+ EntityGraphGenerator g = parseAndCreateGraph("/S1/P1/E1, samples: /S1/S1 /S1/S2\n"
+ + "/S2/P2/E2\n"
+ + "/S1/S1, components: /S1/S2\n");
+
+ reassignSampleToExperiment(g.s(1), g.e(2));
+
+ assertEquals("/S1/P1/E1, samples: /S1/S2\n"
+ + "/S2/P2/E2, samples: /S2/S1\n"
+ + "/S2/S1, components: /S1/S2\n", renderGraph(g));
+ assertModified(g.e(1), g.e(2));
+ assertModified(g.s(1));
+ assertUnmodified(g);
}
@Test
- public void sampleWithoutExperimentCanBeAssignedToExperimentInSameSpaceThroughExperimentUpdate()
- throws Exception
- {
- Sample sample = create(aSample().inSpace(destinationSpace));
-
- perform(anUpdateOf(destinationExperiment).withSamples(sample));
-
- assertThat(sample, is(inExperiment(destinationExperiment)));
- }
-
- @Test(expectedExceptions =
- { UserFailureException.class })
- public void sampleWithoutExperimentCanNotBeAssignedToExperimentInAnotherSpaceThroughExperimentUpdate()
- throws Exception
- {
- Sample sample = create(aSample().inSpace(sourceSpace));
-
- perform(anUpdateOf(destinationExperiment).withSamples(sample));
-
- assertThat(sample, is(inExperiment(destinationExperiment)));
- }
-
- @Test(expectedExceptions =
- { UserFailureException.class })
public void sampleWithExperimentCanNotBeAssignedToAnotherExperimentThroughExperimentUpdate()
- throws Exception
- {
- Experiment destinationExperimentInSameSpace =
- create(anExperiment().inProject(sourceProject));
- Sample sample = create(aSample().inExperiment(sourceExperiment));
-
- perform(anUpdateOf(destinationExperimentInSameSpace).withSamples(sample));
- }
-
- @Test(expectedExceptions =
- { UserFailureException.class })
- public void sharedSampleCanNotBeAssignedToExperimentThroughExperimentUpdate() throws Exception
{
- Sample sample = create(aSample());
-
- perform(anUpdateOf(destinationExperiment).withSamples(sample));
+ EntityGraphGenerator g = parseAndCreateGraph("/S1/P1/E1, samples: /S1/S1\n"
+ + "/S1/P2/E2\n");
- assertThat(sample, is(inExperiment(destinationExperiment)));
+ try
+ {
+ reassignSamplesToExperiment(g.e(2), g.s(1));
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Sample '" + entityGraphManager.getSample(g.s(1)).getIdentifier()
+ + "' is already assigned to the experiment '"
+ + entityGraphManager.getExperimentIdentifierOrNull(g.e(1)) + "'.", ex.getMessage());
+ }
}
@Test
- public void registeringExperimentWithSampleInSameSpaceThatIsNotAssignedToAnyExperimentAssignsTheSampleToTheExperiment()
- throws Exception
+ public void sharedSampleCanNotBeAssignedToExperimentThroughExperimentUpdate()
{
- Sample sample = create(aSample().inSpace(sourceSpace));
-
- Experiment experiment = create(anExperiment().inProject(sourceProject).withSamples(sample));
+ EntityGraphGenerator g = parseAndCreateGraph("/S1/P1/E1\n"
+ + "/S1\n");
- assertThat(sample, is(inExperiment(experiment)));
+ try
+ {
+ reassignSamplesToExperiment(g.e(1), g.s(1));
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Samples with following codes do not exist in the space 'S1': '["
+ + entityGraphManager.getSample(g.s(1)).getCode() + "]'.", ex.getMessage());
+ }
}
Space unrelatedAdmin;
@@ -547,15 +509,7 @@ public class AssignSampleToExperimentTest extends BaseTest
RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
throws Exception
{
- Sample sample = create(aSample().inExperiment(sourceExperiment));
- String user =
- create(aSession().withSpaceRole(sourceSpaceRole, sourceSpace)
- .withSpaceRole(destinationSpaceRole, destinationSpace)
- .withInstanceRole(instanceRole)
- .withSpaceRole(RoleWithHierarchy.SPACE_ADMIN, unrelatedAdmin)
- .withSpaceRole(RoleWithHierarchy.SPACE_OBSERVER, unrelatedObserver));
-
- perform(anUpdateOf(sample).toExperiment(destinationExperiment).as(user));
+ checkAssigningSampleToExperiment(sourceSpaceRole, destinationSpaceRole, instanceRole);
}
@Test(dataProvider = "rolesNotAllowedToAssignSampleToExperiment", expectedExceptions =
@@ -564,15 +518,7 @@ public class AssignSampleToExperimentTest extends BaseTest
RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
throws Exception
{
- Sample sample = create(aSample().inExperiment(sourceExperiment));
- String user =
- create(aSession().withSpaceRole(sourceSpaceRole, sourceSpace)
- .withSpaceRole(destinationSpaceRole, destinationSpace)
- .withInstanceRole(instanceRole)
- .withSpaceRole(RoleWithHierarchy.SPACE_ADMIN, unrelatedAdmin)
- .withSpaceRole(RoleWithHierarchy.SPACE_OBSERVER, unrelatedObserver));
-
- perform(anUpdateOf(sample).toExperiment(destinationExperiment).as(user));
+ checkAssigningSampleToExperiment(sourceSpaceRole, destinationSpaceRole, instanceRole);
}
@Test(dataProvider = "rolesAllowedToAssignSharedSampleToExperiment", groups = "authorization")
@@ -580,14 +526,7 @@ public class AssignSampleToExperimentTest extends BaseTest
RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
throws Exception
{
- Sample sample = create(aSample());
- String user =
- create(aSession().withSpaceRole(destinationSpaceRole, destinationSpace)
- .withInstanceRole(instanceRole)
- .withSpaceRole(RoleWithHierarchy.SPACE_ADMIN, unrelatedAdmin)
- .withSpaceRole(RoleWithHierarchy.SPACE_OBSERVER, unrelatedObserver));
-
- perform(anUpdateOf(sample).toExperiment(destinationExperiment).as(user));
+ checkAssigningSharedSampleToExperiment(destinationSpaceRole, instanceRole);
}
@Test(dataProvider = "rolesNotAllowedToAssignSharedSampleToExperiment", expectedExceptions =
@@ -596,14 +535,7 @@ public class AssignSampleToExperimentTest extends BaseTest
RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
throws Exception
{
- Sample sample = create(aSample());
- String user =
- create(aSession().withSpaceRole(destinationSpaceRole, destinationSpace)
- .withInstanceRole(instanceRole)
- .withSpaceRole(RoleWithHierarchy.SPACE_ADMIN, unrelatedAdmin)
- .withSpaceRole(RoleWithHierarchy.SPACE_OBSERVER, unrelatedObserver));
-
- perform(anUpdateOf(sample).toExperiment(destinationExperiment).as(user));
+ checkAssigningSharedSampleToExperiment(destinationSpaceRole, instanceRole);
}
@Test(dataProvider = "rolesAllowedToAssignSampleToExperimentThroughExperimentUpdate", groups = "authorization")
@@ -611,14 +543,7 @@ public class AssignSampleToExperimentTest extends BaseTest
RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
throws Exception
{
- Sample sample = create(aSample().inSpace(destinationSpace));
- String user =
- create(aSession().withSpaceRole(destinationSpaceRole, destinationSpace)
- .withInstanceRole(instanceRole)
- .withSpaceRole(RoleWithHierarchy.SPACE_ADMIN, unrelatedAdmin)
- .withSpaceRole(RoleWithHierarchy.SPACE_OBSERVER, unrelatedObserver));
-
- perform(anUpdateOf(destinationExperiment).withSamples(sample).as(user));
+ checkAssigningSamplesToExperiment(destinationSpaceRole, instanceRole);
}
@Test(dataProvider = "rolesNotAllowedToAssignSampleToExperimentThroughExperimentUpdate", expectedExceptions =
@@ -627,14 +552,45 @@ public class AssignSampleToExperimentTest extends BaseTest
RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
throws Exception
{
- Sample sample = create(aSample().inSpace(destinationSpace));
+ checkAssigningSamplesToExperiment(destinationSpaceRole, instanceRole);
+ }
+
+ private void checkAssigningSampleToExperiment(RoleWithHierarchy sourceSpaceRole, RoleWithHierarchy destinationSpaceRole,
+ RoleWithHierarchy instanceRole)
+ {
+ String user =
+ create(aSession().withSpaceRole(sourceSpaceRole, sourceSpace)
+ .withSpaceRole(destinationSpaceRole, destinationSpace)
+ .withInstanceRole(instanceRole)
+ .withSpaceRole(RoleWithHierarchy.SPACE_ADMIN, unrelatedAdmin)
+ .withSpaceRole(RoleWithHierarchy.SPACE_OBSERVER, unrelatedObserver));
+
+ Sample sample = create(aSample().inExperiment(sourceExperiment));
+ reassignSampleToExperiment(sample.getPermId(), destinationExperiment.getIdentifier(), user);
+ }
+
+ private void checkAssigningSharedSampleToExperiment(RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
+ {
+ String user =
+ create(aSession().withSpaceRole(destinationSpaceRole, destinationSpace)
+ .withInstanceRole(instanceRole)
+ .withSpaceRole(RoleWithHierarchy.SPACE_ADMIN, unrelatedAdmin)
+ .withSpaceRole(RoleWithHierarchy.SPACE_OBSERVER, unrelatedObserver));
+
+ Sample sample = create(aSample());
+ reassignSampleToExperiment(sample.getPermId(), destinationExperiment.getIdentifier(), user);
+ }
+
+ private void checkAssigningSamplesToExperiment(RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
+ {
String user =
create(aSession().withSpaceRole(destinationSpaceRole, destinationSpace)
.withInstanceRole(instanceRole)
.withSpaceRole(RoleWithHierarchy.SPACE_ADMIN, unrelatedAdmin)
.withSpaceRole(RoleWithHierarchy.SPACE_OBSERVER, unrelatedObserver));
- perform(anUpdateOf(destinationExperiment).withSamples(sample).as(user));
+ Sample sample = create(aSample().inSpace(destinationSpace));
+ reassignSamplesToExperiment(destinationExperiment.getIdentifier(), Arrays.asList(sample.getPermId()), user);
}
@BeforeClass(dependsOnMethods = "loginAsSystem")
@@ -694,7 +650,7 @@ public class AssignSampleToExperimentTest extends BaseTest
and(rule(destination, RoleWithHierarchy.SPACE_USER),
rule(instance, RoleWithHierarchy.INSTANCE_ETL_SERVER));
}
-/*
+
@DataProvider
Object[][] rolesAllowedToAssignSampleToExperiment()
{
@@ -736,7 +692,7 @@ public class AssignSampleToExperimentTest extends BaseTest
return RolePermutator.getAcceptedPermutations(not(assignSharedSampleToExperimentRule),
destination, instance);
}
- */
+
private void reassignSampleToExperiment(SampleNode sampleNode, ExperimentNode experimentNodeOrNull)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/entitygraph/EntityGraphManager.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/entitygraph/EntityGraphManager.java
index 4b7f274af5f9e226fd6e17e53d1c54295300e00e..6f33ccd7599e7fc782d1af76055c315a328638d6 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/entitygraph/EntityGraphManager.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/entitygraph/EntityGraphManager.java
@@ -26,7 +26,6 @@ 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.Map.Entry;
@@ -72,7 +71,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
/**
* Helper class which creates a graph of entities of kind experiment, sample, and data set based on a
- * textual description.
+ * textual description. A simple language defines the entities and its relations.
*
* @author Franz-Josef Elmer
*/
@@ -190,6 +189,8 @@ public class EntityGraphManager
for (SampleNode sampleNode : g.getSamples().values())
{
StringBuilder builder2 = new StringBuilder();
+ render(builder2, "components", repository.getComponentSampleNodes(sampleNode));
+ render(builder2, "children", repository.getChildrenSampleNodes(sampleNode));
render(builder2, "data sets", repository.getDataSetNodes(sampleNode));
appendNodeTo(builder, getIdentifierAndType(sampleNode), builder2);
}
@@ -382,21 +383,27 @@ public class EntityGraphManager
try
{
NewSample sample = new NewSample();
- String prefix = space == null ? "/" : space.getIdentifier() + "/";
- if (sampleNode.isShared())
- {
- prefix = "/";
- } else if (sampleNode.getSpace() != null)
- {
- prefix = createSpace(sampleNode.getSpace()).getIdentifier() + "/";
- }
- sample.setIdentifier(prefix + sampleNode.getCode() + generateUniqueId());
+ sample.setIdentifier(createSampleIdentifier(space, sampleNode));
sample.setSampleType(defaultSampleType);
ExperimentNode experimentNode = sampleNode.getExperiment();
if (experimentNode != null)
{
sample.setExperimentIdentifier(repository.tryGetExperiment(experimentNode).getIdentifier());
}
+ List<String> parentIdentifiers = getParentIdentifiers(sampleNode);
+ sample.setParentsOrNull(parentIdentifiers.toArray(new String[0]));
+ SampleNode container = sampleNode.getContainer();
+ if (container != null)
+ {
+ Sample containerSample = repository.tryGetSample(container);
+ if (containerSample == null)
+ {
+ throw new IllegalStateException("Sample " + container.getCode()
+ + " is specified as container of " + sampleNode.getCode()
+ + " but hasn't yet created.");
+ }
+ sample.setContainerIdentifier(containerSample.getIdentifier());
+ }
sample.setProperties(new IEntityProperty[0]);
sample.setAttachments(Collections.<NewAttachment>emptyList());
service.registerSample(sessionToken, sample, null);
@@ -407,6 +414,36 @@ public class EntityGraphManager
+ ": " + ex.getMessage(), ex);
}
}
+
+ private List<String> getParentIdentifiers(SampleNode sampleNode)
+ {
+ List<String> parentIdentifiers = new ArrayList<String>();
+ for (SampleNode parent : sampleNode.getParents())
+ {
+ Sample parentSample = repository.tryGetSample(parent);
+ if (parentSample == null)
+ {
+ throw new IllegalStateException("Sample " + parent.getCode()
+ + " is specified as parent of " + sampleNode.getCode()
+ + " but hasn't yet created.");
+ }
+ parentIdentifiers.add(parentSample.getIdentifier());
+ }
+ return parentIdentifiers;
+ }
+
+ private String createSampleIdentifier(Space space, SampleNode sampleNode)
+ {
+ String prefix = space == null ? "/" : space.getIdentifier() + "/";
+ if (sampleNode.isShared())
+ {
+ prefix = "/";
+ } else if (sampleNode.getSpace() != null)
+ {
+ prefix = createSpace(sampleNode.getSpace()).getIdentifier() + "/";
+ }
+ return prefix + sampleNode.getCode() + generateUniqueId();
+ }
private Sample refresh(Sample sample)
{
@@ -425,19 +462,7 @@ public class EntityGraphManager
{
dataSetKind = DataSetKind.CONTAINER;
NewContainerDataSet cont = new NewContainerDataSet();
- List<String> componentCodes = new ArrayList<String>();
- for (DataSetNode component : components)
- {
- AbstractExternalData componentDataSet = repository.tryGetDataSet(component);
- if (componentDataSet == null)
- {
- throw new IllegalStateException("Data set " + component.getCode()
- + " is specified as component of " + dataSetNode.getCode()
- + " but hasn't yet created.");
- }
- componentCodes.add(componentDataSet.getCode());
- }
- cont.setContainedDataSetCodes(componentCodes);
+ cont.setContainedDataSetCodes(getRelatedDataSetIdentifiers(dataSetNode, "component", components));
dataSet = cont;
}
dataSet.setCode(dataSetNode.getCode() + generateUniqueId());
@@ -452,29 +477,8 @@ public class EntityGraphManager
dataSet.setLocation(UUID.randomUUID().toString());
dataSet.setStorageFormat(StorageFormat.PROPRIETARY);
dataSet.setDataStoreCode("STANDARD");
- if (dataSetNode.getSample() != null)
- {
- Sample sample = repository.tryGetSample(dataSetNode.getSample());
- dataSet.setSampleIdentifierOrNull(SampleIdentifierFactory.parse(sample));
- } else if (dataSetNode.getExperiment() != null)
- {
- String identifier = repository.tryGetExperiment(dataSetNode.getExperiment()).getIdentifier();
- dataSet.setExperimentIdentifierOrNull(ExperimentIdentifierFactory.parse(identifier));
- }
- List<String> parentCodes = new ArrayList<String>();
- List<DataSetNode> parents = dataSetNode.getParents();
- for (DataSetNode parent : parents)
- {
- AbstractExternalData parentDataSet = repository.tryGetDataSet(parent);
- if (parentDataSet == null)
- {
- throw new IllegalStateException("Data set " + parent.getCode()
- + " is specified as parent of " + dataSetNode.getCode()
- + " but hasn't yet created.");
- }
- parentCodes.add(parentDataSet.getCode());
- }
- dataSet.setParentDataSetCodes(parentCodes);
+ addSampleOrExperimentIdentifier(dataSet, dataSetNode);
+ dataSet.setParentDataSetCodes(getRelatedDataSetIdentifiers(dataSetNode, "parent", dataSetNode.getParents()));
if (dataSet.getSampleIdentifierOrNull() != null)
{
service.registerDataSet(sessionToken, dataSet.getSampleIdentifierOrNull(), dataSet);
@@ -490,6 +494,36 @@ public class EntityGraphManager
}
}
+ private void addSampleOrExperimentIdentifier(NewExternalData dataSet, DataSetNode dataSetNode)
+ {
+ if (dataSetNode.getSample() != null)
+ {
+ Sample sample = repository.tryGetSample(dataSetNode.getSample());
+ dataSet.setSampleIdentifierOrNull(SampleIdentifierFactory.parse(sample));
+ } else if (dataSetNode.getExperiment() != null)
+ {
+ String identifier = repository.tryGetExperiment(dataSetNode.getExperiment()).getIdentifier();
+ dataSet.setExperimentIdentifierOrNull(ExperimentIdentifierFactory.parse(identifier));
+ }
+ }
+
+ private List<String> getRelatedDataSetIdentifiers(DataSetNode dataSetNode, String relationType, List<DataSetNode> dataSetNodes)
+ {
+ List<String> parentCodes = new ArrayList<String>();
+ for (DataSetNode parent : dataSetNodes)
+ {
+ AbstractExternalData parentDataSet = repository.tryGetDataSet(parent);
+ if (parentDataSet == null)
+ {
+ throw new IllegalStateException("Data set " + parent.getCode()
+ + " is specified as " + relationType + " of " + dataSetNode.getCode()
+ + " but hasn't yet created.");
+ }
+ parentCodes.add(parentDataSet.getCode());
+ }
+ return parentCodes;
+ }
+
private AbstractExternalData refresh(AbstractExternalData data)
{
return service.tryGetDataSet(sessionToken, data.getCode());
@@ -524,7 +558,9 @@ public class EntityGraphManager
private void createSamples(Space space, EntityGraphGenerator g)
{
- for (SampleNode sampleNode : g.getSamples().values())
+ ArrayList<SampleNode> sampleNodes = new ArrayList<SampleNode>(g.getSamples().values());
+// Collections.reverse(sampleNodes);
+ for (SampleNode sampleNode : sampleNodes)
{
repository.put(sampleNode, createSample(sampleNode, space));
}
@@ -556,10 +592,12 @@ public class EntityGraphManager
private Set<DataSetNode> modifiedDataSetNodes = new HashSet<DataSetNode>();
private Map<Long, Set<Long>> experimentSamplesMap = new HashMap<Long, Set<Long>>();
+ private Map<Long, Set<Long>> childrenSamplesMap = new HashMap<Long, Set<Long>>();
+ private Map<Long, Set<Long>> componentSamplesMap = new HashMap<Long, Set<Long>>();
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>>();
+ private Map<Long, Set<Long>> parentDataSetsMap = new HashMap<Long, Set<Long>>();
public String renderNodeToDtoMapping()
{
@@ -648,6 +686,18 @@ public class EntityGraphManager
}
void refreshGraph(boolean showWhereIAm)
+ {
+ refreshEntityDtos();
+ refreshSamplesMap();
+ refreshDataSetsMap();
+ if (showWhereIAm)
+ {
+ printWhereIAm();
+ }
+ System.out.println("Entities mapping:\n" + renderNodeToDtoMapping());
+ }
+
+ private void refreshEntityDtos()
{
for (Long id : experimentsNodeToDtoMap.keySet())
{
@@ -661,48 +711,48 @@ public class EntityGraphManager
{
dataSetsNodeToDtoMap.put(id, refresh(dataSetsNodeToDtoMap.get(id)));
}
+ }
+
+ private void refreshSamplesMap()
+ {
experimentSamplesMap.clear();
+ childrenSamplesMap.clear();
+ componentSamplesMap.clear();
for (Sample sample : samplesNodeToDtoMap.values())
{
Experiment experiment = sample.getExperiment();
- if (experiment != null)
+ addToEntitiesMap(experimentSamplesMap, experiment, sample);
+ for (Sample parentSample : sample.getParents())
{
- Long id = experiment.getId();
- Set<Long> sampleIds = experimentSamplesMap.get(id);
- if (sampleIds == null)
- {
- sampleIds = new TreeSet<Long>();
- experimentSamplesMap.put(id, sampleIds);
- }
- sampleIds.add(sample.getId());
+ addToEntitiesMap(childrenSamplesMap, parentSample, sample);
+ }
+ Sample container = sample.getContainer();
+ if (container != null)
+ {
+ addToEntitiesMap(componentSamplesMap, container, sample);
}
}
+ }
+
+ private void refreshDataSetsMap()
+ {
experimentDataSetsMap.clear();
- for (AbstractExternalData dataSet : dataSetsNodeToDtoMap.values())
- {
- addToDataSetsMap(experimentDataSetsMap, dataSet, dataSet.getExperiment());
- }
sampleDataSetsMap.clear();
componentDataSetsMap.clear();
+ parentDataSetsMap.clear();
for (AbstractExternalData dataSet : dataSetsNodeToDtoMap.values())
{
- addToDataSetsMap(sampleDataSetsMap, dataSet, dataSet.getSample());
- List<ContainerDataSet> containerDataSets = dataSet.getContainerDataSets();
- for (ContainerDataSet containerDataSet : containerDataSets)
+ addToEntitiesMap(experimentDataSetsMap, dataSet.getExperiment(), dataSet);
+ addToEntitiesMap(sampleDataSetsMap, dataSet.getSample(), dataSet);
+ for (ContainerDataSet containerDataSet : dataSet.getContainerDataSets())
{
- addToDataSetsMap(componentDataSetsMap, dataSet, containerDataSet);
+ addToEntitiesMap(componentDataSetsMap, containerDataSet, dataSet);
}
- Collection<AbstractExternalData> parents = dataSet.getParents();
- for (AbstractExternalData parentDataSet : parents)
+ for (AbstractExternalData parentDataSet : dataSet.getParents())
{
- addToDataSetsMap(parentsDataSetsMap, parentDataSet, dataSet);
+ addToEntitiesMap(parentDataSetsMap, dataSet, parentDataSet);
}
}
- if (showWhereIAm)
- {
- printWhereIAm();
- }
- System.out.println("Entities mapping:\n" + renderNodeToDtoMapping());
}
private void printWhereIAm()
@@ -716,19 +766,18 @@ public class EntityGraphManager
System.out.println("...");
}
- private void addToDataSetsMap(Map<Long, Set<Long>> holderDataSetsMap,
- AbstractExternalData dataSet, IIdHolder idHolder)
+ private void addToEntitiesMap(Map<Long, Set<Long>> entityToEntitiesMap, IIdHolder keyEntity, IIdHolder valueEntity)
{
- if (idHolder != null)
+ if (keyEntity != null)
{
- Long id = idHolder.getId();
- Set<Long> dataSetIds = holderDataSetsMap.get(id);
- if (dataSetIds == null)
+ Long id = keyEntity.getId();
+ Set<Long> entityIds = entityToEntitiesMap.get(id);
+ if (entityIds == null)
{
- dataSetIds = new TreeSet<Long>();
- holderDataSetsMap.put(id, dataSetIds);
+ entityIds = new TreeSet<Long>();
+ entityToEntitiesMap.put(id, entityIds);
}
- dataSetIds.add(dataSet.getId());
+ entityIds.add(valueEntity.getId());
}
}
@@ -839,20 +888,20 @@ public class EntityGraphManager
Set<SampleNode> getSampleNodes(ExperimentNode experimentNode)
{
- Set<SampleNode> result = new LinkedHashSet<SampleNode>();
- Experiment experiment = experimentsNodeToDtoMap.get(experimentNode.getId());
- if (experiment != null)
- {
- Set<Long> sampleDtoIds = experimentSamplesMap.get(experiment.getId());
- if (sampleDtoIds != null)
- {
- for (Long dtoId : sampleDtoIds)
- {
- result.add(samplesDtoToNodeMap.get(dtoId));
- }
- }
- }
- return result;
+ return getEntityNodes(experimentSamplesMap, experimentsNodeToDtoMap.get(experimentNode.getId()),
+ samplesDtoToNodeMap);
+ }
+
+ Set<SampleNode> getChildrenSampleNodes(SampleNode sampleNode)
+ {
+ return getEntityNodes(childrenSamplesMap, samplesNodeToDtoMap.get(sampleNode.getId()),
+ samplesDtoToNodeMap);
+ }
+
+ Set<SampleNode> getComponentSampleNodes(SampleNode sampleNode)
+ {
+ return getEntityNodes(componentSamplesMap, samplesNodeToDtoMap.get(sampleNode.getId()),
+ samplesDtoToNodeMap);
}
Set<DataSetNode> getDataSetNodes(ExperimentNode experimentNode)
@@ -872,20 +921,26 @@ public class EntityGraphManager
Set<DataSetNode> getParentDataSetNodes(DataSetNode childDataSetNode)
{
- return getDataSetNodes(parentsDataSetsMap, dataSetsNodeToDtoMap.get(childDataSetNode.getId()));
+ return getDataSetNodes(parentDataSetsMap, dataSetsNodeToDtoMap.get(childDataSetNode.getId()));
}
- private Set<DataSetNode> getDataSetNodes(Map<Long, Set<Long>> idHolderDataSetsMap, IIdHolder experiment)
+ private Set<DataSetNode> getDataSetNodes(Map<Long, Set<Long>> idHolderDataSetsMap, IIdHolder idHolder)
{
- Set<DataSetNode> result = new TreeSet<DataSetNode>();
- if (experiment != null)
+ return getEntityNodes(idHolderDataSetsMap, idHolder, dataSetsDtoToNodeMap);
+ }
+
+ private <T extends EntityNode> Set<T> getEntityNodes(Map<Long, Set<Long>> idHolderEntitiesMap, IIdHolder idHolder,
+ Map<Long, T> dtoToNodeMap)
+ {
+ Set<T> result = new TreeSet<T>();
+ if (idHolder != null)
{
- Set<Long> dataSetDtoIds = idHolderDataSetsMap.get(experiment.getId());
- if (dataSetDtoIds != null)
+ Set<Long> entityDtoIds = idHolderEntitiesMap.get(idHolder.getId());
+ if (entityDtoIds != null)
{
- for (Long dtoId : dataSetDtoIds)
+ for (Long dtoId : entityDtoIds)
{
- result.add(dataSetsDtoToNodeMap.get(dtoId));
+ result.add(dtoToNodeMap.get(dtoId));
}
}
}