diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/RelationshipService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/RelationshipService.java
index 50644afd58f751dc1ae2ea3c0b0d6987bd08ec82..bf61d70e73ce1dfdac3500f56a75aaf97cc780a7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/RelationshipService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/RelationshipService.java
@@ -23,6 +23,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.util.SampleUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.RelationshipUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.DAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetRelationshipPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
@@ -144,21 +145,17 @@ public class RelationshipService implements IRelationshipService
public void assignDataSetToExperiment(IAuthSession session, DataPE data, ExperimentPE experimentOrNull)
{
RelationshipUtils.setExperimentForDataSet(data, experimentOrNull, session);
- if (experimentOrNull != null)
- {
- RelationshipUtils.setSampleForDataSet(data, null, session);
- }
}
@Override
- public void assignDataSetToSample(IAuthSession session, DataPE data, SamplePE sampleOrNull)
+ public void assignDataSetToSample(IAuthSession session, DataPE data, SamplePE sample)
{
- if (sampleOrNull != null)
+ SamplePE currentSample = data.tryGetSample();
+ if (equalEntities(currentSample, sample))
{
- ExperimentPE experiment = sampleOrNull.getExperiment();
- RelationshipUtils.setExperimentForDataSet(data, experiment, session);
+ return;
}
- RelationshipUtils.setSampleForDataSet(data, sampleOrNull, session);
+ RelationshipUtils.setSampleForDataSet(data, sample, session);
}
@Override
@@ -281,4 +278,16 @@ public class RelationshipService implements IRelationshipService
return RelationshipUtils.getParentChildRelationshipType(daoFactory.getRelationshipTypeDAO());
}
+ private static <T extends IIdHolder >boolean equalEntities(T entity1OrNull, T entity2OrNull)
+ {
+ Long id1 = getIdOrNull(entity1OrNull);
+ Long id2 = getIdOrNull(entity2OrNull);
+ return id1 == null ? id1 == id2 : id1.equals(id2);
+ }
+
+ private static Long getIdOrNull(IIdHolder idHolderOrNull)
+ {
+ return idHolderOrNull == null ? null : idHolderOrNull.getId();
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractDataSetBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractDataSetBusinessObject.java
index c3c0c44ee1fbab34cfb651dfac762693a61aaecc..d9e66090a2a4088c8aa7024b3affb07108d8f5d8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractDataSetBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractDataSetBusinessObject.java
@@ -34,6 +34,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.util.DataSetTypeWitho
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityPropertiesConverter;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetRelationshipPE;
@@ -118,30 +119,99 @@ public abstract class AbstractDataSetBusinessObject extends AbstractSampleIdenti
{
throw createWrongSampleException(data, newSample, "the new sample is shared");
}
- ExperimentPE experiment = newSample.getExperiment();
- String dataSetTypeCode = data.getDataSetType().getCode();
+ assignDataSetToSampleAndExperiment(data, newSample, newSample.getExperiment());
+ }
+
+ private void assignDataSetToSampleAndExperiment(DataPE data, SamplePE newSample, ExperimentPE experiment)
+ {
+ List<DataSetSampleExperiment> assignments = new ArrayList<DataSetSampleExperiment>();
+ gatherNewAssigments(assignments, data, data, newSample, experiment);
+ for (DataSetSampleExperiment assignment : assignments)
+ {
+ assignment.assignDataSet(relationshipService, session);
+ }
+ }
+
+ private void gatherNewAssigments(List<DataSetSampleExperiment> assignments,
+ DataPE dataSet, DataPE rootDataSet, SamplePE sample, ExperimentPE experiment)
+ {
+ String dataSetTypeCode = dataSet.getDataSetType().getCode();
if (experiment == null && dataSetTypeChecker.isDataSetTypeWithoutExperiment(dataSetTypeCode) == false)
{
- throw createWrongSampleException(data, newSample,
- "the new sample is not connected to any experiment");
+ throw createWrongSampleException(dataSet, sample,
+ "the new sample is not connected to any experiment and the data set type ("
+ + dataSetTypeCode + ") doesn't match one of the following regular expressions: "
+ + dataSetTypeChecker.getRegularExpressions());
+ }
+ if (rootDataSet == dataSet)
+ {
+ assignments.add(new DataSetSampleExperiment(dataSet, sample, experiment));
+ }
+ SamplePE rootSample = rootDataSet.tryGetSample();
+ ExperimentPE rootExperiment = getExperimentOf(rootDataSet);
+ List<DataPE> components = dataSet.getContainedDataSets();
+ for (DataPE component : components)
+ {
+ SamplePE componentSample = component.tryGetSample();
+ ExperimentPE componentExperiment = getExperimentOf(component);
+ if ((equalEntities(rootSample, componentSample) || componentSample == null)
+ && equalEntities(rootExperiment, componentExperiment))
+ {
+ SamplePE newSample = componentSample == null && rootSample != null ? null : sample;
+ assignments.add(new DataSetSampleExperiment(component, newSample, experiment));
+ gatherNewAssigments(assignments, component, rootDataSet, sample, experiment);
+ }
}
-
- relationshipService.assignDataSetToSample(session, data, newSample);
+ }
+
+ private ExperimentPE getExperimentOf(DataPE data)
+ {
+ SamplePE sample = data.tryGetSample();
+ return sample == null ? data.getExperiment() : sample.getExperiment();
+ }
+
+ private static <T extends IIdHolder >boolean equalEntities(T entity1OrNull, T entity2OrNull)
+ {
+ Long id1 = getIdOrNull(entity1OrNull);
+ Long id2 = getIdOrNull(entity2OrNull);
+ return id1 == null ? id1 == id2 : id1.equals(id2);
}
- protected void updateExperiment(DataPE data, ExperimentIdentifier experimentIdentifier)
+ private static Long getIdOrNull(IIdHolder idHolderOrNull)
{
- assert experimentIdentifier != null;
- ExperimentPE experiment = getExperimentByIdentifier(experimentIdentifier);
- updateExperiment(data, experiment);
+ return idHolderOrNull == null ? null : idHolderOrNull.getId();
}
- protected void updateExperiment(DataPE data, ExperimentPE experiment)
+ private static final class DataSetSampleExperiment
{
- if (experiment.equals(data.getExperiment()) == false)
+ private DataPE dataSet;
+ private SamplePE sample;
+ private ExperimentPE experiment;
+
+ DataSetSampleExperiment(DataPE dataSet, SamplePE sample, ExperimentPE experiment)
{
- relationshipService.assignDataSetToExperiment(session, data, experiment);
+ this.dataSet = dataSet;
+ this.sample = sample;
+ this.experiment = experiment;
}
+
+ public void assignDataSet(IRelationshipService relationshipService, Session session)
+ {
+ if (equalEntities(dataSet.tryGetSample(), sample) == false)
+ {
+ relationshipService.assignDataSetToSample(session, dataSet, sample);
+ }
+ if (equalEntities(dataSet.getExperiment(), experiment) == false)
+ {
+ relationshipService.assignDataSetToExperiment(session, dataSet, experiment);
+ }
+ }
+ }
+
+ protected void updateExperiment(DataPE data, ExperimentIdentifier experimentIdentifier)
+ {
+ assert experimentIdentifier != null;
+ assignDataSetToSampleAndExperiment(data, null, getExperimentByIdentifier(experimentIdentifier));
}
protected ExperimentPE getExperimentByIdentifier(final ExperimentIdentifier identifier)
@@ -155,9 +225,7 @@ public abstract class AbstractDataSetBusinessObject extends AbstractSampleIdenti
throw new UserFailureException("Unkown experiment because of unkown project: "
+ identifier);
}
- final ExperimentPE exp =
- getExperimentDAO().tryFindByCodeAndProject(project, identifier.getExperimentCode());
- return exp;
+ return getExperimentDAO().tryFindByCodeAndProject(project, identifier.getExperimentCode());
}
protected void setContainedDataSets(final DataPE container,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBO.java
index a4fd29fa9df561024c87aeddaf9bc30720345d73..fe6956e8ba1d67ba758954763a1dcf5be9419fff 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBO.java
@@ -616,10 +616,10 @@ public class DataBO extends AbstractDataSetBusinessObject implements IDataBO
{
// update sample and indirectly experiment
updateSample(data, sampleIdentifierOrNull);
- } else
+ } else if (updates.getExperimentIdentifierOrNull() != null)
{
- relationshipService.assignDataSetToSample(session, data, null);
updateExperiment(data, updates.getExperimentIdentifierOrNull());
+ relationshipService.assignDataSetToSample(session, data, null);
}
setParents(data, asListOrNull(updates.getModifiedParentDatasetCodesOrNull()));
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/DataSetTypeWithoutExperimentChecker.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/DataSetTypeWithoutExperimentChecker.java
index 0841024ff0d99858e04a6904338b8765ba5fe6cf..fc9d912efb045eb3049639e8a549084465595337 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/DataSetTypeWithoutExperimentChecker.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/DataSetTypeWithoutExperimentChecker.java
@@ -35,11 +35,13 @@ public class DataSetTypeWithoutExperimentChecker
{
public static final String PROPERTY_KEY = "data-set-types-with-no-experiment-needed";
- private List<Pattern> patternsForDataSetTypesWithoutExperiment = new ArrayList<Pattern>();
+ private final String regularExpressions;
+ private List<Pattern> patternsForDataSetTypesWithoutExperiment = new ArrayList<Pattern>();
+
public DataSetTypeWithoutExperimentChecker(Properties properties)
{
- String regularExpressions = properties.getProperty(PROPERTY_KEY);
+ regularExpressions = properties.getProperty(PROPERTY_KEY);
if (StringUtils.isNotBlank(regularExpressions))
{
String[] splittedRegexes = regularExpressions.split(",");
@@ -57,6 +59,11 @@ public class DataSetTypeWithoutExperimentChecker
}
}
+ public String getRegularExpressions()
+ {
+ return regularExpressions;
+ }
+
public boolean isDataSetTypeWithoutExperiment(String dataSetTypeCode)
{
for (Pattern pattern : patternsForDataSetTypesWithoutExperiment)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
index ebff4c49f5e8cd1e8bd9c9afceeb34ec5c97aff4..b0f030f8903b9e7ab57382698eb9a0996f85c5e4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
@@ -637,13 +637,6 @@ public class DataPE extends AbstractIdAndCodeHolder<DataPE> implements
if (experiment != null)
{
experiment.addDataSet(this);
- for (DataPE contained : getContainedDataSets())
- {
- if (false == contained.equals(this))
- {
- contained.setExperiment(experiment);
- }
- }
} else
{
ExperimentPE previous = getExperiment();
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 7e6e22ea9dc1e7ec4e4e3474db666dd632c39456..a4e25ff5e772f160d2c036485a8b112cf3626d35 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
@@ -103,7 +103,7 @@ public final class DataSetNode extends EntityNode
@Override
public String toString()
{
- StringBuilder builder = new StringBuilder(getCode());
+ StringBuilder builder = new StringBuilder(super.toString());
if (deletable == false)
{
builder.append(" (non deletable)");
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityNode.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityNode.java
index a049dd9cfe4616048458d5a183801035c729837a..dfa18463e03ef45c61612f98a6bc3112d85424d3 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityNode.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityNode.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo.entitygraph;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
-public class EntityNode implements IIdHolder
+public class EntityNode implements IIdHolder, Comparable<EntityNode>
{
private final long id;
@@ -47,9 +47,32 @@ public class EntityNode implements IIdHolder
{
return type;
}
+
+ public String getCodeAndType()
+ {
+ StringBuilder builder = new StringBuilder(code);
+ if (type != null)
+ {
+ builder.append("[").append(type).append("]");
+ }
+ return builder.toString();
+ }
public void setType(String type)
{
this.type = type;
}
+
+ @Override
+ public int compareTo(EntityNode that)
+ {
+ return this.getCode().compareTo(that.getCode());
+ }
+
+ @Override
+ public String toString()
+ {
+ return getCodeAndType();
+ }
+
}
\ No newline at end of file
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/ExperimentNode.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/ExperimentNode.java
index d904a9513b61d5b791e1bacf2e2193ac8d06de42..5072c31effc24e9deeb3d6e521c19c761f3bc7a3 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/ExperimentNode.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/ExperimentNode.java
@@ -60,7 +60,7 @@ public final class ExperimentNode extends EntityNode
@Override
public String toString()
{
- StringBuilder builder = new StringBuilder(getCode());
+ StringBuilder builder = new StringBuilder(super.toString());
Utils.appendTo(builder, "samples", samples);
Utils.appendTo(builder, "data sets", dataSets);
return builder.toString();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/SampleNode.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/SampleNode.java
index 6a106977b85d922ad3dfe847811f557084391beb..b8fee0d01ee12211e453f62dfea73f89c8a15559 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/SampleNode.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/SampleNode.java
@@ -98,7 +98,7 @@ public final class SampleNode extends EntityNode
public String toString()
{
- StringBuilder builder = new StringBuilder(getCode());
+ StringBuilder builder = new StringBuilder(super.toString());
Utils.appendTo(builder, "experiment", experiment);
Utils.appendTo(builder, "children", children);
Utils.appendTo(builder, "parents", parents);
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 f0b54bb7a9f7ebd7e5f23ecf4b9bc96c42b393d0..cee14dbe3d7c4acf388ab3298e46d6499b50e43c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToSampleTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToSampleTest.java
@@ -63,134 +63,234 @@ public class AssignDataSetToSampleTest extends BaseTest
Space destinationSpace;
@Test
- public void dataSetReassignedFromExperimentToExperiment()
+ public void containerWithSomeComponentsReassignedFromExperimentToExperiment()
{
- EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1\n"
- + "E2, samples: S2\n");
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1 DS2 DS4\n"
+ + "E2, samples: S2\n"
+ + "E3, data sets: DS3\n"
+ + "DS1, components: DS2 DS3\n"
+ + "DS2, components: DS4");
reassignToExperiment(g.ds(1), g.e(2));
assertEquals("E1, samples: S1\n"
- + "E2, samples: S2, data sets: DS1\n", renderGraph(g));
+ + "E2, samples: S2, data sets: DS1 DS2 DS4\n"
+ + "E3, data sets: DS3\n"
+ + "DS1, components: DS2 DS3\n"
+ + "DS2, components: DS4\n", renderGraph(g));
repository.assertModified(g.e(1), g.e(2));
- repository.assertModified(g.ds(1));
- repository.assertUnmodified(g.s(1), g.s(2));
+ repository.assertModified(g.ds(1), g.ds(2), g.ds(4));
+ repository.assertUnmodified(g);
}
@Test
- public void dataSetReassignedFromExperimentToSampleWithExperiment()
+ public void containerWithSomeComponentsReassignedFromExperimentToSampleWithExperiment()
+ {
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1 DS2 DS4\n"
+ + "E2, samples: S2\n"
+ + "E3, data sets: DS3\n"
+ + "DS1, components: DS2 DS3\n"
+ + "DS2, components: DS4");
+
+ reassignToSample(g.ds(1), g.s(2));
+
+ assertEquals("E1, samples: S1\n"
+ + "E2, samples: S2, data sets: DS1 DS2 DS4\n"
+ + "E3, data sets: DS3\n"
+ + "S2, data sets: DS1 DS2 DS4\n"
+ + "DS1, components: DS2 DS3\n"
+ + "DS2, components: DS4\n", renderGraph(g));
+ repository.assertModified(g.e(1), g.e(2));
+ repository.assertModified(g.ds(1), g.ds(2), g.ds(4));
+ repository.assertModified(g.s(2));
+ repository.assertUnmodified(g);
+ }
+
+ @Test
+ public void containerWithSomeComponentsReassignedFromExperimentToSampleWithExperiment2()
{
- EntityGraphGenerator g = parseAndCreateGraph("E1, data sets: DS1\nE2, samples: S2\n");
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1 DS2 DS4\n"
+ + "E2, samples: S2\n"
+ + "E3, data sets: DS3\n"
+ + "S1, data sets: DS2\n"
+ + "DS1, components: DS2 DS3\n"
+ + "DS2, components: DS4");
+
+ reassignToSample(g.ds(1), g.s(2));
+
+ assertEquals("E1, samples: S1, data sets: DS2 DS4\n"
+ + "E2, samples: S2, data sets: DS1\n"
+ + "E3, data sets: DS3\n"
+ + "S1, data sets: DS2\n"
+ + "S2, data sets: DS1\n"
+ + "DS1, components: DS2 DS3\n"
+ + "DS2, components: DS4\n", renderGraph(g));
+ repository.assertModified(g.e(1), g.e(2));
+ repository.assertModified(g.s(2));
+ repository.assertModified(g.ds(1));
+ repository.assertUnmodified(g);
+ }
+
+ @Test
+ public void containerWithAllItsComponentsReassignedFromExperimentToExperiment()
+ {
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1 DS2\n"
+ + "E2, samples: S2\n"
+ + "DS1, components: DS2\n");
+
+ reassignToExperiment(g.ds(1), g.e(2));
+
+ assertEquals("E1, samples: S1\n"
+ + "E2, samples: S2, data sets: DS1 DS2\n"
+ + "DS1, components: DS2\n", renderGraph(g));
+ repository.assertModified(g.e(1), g.e(2));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
+ }
+
+ @Test
+ public void containerWithAllItsComponentsReassignedFromExperimentToSampleWithExperiment()
+ {
+ EntityGraphGenerator g = parseAndCreateGraph("E1, data sets: DS1 DS2\n"
+ + "E2, samples: S2\n"
+ + "DS1, components: DS2\n");
reassignToSample(g.ds(1), g.s(2));
- assertEquals("E2, samples: S2, data sets: DS1\nS2, data sets: DS1\n", renderGraph(g));
+ assertEquals("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(2));
- repository.assertModified(g.ds(1));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
}
@Test
- public void dataSetReassignedFromExperimentToSampleWithoutExperiment()
+ public void containerWithAllItsComponentsReassignedFromExperimentToSampleWithoutExperiment()
{
- EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1[NEXP-TYPE]\n"
- + "S2\n");
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1[NECT] DS2[NET]\n"
+ + "S2\n"
+ + "DS1[NECT], components: DS2[NET]\n");
reassignToSample(g.ds(1), g.s(2));
- assertEquals("E1, samples: S1\nS2, data sets: DS1[NEXP-TYPE]\n", renderGraph(g));
+ assertEquals("E1, samples: S1\n"
+ + "S2, data sets: DS1[NECT] DS2[NET]\n"
+ + "DS1[NECT], components: DS2[NET]\n", renderGraph(g));
repository.assertModified(g.e(1));
- repository.assertUnmodified(g.s(1));
repository.assertModified(g.s(2));
- repository.assertModified(g.ds(1));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
}
@Test
- public void dataSetReassignedFromSampleWithExperimentToExperiment()
+ public void containerWithAllItsComponentsReassignedFromSampleWithExperimentToExperiment()
{
- EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1\n"
- + "E2, samples: S2\nS1, data sets: DS1\n");
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1 DS2\n"
+ + "E2, samples: S2\n"
+ + "S1, data sets: DS1\n"
+ + "DS1, components: DS2");
reassignToExperiment(g.ds(1), g.e(2));
assertEquals("E1, samples: S1\n"
- + "E2, samples: S2, data sets: DS1\n", renderGraph(g));
+ + "E2, samples: 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));
- repository.assertModified(g.ds(1));
- repository.assertUnmodified(g.s(2));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
}
@Test
- public void dataSetReassignedFromSampleWithExperimentToSampleWithExperiment()
+ public void containerWithAllItsComponentsReassignedFromSampleWithExperimentToSampleWithExperiment()
{
- EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1\n"
- + "E2, samples: S2\nS1, data sets: DS1\n");
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1 DS2\n"
+ + "E2, samples: S2\n"
+ + "S1, data sets: DS1\n"
+ + "DS1, components: DS2");
reassignToSample(g.ds(1), g.s(2));
assertEquals("E1, samples: S1\n"
- + "E2, samples: S2, data sets: DS1\nS2, data sets: DS1\n", renderGraph(g));
+ + "E2, samples: S2, data sets: DS1 DS2\n"
+ + "S2, data sets: DS1\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));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
}
@Test
- public void dataSetReassignedFromSampleWithExperimentToSampleWithoutExperiment()
+ public void containerWithAllItsComponentsReassignedFromSampleWithExperimentToSampleWithoutExperiment()
{
- EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1[NEXP-TYPE]\n"
- + "S1, data sets: DS1[NEXP-TYPE]\nS2\n");
+ EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1[NECT] DS2[NET]\n"
+ + "S1, data sets: DS1[NECT] DS2[NET]\n"
+ + "S2\n"
+ + "DS1[NECT], components: DS2[NET]\n");
reassignToSample(g.ds(1), g.s(2));
assertEquals("E1, samples: S1\n"
- + "S2, data sets: DS1[NEXP-TYPE]\n", renderGraph(g));
+ + "S2, data sets: DS1[NECT] DS2[NET]\n"
+ + "DS1[NECT], components: DS2[NET]\n", renderGraph(g));
repository.assertModified(g.e(1));
repository.assertModified(g.s(1), g.s(2));
- repository.assertModified(g.ds(1));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
}
@Test
- public void dataSetReassignedFromSampleWithoutExperimentToExperiment()
+ public void containerWithAllItsComponentsReassignedFromSampleWithoutExperimentToExperiment()
{
EntityGraphGenerator g = parseAndCreateGraph("E1\n"
- + "S1, data sets: DS1[NEXP-TYPE]\n");
+ + "S1, data sets: DS1[NECT] DS2[NET]\n"
+ + "DS1[NECT], components: DS2[NET]\n");
reassignToExperiment(g.ds(1), g.e(1));
- assertEquals("E1, data sets: DS1[NEXP-TYPE]\n", renderGraph(g));
+ assertEquals("E1, data sets: DS1[NECT] DS2[NET]\n"
+ + "DS1[NECT], components: DS2[NET]\n", renderGraph(g));
repository.assertModified(g.e(1));
repository.assertModified(g.s(1));
- repository.assertModified(g.ds(1));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
}
@Test
- public void dataSetReassignedFromSampleWithoutExperimentToSampleWithExperiment()
+ public void containerWithAllItsComponentsReassignedFromSampleWithoutExperimentToSampleWithExperiment()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1\n"
- + "S2, data sets: DS1[NEXP-TYPE]\n");
+ + "S2, data sets: DS1[NECT] DS2[NET]\n"
+ + "DS1[NECT], components: DS2[NET]\n");
reassignToSample(g.ds(1), g.s(1));
- assertEquals("E1, samples: S1, data sets: DS1[NEXP-TYPE]\n"
- + "S1, data sets: DS1[NEXP-TYPE]\n", renderGraph(g));
+ assertEquals("E1, samples: S1, data sets: DS1[NECT] DS2[NET]\n"
+ + "S1, data sets: DS1[NECT] DS2[NET]\n"
+ + "DS1[NECT], components: DS2[NET]\n", renderGraph(g));
repository.assertModified(g.e(1));
repository.assertModified(g.s(1), g.s(2));
- repository.assertModified(g.ds(1));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
}
@Test
- public void dataSetReassignedFromSampleWithoutExperimentToSampleWithoutExperiment()
+ public void containerWithAllItsComponentsReassignedFromSampleWithoutExperimentToSampleWithoutExperiment()
{
- EntityGraphGenerator g = parseAndCreateGraph("S1, data sets: DS1[NO-EXP-TYPE]\n"
- + "S2\n");
+ EntityGraphGenerator g = parseAndCreateGraph("S1, data sets: DS1[NECT] DS2[NET]\n"
+ + "S2\n"
+ + "DS1[NECT], components: DS2[NET]\n");
reassignToSample(g.ds(1), g.s(2));
- assertEquals("S2, data sets: DS1[NO-EXP-TYPE]\n", renderGraph(g));
+ assertEquals("S2, data sets: DS1[NECT] DS2[NET]\n"
+ + "DS1[NECT], components: DS2[NET]\n", renderGraph(g));
repository.assertModified(g.s(1), g.s(2));
- repository.assertModified(g.ds(1));
+ repository.assertModified(g.ds(1), g.ds(2));
+ repository.assertUnmodified(g);
}
@Test(expectedExceptions =
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 e2fb6d78a1195de85261e2cedcfd089f7685150e..570825d19f59ea83b953d72f45adb8572c0bb4e1 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
@@ -20,11 +20,17 @@ import static org.hamcrest.CoreMatchers.is;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
+import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
+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;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
@@ -62,6 +68,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeWithRegistrationAndModificationDate;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
@@ -165,7 +172,7 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
System.setProperty("hibernate.search.index-mode", IndexMode.INDEX_FROM_SCRATCH.name());
System.setProperty("hibernate.search.index-base", "../openbis/targets/lucene/cleandb");
System.setProperty("hibernate.search.worker.execution", "sync");
- System.setProperty(DataSetTypeWithoutExperimentChecker.PROPERTY_KEY, " NO-EXP-.* , NEXP-.* ");
+ System.setProperty(DataSetTypeWithoutExperimentChecker.PROPERTY_KEY, " NO-EXP-.* , NE.* ");
}
private void setContext() throws Exception
@@ -485,8 +492,9 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
{
EntityGraphGenerator g = new EntityGraphGenerator();
g.parse(graphDefinition);
- prepare(g);
- assertEquals(removeSolitaryNodes(graphDefinition), renderGraph(g));
+ createGraph(g);
+ assertEquals(removeSolitaryNodes(graphDefinition), renderGraph(g, true));
+ repository.gatherModifictaionInfos();
return g;
}
@@ -506,31 +514,44 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
protected String renderGraph(EntityGraphGenerator g)
{
- repository.refreshGraph();
+ return renderGraph(g, false);
+ }
+
+ private String renderGraph(EntityGraphGenerator g, boolean showWhereIAm)
+ {
+ repository.refreshGraph(showWhereIAm);
StringBuilder builder = new StringBuilder();
for (ExperimentNode experimentNode : g.getExperiments().values())
{
StringBuilder builder2 = new StringBuilder();
render(builder2, "samples", repository.getSampleNode(experimentNode));
render(builder2, "data sets", repository.getDataSetNodes(experimentNode));
- if (builder2.length() > 0)
- {
- builder.append(experimentNode.getCode());
- builder.append(builder2).append("\n");
- }
+ appendNodeTo(builder, experimentNode, builder2);
}
for (SampleNode sampleNode : g.getSamples().values())
{
StringBuilder builder2 = new StringBuilder();
render(builder2, "data sets", repository.getDataSetNodes(sampleNode));
- if (builder2.length() > 0)
- {
- builder.append(sampleNode.getCode());
- builder.append(builder2).append("\n");
- }
+ appendNodeTo(builder, sampleNode, builder2);
+ }
+ for (DataSetNode dataSetNode : g.getDataSets().values())
+ {
+ StringBuilder builder2 = new StringBuilder();
+ render(builder2, "components", repository.getComponentDataSetNodes(dataSetNode));
+ appendNodeTo(builder, dataSetNode, builder2);
}
return builder.toString();
}
+
+ private void appendNodeTo(StringBuilder builder, EntityNode entityNode, StringBuilder builder2)
+ {
+ if (builder2.length() > 0)
+ {
+ builder.append(entityNode.getCodeAndType());
+
+ builder.append(builder2).append("\n");
+ }
+ }
private void render(StringBuilder builder, String name, Collection<? extends EntityNode> nodes)
{
@@ -541,22 +562,18 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
builder.append(", ").append(name).append(":");
for (EntityNode node : nodes)
{
- builder.append(' ').append(node.getCode());
- if (node.getType() != null)
- {
- builder.append("[").append(node.getType()).append("]");
- }
+ builder.append(' ').append(node.getCodeAndType());
}
}
- private void prepare(EntityGraphGenerator g)
+ private void createGraph(EntityGraphGenerator g)
{
repository = new EntityRepository();
Space space = create(aSpace());
Project project = create(aProject().inSpace(space));
for (ExperimentNode experimentNode : g.getExperiments().values())
{
- repository.put(experimentNode, create(anExperiment().inProject(project)));
+ addToRepository(experimentNode, create(anExperiment().inProject(project)));
}
for (SampleNode sampleNode : g.getSamples().values())
{
@@ -566,9 +583,11 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
{
sample.inExperiment(repository.getExperiment(experimentNode));
}
- repository.put(sampleNode, create(sample));
+ addToRepository(sampleNode, sample);
}
- for (DataSetNode dataSetNode : g.getDataSets().values())
+ List<DataSetNode> dataSetNodes = new ArrayList<DataSetNode>(g.getDataSets().values());
+ Collections.reverse(dataSetNodes);
+ for (DataSetNode dataSetNode : dataSetNodes)
{
ExternalDataBuilder dataSet = aDataSet().withType(dataSetNode.getType());
if (dataSetNode.getSample() != null)
@@ -578,10 +597,62 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
{
dataSet.inExperiment(repository.getExperiment(dataSetNode.getExperiment()));
}
+ List<DataSetNode> components = dataSetNode.getComponents();
+ if (components.isEmpty() == false)
+ {
+ dataSet.asContainer();
+ for (DataSetNode component : components)
+ {
+ AbstractExternalData componentDataSet = repository.getDataSet(component);
+ if (componentDataSet == null)
+ {
+ throw new IllegalStateException("Data set " + component.getCode()
+ + " is specified as component of " + dataSetNode.getCode()
+ + " but hasn't yet created.");
+ }
+ dataSet.withComponent(componentDataSet);
+ }
+ }
+ addToRepository(dataSetNode, dataSet);
+ }
+ }
+
+ private void addToRepository(ExperimentNode experimentNode, Experiment experiment)
+ {
+ try
+ {
+ repository.put(experimentNode, experiment);
+ } catch (Exception ex)
+ {
+ throw new RuntimeException("Error while creating experiment for node " + experimentNode.getCode()
+ + ": " + ex.getMessage(), ex);
+ }
+ }
+
+ private void addToRepository(SampleNode sampleNode, SampleBuilder sample)
+ {
+ try
+ {
+ repository.put(sampleNode, create(sample));
+ } catch (Exception ex)
+ {
+ throw new RuntimeException("Error while creating sample for node " + sampleNode.getCode()
+ + ": " + ex.getMessage(), ex);
+ }
+ }
+
+ private void addToRepository(DataSetNode dataSetNode, ExternalDataBuilder dataSet)
+ {
+ try
+ {
repository.put(dataSetNode, create(dataSet));
+ } catch (Exception ex)
+ {
+ throw new RuntimeException("Error while creating data set for node " + dataSetNode.getCodeAndType()
+ + ": " + ex.getMessage(), ex);
}
}
-
+
public static ExperimentIdentifier id(Experiment experiment)
{
return new ExperimentIdentifier(id(experiment.getProject()), experiment.getCode());
@@ -680,18 +751,48 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
private Map<Long, Experiment> experimentsNodeToDtoMap = new TreeMap<Long, Experiment>();
private Map<Long, ExperimentNode> experimentDtoToNodeMap = new TreeMap<Long, ExperimentNode>();
private Map<Long, ModificationInfo> experimentModificationInfoByNodeId = new HashMap<Long, ModificationInfo>();
+ private Set<ExperimentNode> modifiedExperimentNodes = new HashSet<ExperimentNode>();
private Map<Long, Sample> samplesNodeToDtoMap = new TreeMap<Long, Sample>();
private Map<Long, SampleNode> samplesDtoToNodeMap = new TreeMap<Long, SampleNode>();
private Map<Long, ModificationInfo> sampleModificationInfoByNodeId = new HashMap<Long, ModificationInfo>();
+ private Set<SampleNode> modifiedSampleNodes = new HashSet<SampleNode>();
private Map<Long, AbstractExternalData> dataSetsNodeToDtoMap = new TreeMap<Long, AbstractExternalData>();
private Map<Long, DataSetNode> dataSetsDtoToNodeMap = new TreeMap<Long, DataSetNode>();
private Map<Long, ModificationInfo> dataSetModificationInfoByNodeId = new HashMap<Long, ModificationInfo>();
-
+ private Set<DataSetNode> modifiedDataSetNodes = new HashSet<DataSetNode>();
+
private Map<Long, Set<Long>> experimentSamplesMap = 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>>();
+
+ public String renderNodeToDtoMapping()
+ {
+ StringBuilder builder = new StringBuilder();
+ for (Entry<Long, Experiment> entry : experimentsNodeToDtoMap.entrySet())
+ {
+ render(builder, "E", entry.getKey(), entry.getValue());
+ }
+ for (Entry<Long, Sample> entry : samplesNodeToDtoMap.entrySet())
+ {
+ render(builder, "S", entry.getKey(), entry.getValue());
+ }
+ for (Entry<Long, AbstractExternalData> entry : dataSetsNodeToDtoMap.entrySet())
+ {
+ render(builder, "DS", entry.getKey(), entry.getValue());
+ }
+ return builder.toString();
+ }
+
+ private void render(StringBuilder builder, String prefix, Long id,
+ CodeWithRegistrationAndModificationDate<?> entity)
+ {
+ builder.append(prefix).append(id).append(" -> ").append(entity.getCode()).append(" (");
+ builder.append(entity.getModifier().getUserId()).append(", ");
+ builder.append(entity.getModificationDate()).append(")\n");
+ }
public Experiment getExperiment(ExperimentNode experimentNode)
{
@@ -708,19 +809,19 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
return dataSetsNodeToDtoMap.get(dataSetNode.getId());
}
- void refreshGraph()
+ void refreshGraph(boolean showWhereIAm)
{
for (Long id : experimentsNodeToDtoMap.keySet())
{
- experimentsNodeToDtoMap.put(id, refresh(experimentsNodeToDtoMap.get(id)));
+ experimentsNodeToDtoMap.put(id, refresh(experimentsNodeToDtoMap.get(id)));
}
for (Long id : samplesNodeToDtoMap.keySet())
{
- samplesNodeToDtoMap.put(id, refresh(samplesNodeToDtoMap.get(id)));
+ samplesNodeToDtoMap.put(id, refresh(samplesNodeToDtoMap.get(id)));
}
for (Long id : dataSetsNodeToDtoMap.keySet())
{
- dataSetsNodeToDtoMap.put(id, refresh(dataSetsNodeToDtoMap.get(id)));
+ dataSetsNodeToDtoMap.put(id, refresh(dataSetsNodeToDtoMap.get(id)));
}
experimentSamplesMap.clear();
for (Sample sample : samplesNodeToDtoMap.values())
@@ -744,12 +845,34 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
addToDataSetsMap(experimentDataSetsMap, dataSet, dataSet.getExperiment());
}
sampleDataSetsMap.clear();
+ componentDataSetsMap.clear();
for (AbstractExternalData dataSet : dataSetsNodeToDtoMap.values())
{
addToDataSetsMap(sampleDataSetsMap, dataSet, dataSet.getSample());
+ List<ContainerDataSet> containerDataSets = dataSet.getContainerDataSets();
+ for (ContainerDataSet containerDataSet : containerDataSets)
+ {
+ addToDataSetsMap(componentDataSetsMap, dataSet, containerDataSet);
+ }
}
+ if (showWhereIAm)
+ {
+ printWhereIAm();
+ }
+ System.out.println("Entities mapping:\n" + renderNodeToDtoMapping());
}
+ private void printWhereIAm()
+ {
+ StackTraceElement[] stackTrace = Thread.currentThread().getStackTrace();
+ for (int i = 5, n = Math.min(stackTrace.length, 9); i < n; i++)
+ {
+ StackTraceElement element = stackTrace[i];
+ System.out.print(element.getMethodName() + " <- ");
+ }
+ System.out.println("...");
+ }
+
private void addToDataSetsMap(Map<Long, Set<Long>> holderDataSetsMap,
AbstractExternalData dataSet, IIdHolder idHolder)
{
@@ -766,57 +889,101 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
}
}
+ void gatherModifictaionInfos()
+ {
+ for (Entry<Long, Experiment> entry : experimentsNodeToDtoMap.entrySet())
+ {
+ experimentModificationInfoByNodeId.put(entry.getKey(), new ModificationInfo(entry.getValue()));
+ }
+ for (Entry<Long, Sample> entry : samplesNodeToDtoMap.entrySet())
+ {
+ sampleModificationInfoByNodeId.put(entry.getKey(), new ModificationInfo(entry.getValue()));
+ }
+ for (Entry<Long, AbstractExternalData> entry : dataSetsNodeToDtoMap.entrySet())
+ {
+ dataSetModificationInfoByNodeId.put(entry.getKey(), new ModificationInfo(entry.getValue()));
+ }
+ }
+
void put(ExperimentNode experimentNode, Experiment experiment)
{
experimentsNodeToDtoMap.put(experimentNode.getId(), experiment);
experimentDtoToNodeMap.put(experiment.getId(), experimentNode);
- experimentModificationInfoByNodeId.put(experimentNode.getId(), new ModificationInfo(experiment));
}
public void assertModified(ExperimentNode...experimentNodes)
{
- assertModificationInfo(true, experimentModificationInfoByNodeId, experimentsNodeToDtoMap, experimentNodes);
- }
-
- public void assertUnmodified(ExperimentNode...experimentNodes)
- {
- assertModificationInfo(false, experimentModificationInfoByNodeId, experimentsNodeToDtoMap, experimentNodes);
+ assertModificationInfo(true, experimentModificationInfoByNodeId, experimentsNodeToDtoMap,
+ Arrays.<EntityNode>asList(experimentNodes));
+ modifiedExperimentNodes.addAll(Arrays.asList(experimentNodes));
}
void put(SampleNode sampleNode, Sample sample)
{
samplesNodeToDtoMap.put(sampleNode.getId(), sample);
samplesDtoToNodeMap.put(sample.getId(), sampleNode);
- sampleModificationInfoByNodeId.put(sampleNode.getId(), new ModificationInfo(sample));
}
public void assertModified(SampleNode...sampleNodes)
{
- assertModificationInfo(true, sampleModificationInfoByNodeId, samplesNodeToDtoMap, sampleNodes);
- }
-
- public void assertUnmodified(SampleNode...sampleNodes)
- {
- assertModificationInfo(false, sampleModificationInfoByNodeId, samplesNodeToDtoMap, sampleNodes);
+ assertModificationInfo(true, sampleModificationInfoByNodeId, samplesNodeToDtoMap,
+ Arrays.<EntityNode>asList(sampleNodes));
+ modifiedSampleNodes.addAll(Arrays.asList(sampleNodes));
}
void put(DataSetNode dataSetNode, AbstractExternalData dataSet)
{
dataSetsNodeToDtoMap.put(dataSetNode.getId(), dataSet);
dataSetsDtoToNodeMap.put(dataSet.getId(), dataSetNode);
- dataSetModificationInfoByNodeId.put(dataSetNode.getId(), new ModificationInfo(dataSet));
}
-
+
public void assertModified(DataSetNode...dataSetNodes)
{
- assertModificationInfo(true, dataSetModificationInfoByNodeId, dataSetsNodeToDtoMap, dataSetNodes);
+ assertModificationInfo(true, dataSetModificationInfoByNodeId, dataSetsNodeToDtoMap,
+ Arrays.<EntityNode>asList(dataSetNodes));
+ modifiedDataSetNodes.addAll(Arrays.asList(dataSetNodes));
}
- public void assertUnmodified(DataSetNode...dataSetNodes)
+ public void assertUnmodified(EntityGraphGenerator g)
{
- assertModificationInfo(false, dataSetModificationInfoByNodeId, dataSetsNodeToDtoMap, dataSetNodes);
+ Set<EntityNode> unmodifiedExperimentNodes = new HashSet<EntityNode>(g.getExperiments().values());
+ unmodifiedExperimentNodes.removeAll(modifiedExperimentNodes);
+ assertModificationInfo(false, experimentModificationInfoByNodeId, experimentsNodeToDtoMap, unmodifiedExperimentNodes);
+ Set<EntityNode> unmodifiedSampleNodes = new HashSet<EntityNode>(g.getSamples().values());
+ unmodifiedSampleNodes.removeAll(modifiedSampleNodes);
+ assertModificationInfo(false, sampleModificationInfoByNodeId, samplesNodeToDtoMap, unmodifiedSampleNodes);
+ Set<EntityNode> unmodifiedDataSetNodes = new HashSet<EntityNode>(g.getDataSets().values());
+ unmodifiedDataSetNodes.removeAll(modifiedDataSetNodes);
+ assertModificationInfo(false, dataSetModificationInfoByNodeId, dataSetsNodeToDtoMap, unmodifiedDataSetNodes);
}
+ private void assertModificationInfo(boolean modified, Map<Long, ModificationInfo> previousInfos,
+ Map<Long, ? extends CodeWithRegistrationAndModificationDate<?>> nodeToDtoMap,
+ Collection<EntityNode> entityNodes)
+ {
+ for (EntityNode node : entityNodes)
+ {
+ ModificationInfo previous = previousInfos.get(node.getId());
+ assertNotNull(node.getCode() + " no previous modification info", previous);
+ CodeWithRegistrationAndModificationDate<?> entity = nodeToDtoMap.get(node.getId());
+ assertNotNull(node.getCode() + " unknown", entity);
+ ModificationInfo current = new ModificationInfo(entity);
+ if (modified)
+ {
+ assertEquals(node.getCode() + " has unexpectedly still the old modifier: " + current.modifier,
+ false, current.modifier.equals(previous.modifier));
+ assertEquals(node.getCode() + " has unexpectedly still the old modification date: " + current.modificationDate,
+ true, current.modificationDate.getTime() > previous.modificationDate.getTime());
+ } else
+ {
+ assertEquals(node.getCode() + " has unexpectedly a new modifier: ",
+ previous.modifier, current.modifier);
+ assertEquals(node.getCode() + " has unexpectedly a new modification date:",
+ previous.modificationDate, current.modificationDate);
+ }
+ }
+ }
+
Set<SampleNode> getSampleNode(ExperimentNode experimentNode)
{
Set<SampleNode> result = new LinkedHashSet<SampleNode>();
@@ -845,9 +1012,14 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
return getDataSetNodes(sampleDataSetsMap, samplesNodeToDtoMap.get(sampleNode.getId()));
}
+ Set<DataSetNode> getComponentDataSetNodes(DataSetNode containerDataSetNode)
+ {
+ return getDataSetNodes(componentDataSetsMap, dataSetsNodeToDtoMap.get(containerDataSetNode.getId()));
+ }
+
private Set<DataSetNode> getDataSetNodes(Map<Long, Set<Long>> idHolderDataSetsMap, IIdHolder experiment)
{
- Set<DataSetNode> result = new LinkedHashSet<DataSetNode>();
+ Set<DataSetNode> result = new TreeSet<DataSetNode>();
if (experiment != null)
{
Set<Long> dataSetDtoIds = idHolderDataSetsMap.get(experiment.getId());
@@ -861,33 +1033,6 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
}
return result;
}
-
- private void assertModificationInfo(boolean modified, Map<Long, ModificationInfo> previousInfos,
- Map<Long, ? extends CodeWithRegistrationAndModificationDate<?>> nodeToDtoMap, EntityNode...entityNodes)
- {
- for (EntityNode node : entityNodes)
- {
- ModificationInfo previous = previousInfos.get(node.getId());
- assertNotNull(node.getCode() + " no previous modification info", previous);
- CodeWithRegistrationAndModificationDate<?> entity = nodeToDtoMap.get(node.getId());
- assertNotNull(node.getCode() + " unknown", entity);
- ModificationInfo current = new ModificationInfo(entity);
- if (modified)
- {
- assertEquals(node.getCode() + " still same modifier: " + current.modifier, false,
- current.modifier.equals(previous.modifier));
- assertEquals(node.getCode() + " still same modification date: " + current.modificationDate,
- true, current.modificationDate.getTime() > previous.modificationDate.getTime());
- } else
- {
- assertEquals(node.getCode() + " different modifiers: " + previous.modifier + " " + previous.modifier,
- previous.modifier, current.modifier);
- assertEquals(node.getCode() + " different modification date: " + previous.modificationDate
- + " " + current.modificationDate, previous.modificationDate, current.modificationDate);
- }
- }
- }
-
}
private static final class ModificationInfo
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/ExternalDataBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/ExternalDataBuilder.java
index b15d7e0cfeccef056bd580ca21709054ed0b2c39..ecaacc7e6984a9f6745191ddbb8f008487a660bd 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/ExternalDataBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/ExternalDataBuilder.java
@@ -131,9 +131,13 @@ public class ExternalDataBuilder extends Builder<AbstractExternalData>
if (this.sampleIdentifier != null)
{
etlService.registerDataSet(systemSession, sampleIdentifier, data);
- } else
+ } else if (experimentIdentifier != null)
{
etlService.registerDataSet(systemSession, experimentIdentifier, data);
+ } else
+ {
+ throw new IllegalStateException("Neither sample nor experiment has been specified for data set "
+ + data.getCode());
}
return etlService.tryGetDataSet(systemSession, this.code);
@@ -151,7 +155,7 @@ public class ExternalDataBuilder extends Builder<AbstractExternalData>
{
dataSetType.setDataSetKind(DataSetKind.PHYSICAL);
}
- commonServer.registerDataSetType(systemSession, dataSetType);
+ registerDataSetType(dataSetType);
NewExternalData data;
if (this.container)
@@ -175,4 +179,17 @@ public class ExternalDataBuilder extends Builder<AbstractExternalData>
data.setParentDataSetCodes(this.parentCodes);
return data;
}
+
+ private void registerDataSetType(DataSetType dataSetType)
+ {
+ List<DataSetType> dataSetTypes = commonServer.listDataSetTypes(systemSession);
+ for (DataSetType type : dataSetTypes)
+ {
+ if (type.getCode().equals(dataSetType.getCode()))
+ {
+ return;
+ }
+ }
+ commonServer.registerDataSetType(systemSession, dataSetType);
+ }
}
\ No newline at end of file