diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
index 3ac72d2c4bb6f9dbc081c40f3f61a67056a585a6..f917a7efe9f346ac1d1acb5282b14823ae96fc1e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
@@ -462,8 +462,7 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
throw UserFailureException.fromTemplate("Sample type with code '%s' does not exist.",
sampleTypeCode);
}
- getPropertiesBatchManager().manageProperties(sampleTypePE, newSamplesWithType,
- registratorOrNull);
+ getPropertiesBatchManager().manageProperties(sampleTypePE, newSamples, registratorOrNull);
getSampleTypeSlaveServerPlugin(sampleTypePE).registerSamples(session, newSamples,
registratorOrNull);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IPropertiesBatchManager.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IPropertiesBatchManager.java
index 4773ce1c1174a6c11257d0c2a23cf294914ca87b..5421fb5849e514a75448d7b0f30c40f00de68cd8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IPropertiesBatchManager.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IPropertiesBatchManager.java
@@ -18,9 +18,9 @@ package ch.systemsx.cisd.openbis.generic.server.business;
import java.util.List;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperimentsWithType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewBasicExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
@@ -33,11 +33,11 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
*/
public interface IPropertiesBatchManager
{
- public void manageProperties(SampleTypePE sampleType, NewSamplesWithTypes newSamplesWithTypes,
+ public void manageProperties(SampleTypePE sampleType, List<NewSample> newSamples,
PersonPE registrator);
public void manageProperties(ExperimentTypePE experimentType,
- NewExperimentsWithType experiments, PersonPE registrator);
+ List<? extends NewBasicExperiment> experiments, PersonPE registrator);
public void manageProperties(MaterialTypePE materialType, List<NewMaterial> newMaterials,
PersonPE registrator);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchManager.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchManager.java
index 30004e9f67f87c986135e4296d80f30a11fb3438..1cefc1673836d08b4e3ddc92be418b8e8e52a7f5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchManager.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchManager.java
@@ -36,9 +36,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IPropertiesBean;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ManagedProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperimentsWithType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewBasicExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.ValidationException;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
@@ -52,7 +52,7 @@ import ch.systemsx.cisd.openbis.generic.shared.managed_property.ManagedPropertyE
/**
* Handles Managed Properties of batch uploads/updates.
- *
+ *
* @author Franz-Josef Elmer
*/
public class PropertiesBatchManager implements IPropertiesBatchManager
@@ -67,27 +67,24 @@ public class PropertiesBatchManager implements IPropertiesBatchManager
private final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY, getClass());
-
-
- public void manageProperties(SampleTypePE sampleType, NewSamplesWithTypes newSamplesWithTypes,
+ public void manageProperties(SampleTypePE sampleType, List<NewSample> samples,
PersonPE registrator)
{
Set<? extends EntityTypePropertyTypePE> sampleTypePropertyTypes =
sampleType.getSampleTypePropertyTypes();
-
- managePropertiesBeans(newSamplesWithTypes.getNewSamples(), sampleTypePropertyTypes,
- registrator);
+
+ managePropertiesBeans(samples, sampleTypePropertyTypes, registrator);
}
-
+
public void manageProperties(ExperimentTypePE experimentType,
- NewExperimentsWithType experiments, PersonPE registrator)
+ List<? extends NewBasicExperiment> experiments, PersonPE registrator)
{
Set<? extends EntityTypePropertyTypePE> entityTypePropertyTypes =
experimentType.getExperimentTypePropertyTypes();
- managePropertiesBeans(experiments.getNewExperiments(), entityTypePropertyTypes, registrator);
+ managePropertiesBeans(experiments, entityTypePropertyTypes, registrator);
}
-
+
public void manageProperties(MaterialTypePE materialType, List<NewMaterial> newMaterials,
PersonPE registrator)
{
@@ -99,9 +96,9 @@ public class PropertiesBatchManager implements IPropertiesBatchManager
private void managePropertiesBeans(List<? extends IPropertiesBean> propertiesBeans,
Set<? extends EntityTypePropertyTypePE> entityTypePropertyTypes, PersonPE registrator)
{
- Map<String, EvaluationContext> contexts =
- createEvaluationContexts(entityTypePropertyTypes);
- PropertiesBatchEvaluationErrors errors = new PropertiesBatchEvaluationErrors(registrator, propertiesBeans.size());
+ Map<String, EvaluationContext> contexts = createEvaluationContexts(entityTypePropertyTypes);
+ PropertiesBatchEvaluationErrors errors =
+ new PropertiesBatchEvaluationErrors(registrator, propertiesBeans.size());
int rowNumber = 0;
for (IPropertiesBean propertiesBean : propertiesBeans)
@@ -160,8 +157,8 @@ public class PropertiesBatchManager implements IPropertiesBatchManager
EntityProperty entityProperty = createNewEntityProperty(code);
if (evalContext == null)
{
- ManagedPropertyEvaluator.assertBatchColumnNames(code,
- Collections.<String> emptyList(), bindings);
+ ManagedPropertyEvaluator.assertBatchColumnNames(code, Collections.<String> emptyList(),
+ bindings);
entityProperty.setValue(bindings.get(""));
} else
{
@@ -229,4 +226,4 @@ public class PropertiesBatchManager implements IPropertiesBatchManager
}
return result;
}
-}
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
index e57769834d9bf2c2fa825f526d5f252de1e93b24..7ec512d000fa79cd9753237a07be399a796ddb29 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
@@ -425,7 +425,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
throw UserFailureException.fromTemplate("Sample type with code '%s' does not exist.",
sampleTypeCode);
}
- getPropertiesBatchManager().manageProperties(sampleTypePE, updatedSamplesWithType,
+ getPropertiesBatchManager().manageProperties(sampleTypePE, updatedSamples,
session.tryGetPerson());
getSampleTypeSlaveServerPlugin(sampleTypePE).updateSamples(session,
convertSamples(updatedSamples));
@@ -839,7 +839,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
throw UserFailureException.fromTemplate(
"Experiment type with code '%s' does not exist.", experimentTypePE);
}
- getPropertiesBatchManager().manageProperties(experimentTypePE, experiments,
+ getPropertiesBatchManager().manageProperties(experimentTypePE, newExperiments,
session.tryGetPerson());
BatchOperationExecutor.executeInBatches(new ExperimentBatchRegistration(
businessObjectFactory.createExperimentTable(session), newExperiments,
@@ -874,6 +874,8 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
throw UserFailureException.fromTemplate(
"Experiment type with code '%s' does not exist.", experimentTypePE);
}
+ getPropertiesBatchManager().manageProperties(experimentTypePE, newExperiments,
+ session.tryGetPerson());
BatchOperationExecutor.executeInBatches(new ExperimentBatchUpdate(businessObjectFactory
.createExperimentTable(session), convertExperiments(newExperiments),
experimentTypePE));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchManagerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchManagerTest.java
index 6ed9c440ca813aa238323fb016f8bc7291e317ba..164464cf60f5fc2d9313924407fe7feee4e60de2 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchManagerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchManagerTest.java
@@ -25,9 +25,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IPropertiesBean;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewBasicExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperimentsWithType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ScriptType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.PropertyBuilder;
import ch.systemsx.cisd.openbis.generic.shared.dto.builders.ExperimentTypePEBuilder;
@@ -39,8 +37,12 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.builders.SampleTypePEBuilder;
public class PropertiesBatchManagerTest extends AssertJUnit
{
private static final String MANAGED_SUBCOLUMNS = "MANAGED_SUBCOLUMNS";
- private static final String MANAGED_NO_SUBCOLUMNS_BUT_UPDATE = "MANAGED-NO-SUBCOLUMNS-BUT-UPDATE";
+
+ private static final String MANAGED_NO_SUBCOLUMNS_BUT_UPDATE =
+ "MANAGED-NO-SUBCOLUMNS-BUT-UPDATE";
+
private static final String MANAGED_NO_SUBCOLUMNS_NO_UPDATE = "MANAGED-NO-SUBCOLUMNS";
+
private static final String UN_MANAGED = "UN-MANAGED";
@Test
@@ -49,9 +51,10 @@ public class PropertiesBatchManagerTest extends AssertJUnit
ExperimentTypePEBuilder builder = new ExperimentTypePEBuilder();
builder.assign(UN_MANAGED);
builder.assign(MANAGED_NO_SUBCOLUMNS_NO_UPDATE).script(ScriptType.MANAGED_PROPERTY, "");
- builder.assign(MANAGED_NO_SUBCOLUMNS_BUT_UPDATE).script(ScriptType.MANAGED_PROPERTY,
- "def updateFromBatchInput(columnValues):\n" +
- " property.setValue(columnValues.get('') + ' alpha')");
+ builder.assign(MANAGED_NO_SUBCOLUMNS_BUT_UPDATE).script(
+ ScriptType.MANAGED_PROPERTY,
+ "def updateFromBatchInput(columnValues):\n"
+ + " property.setValue(columnValues.get('') + ' alpha')");
builder.assign(MANAGED_SUBCOLUMNS).script(
ScriptType.MANAGED_PROPERTY,
"def batchColumnNames():\n return ['1', '2']\n"
@@ -66,33 +69,33 @@ public class PropertiesBatchManagerTest extends AssertJUnit
PropertyBuilder p4 = new PropertyBuilder(MANAGED_SUBCOLUMNS + ":1").value("ab");
PropertyBuilder p5 = new PropertyBuilder(MANAGED_SUBCOLUMNS + ":2").value("12");
addProperties(e2, p3, p4, p5);
- NewExperimentsWithType experiments = new NewExperimentsWithType("T", Arrays.asList(e1, e2));
-
- new PropertiesBatchManager().manageProperties(builder.getExperimentTypePE(), experiments,
- null);
-
+
+ new PropertiesBatchManager().manageProperties(builder.getExperimentTypePE(),
+ Arrays.asList(e1, e2), null);
+
assertProperties("UN-MANAGED:hello, MANAGED-NO-SUBCOLUMNS:hi", e1);
assertProperties("MANAGED-NO-SUBCOLUMNS-BUT-UPDATE:hi alpha, MANAGED_SUBCOLUMNS:ab12", e2);
}
-
+
@Test
public void testScriptErrorWhenExecutingUpdateFromBatchInput()
{
SampleTypePEBuilder builder = new SampleTypePEBuilder();
- builder.assign(MANAGED_NO_SUBCOLUMNS_BUT_UPDATE).script(ScriptType.MANAGED_PROPERTY,
- "def updateFromBatchInput(columnValues):\n" +
- " property.setValue(str(int(columnValues.get('')) + 42))");
+ builder.assign(MANAGED_NO_SUBCOLUMNS_BUT_UPDATE).script(
+ ScriptType.MANAGED_PROPERTY,
+ "def updateFromBatchInput(columnValues):\n"
+ + " property.setValue(str(int(columnValues.get('')) + 42))");
NewSample s1 = new NewSample();
PropertyBuilder p1 = new PropertyBuilder(MANAGED_NO_SUBCOLUMNS_BUT_UPDATE).value("1");
addProperties(s1, p1);
NewSample s2 = new NewSample();
PropertyBuilder p2 = new PropertyBuilder(MANAGED_NO_SUBCOLUMNS_BUT_UPDATE).value("two");
addProperties(s2, p2);
- NewSamplesWithTypes samples = new NewSamplesWithTypes(null, Arrays.asList(s1, s2));
-
+
try
{
- new PropertiesBatchManager().manageProperties(builder.getSampleType(), samples, null);
+ new PropertiesBatchManager().manageProperties(builder.getSampleType(),
+ Arrays.asList(s1, s2), null);
} catch (UserFailureException ufe)
{
assertEquals(
@@ -103,34 +106,34 @@ public class PropertiesBatchManagerTest extends AssertJUnit
+ "A detailed error report has been sent to your system administrator.",
ufe.getMessage());
}
-
+
assertProperties("MANAGED-NO-SUBCOLUMNS-BUT-UPDATE:43", s1);
}
-
+
@Test
public void testScriptThrowingValidationException()
{
ExperimentTypePEBuilder builder = new ExperimentTypePEBuilder();
- builder.assign(MANAGED_NO_SUBCOLUMNS_BUT_UPDATE).script(ScriptType.MANAGED_PROPERTY,
- "def updateFromBatchInput(columnValues):\n" +
- " raise ValidationException('Oops!')");
+ builder.assign(MANAGED_NO_SUBCOLUMNS_BUT_UPDATE).script(
+ ScriptType.MANAGED_PROPERTY,
+ "def updateFromBatchInput(columnValues):\n"
+ + " raise ValidationException('Oops!')");
NewBasicExperiment e1 = new NewBasicExperiment();
PropertyBuilder p1 = new PropertyBuilder(MANAGED_NO_SUBCOLUMNS_BUT_UPDATE).value("hello");
addProperties(e1, p1);
- NewExperimentsWithType experiments = new NewExperimentsWithType("T", Arrays.asList(e1));
-
+
try
{
new PropertiesBatchManager().manageProperties(builder.getExperimentTypePE(),
- experiments, null);
+ Arrays.asList(e1), null);
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
assertEquals("Error in row 1: Oops!", ex.getMessage());
}
-
+
}
-
+
@Test
public void testSubColumnsButNoScript()
{
@@ -139,19 +142,18 @@ public class PropertiesBatchManagerTest extends AssertJUnit
NewBasicExperiment e1 = new NewBasicExperiment();
PropertyBuilder p1 = new PropertyBuilder(UN_MANAGED + ":1").value("hello");
addProperties(e1, p1);
- NewExperimentsWithType experiments = new NewExperimentsWithType("T", Arrays.asList(e1));
-
+
try
{
new PropertiesBatchManager().manageProperties(builder.getExperimentTypePE(),
- experiments, null);
+ Arrays.asList(e1), null);
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
assertEquals("No subcolumns expected for property 'UN-MANAGED': [1]", ex.getMessage());
}
}
-
+
private void assertProperties(String expectedProperties, IPropertiesBean propertiesBean)
{
StringBuilder builder = new StringBuilder();
@@ -167,7 +169,7 @@ public class PropertiesBatchManagerTest extends AssertJUnit
}
assertEquals(expectedProperties, builder.toString());
}
-
+
private void addProperties(IPropertiesBean propertiesBean, PropertyBuilder... builders)
{
IEntityProperty[] properties = new IEntityProperty[builders.length];
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
index b08783e5049ae670735ef8c1141202a510325e49..891e6d18819a4f3e8c6b65f1f016f039f793d347 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
@@ -280,8 +280,7 @@ public final class GenericServerTest extends AbstractServerTestCase
one(sampleTypeSlaveServerPlugin).registerSamples(SESSION, newSamples, null);
- one(propertiesBatchManager).manageProperties(sampleTypePE, newSamplesWithType,
- null);
+ one(propertiesBatchManager).manageProperties(sampleTypePE, newSamples, null);
}
});
createServer().registerOrUpdateSamples(SESSION_TOKEN, samplesWithTypes);
@@ -310,8 +309,7 @@ public final class GenericServerTest extends AbstractServerTestCase
one(sampleTypeSlaveServerPlugin).registerSamples(SESSION, newSamples, null);
- one(propertiesBatchManager).manageProperties(sampleTypePE, newSamplesWithType,
- null);
+ one(propertiesBatchManager).manageProperties(sampleTypePE, newSamples, null);
}
});
createServer().registerSamples(SESSION_TOKEN, samplesWithTypes);
@@ -840,8 +838,7 @@ public final class GenericServerTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- one(propertiesBatchManager).manageProperties(experimentTypePE, experiments,
- null);
+ one(propertiesBatchManager).manageProperties(experimentTypePE, entities, null);
one(daoFactory).getEntityTypeDAO(EntityKind.EXPERIMENT);
will(returnValue(entityTypeDAO));
one(entityTypeDAO).tryToFindEntityTypeByCode(EXPERIMENT_TYPE);