diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/BundleDataSetHelper.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/BundleDataSetHelper.java
deleted file mode 100644
index 332453ce605a9bedb05cdbd61f57962f72cff33d..0000000000000000000000000000000000000000
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/BundleDataSetHelper.java
+++ /dev/null
@@ -1,119 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.cina.dss.bundle;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import ch.systemsx.cisd.etlserver.IDataSetHandler;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-
-/**
- * Helper to help registering bundle data sets.
- * <p>
- * This helper registers the entire bundle as one data set.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-class BundleDataSetHelper
-{
-
- static class BundleRegistrationGlobalState
- {
- private final IDataSetHandler delegator;
-
- private final IEncapsulatedOpenBISService openbisService;
-
- private final SampleType replicaSampleType;
-
- private final DataSetTypeWithVocabularyTerms imageDataSetType;
-
- BundleRegistrationGlobalState(IDataSetHandler delegator,
- IEncapsulatedOpenBISService openbisService, SampleType replicaSampleType,
- DataSetTypeWithVocabularyTerms imageDataSetType)
- {
- this.delegator = delegator;
- this.openbisService = openbisService;
- this.replicaSampleType = replicaSampleType;
- this.imageDataSetType = imageDataSetType;
- }
-
- IDataSetHandler getDelegator()
- {
- return delegator;
- }
-
- IEncapsulatedOpenBISService getOpenbisService()
- {
- return openbisService;
- }
-
- SampleType getReplicaSampleType()
- {
- return replicaSampleType;
- }
-
- DataSetTypeWithVocabularyTerms getImageDataSetType()
- {
- return imageDataSetType;
- }
- }
-
- protected final BundleRegistrationGlobalState globalState;
-
- protected final File dataSet;
-
- protected final ArrayList<DataSetInformation> dataSetInformation;
-
- BundleDataSetHelper(BundleRegistrationGlobalState globalState, File dataSet)
- {
- this.globalState = globalState;
- this.dataSet = dataSet;
- this.dataSetInformation = new ArrayList<DataSetInformation>();
- }
-
- public void process()
- {
- // Register the bundle as one data set
- List<DataSetInformation> bigDataSet = getDelegator().handleDataSet(dataSet);
- dataSetInformation.addAll(bigDataSet);
- }
-
- protected IDataSetHandler getDelegator()
- {
- return globalState.getDelegator();
- }
-
- protected IEncapsulatedOpenBISService getOpenbisService()
- {
- return globalState.getOpenbisService();
- }
-
- /**
- * Get all the data set information that has been created as a result of {@link #process}. Only
- * makes sense to invoke after process has been called
- */
- public ArrayList<DataSetInformation> getDataSetInformation()
- {
- return dataSetInformation;
- }
-
-}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/BundleDataSetHelperRpc.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/BundleDataSetHelperRpc.java
deleted file mode 100644
index 3ee3aea11930cceaf89058124c3ba7e95b2039e5..0000000000000000000000000000000000000000
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/BundleDataSetHelperRpc.java
+++ /dev/null
@@ -1,211 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.cina.dss.bundle;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import ch.systemsx.cisd.cina.shared.metadata.BundleMetadataExtractor;
-import ch.systemsx.cisd.cina.shared.metadata.ImageMetadataExtractor;
-import ch.systemsx.cisd.cina.shared.metadata.ReplicaMetadataExtractor;
-import ch.systemsx.cisd.etlserver.IDataSetHandler;
-import ch.systemsx.cisd.etlserver.IDataSetHandlerRpc;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyTypeWithVocabulary;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-
-/**
- * Helper class for processing bundle data sets.
- * <p>
- * This helper registers the entire bundle as one data set, generates samples for each replica, and
- * registers each file as a data set associated with the sample.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-class BundleDataSetHelperRpc extends BundleDataSetHelper
-{
- private static final String MISC_DATA_SET_PROPERTY_CODE = "MISC";
-
- // Invocation-specific State
- private final SessionContextDTO sessionContext;
-
- private final IDataSetHandlerRpc delegatorRpc;
-
- BundleDataSetHelperRpc(BundleRegistrationGlobalState globalState, File dataSet)
- {
- super(globalState, dataSet);
- IDataSetHandler delegator = globalState.getDelegator();
- if (delegator instanceof IDataSetHandlerRpc)
- {
- delegatorRpc = (IDataSetHandlerRpc) delegator;
- this.sessionContext = delegatorRpc.getSessionContext();
- } else
- {
- throw new IllegalArgumentException(
- "BundleDataSetHelperRpc used with non-RPC data set handler.");
- }
- }
-
- /**
- *
- */
- @Override
- public void process()
- {
- String dataSetName = dataSet.getName();
- // Register the bundle as one data set
- super.process();
- if (dataSetInformation.isEmpty())
- {
- return;
- }
-
- ExternalData bigData =
- getOpenbisService().tryGetDataSet(sessionContext.getSessionToken(),
- getBigDataSetInformation().getDataSetCode());
- File containerFile = delegatorRpc.getFileForExternalData(bigData);
- File bundle = new File(containerFile, dataSetName);
-
- BundleMetadataExtractor bundleMetadata = new BundleMetadataExtractor(bundle);
- bundleMetadata.prepare();
- for (ReplicaMetadataExtractor replicaMetadata : bundleMetadata.getReplicaMetadataExtractors())
- {
- handleDerivedDataSets(replicaMetadata);
- }
- }
-
- private void handleDerivedDataSets(ReplicaMetadataExtractor replicaMetadata)
- {
- SampleIdentifier sampleId = registerReplicaSample();
-
- // Register all the data sets derived from this sample
- for (ImageMetadataExtractor imageMetadata : replicaMetadata.getImageMetadataExtractors())
- {
- handleDerivedDataSet(sampleId, imageMetadata);
- }
- }
-
- /**
- * Register a sample with this ID of type GRID_REPLICA, either derived from the GRID_TEMPLATE
- * registered by the client or associated with the experiment.
- */
- private SampleIdentifier registerReplicaSample()
- {
- DataSetInformation bigDataSetInfo = getBigDataSetInformation();
- SampleType replicaSampleType = globalState.getReplicaSampleType();
- long sampleCodeSuffix = getOpenbisService().drawANewUniqueID();
- String sampleCode =
- String.format("%s%d", replicaSampleType.getGeneratedCodePrefix(), sampleCodeSuffix);
- ExperimentIdentifier experimentIdOrNull = bigDataSetInfo.getExperimentIdentifier();
- SampleIdentifier parentIdOrNull = bigDataSetInfo.getSampleIdentifier();
-
- // Either the experimentId or the parentId must be non-null
- assert experimentIdOrNull != null || parentIdOrNull != null;
-
- SampleIdentifier sampleId = null;
- NewSample sample = null;
- if (parentIdOrNull != null)
- {
- Sample parentSample = getOpenbisService().tryGetSampleWithExperiment(parentIdOrNull);
- sampleId = new SampleIdentifier(parentIdOrNull.getSpaceLevel(), sampleCode);
- sample =
- NewSample.createWithParent(sampleId.toString(), replicaSampleType, null,
- parentIdOrNull.toString());
- sample.setExperimentIdentifier(parentSample.getExperiment().getIdentifier());
- } else if (experimentIdOrNull != null)
- {
- SpaceIdentifier spaceId =
- new SpaceIdentifier(experimentIdOrNull.getDatabaseInstanceCode(),
- experimentIdOrNull.getSpaceCode());
- sampleId = new SampleIdentifier(spaceId, sampleCode);
- sample = NewSample.createWithParent(sampleId.toString(), replicaSampleType, null, null);
- sample.setExperimentIdentifier(experimentIdOrNull.toString());
- }
-
- String userIdOrNull = (sessionContext == null) ? null : sessionContext.getUserName();
- getOpenbisService().registerSample(sample, userIdOrNull);
- return sampleId;
- }
-
- private void handleDerivedDataSet(SampleIdentifier sampleId,
- ImageMetadataExtractor imageMetadata)
- {
- // Create a DataSetInformation
- DataSetInformation imageDataSetInfo = createDataSetInformation(sampleId);
-
- // Import the metadata
- ArrayList<NewProperty> properties = createDataSetProperties(imageMetadata);
- imageDataSetInfo.setDataSetProperties(properties);
-
- File imageDataSet = imageMetadata.getFolder();
-
- delegatorRpc.linkAndHandleDataSet(imageDataSet, imageDataSetInfo);
- }
-
- private ArrayList<NewProperty> createDataSetProperties(ImageMetadataExtractor imageMetadata)
- {
- List<PropertyTypeWithVocabulary> propertyTypes =
- globalState.getImageDataSetType().getPropertyTypes();
- ArrayList<NewProperty> properties = new ArrayList<NewProperty>();
- for (PropertyTypeWithVocabulary propertyType : propertyTypes)
- {
- String value = imageMetadata.getMetadataMap().get(propertyType.getCode().toLowerCase());
- if (null != value)
- {
- NewProperty prop;
- prop = new NewProperty(propertyType.getCode(), value);
- properties.add(prop);
- }
- }
-
- // Add a property with everything
- properties.add(new NewProperty(MISC_DATA_SET_PROPERTY_CODE, imageMetadata.getMetadataMap()
- .toString()));
- return properties;
- }
-
- private DataSetInformation createDataSetInformation(SampleIdentifier sampleId)
- {
- DataSetInformation imageDataSetInfo = new DataSetInformation();
- imageDataSetInfo.setSampleCode(sampleId.getSampleCode());
- imageDataSetInfo.setSpaceCode(sampleId.getSpaceLevel().getSpaceCode());
- imageDataSetInfo.setInstanceCode(sampleId.getSpaceLevel().getDatabaseInstanceCode());
- imageDataSetInfo.setDataSetType(globalState.getImageDataSetType().getDataSetType());
- imageDataSetInfo.setParentDataSetCodes(Collections.singletonList(getBigDataSetInformation()
- .getDataSetCode()));
- return imageDataSetInfo;
- }
-
- /**
- * Get the "big data set" -- the one that is the parent of all the derived data sets I register
- */
- private DataSetInformation getBigDataSetInformation()
- {
- // The big data set is the first one registered.
- return dataSetInformation.get(0);
- }
-}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandler.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandler.java
index fe4ce92f5d6fa7f5b8432f81f8ae090cd90f06b6..d0f978419c315208460dbd33d78687c43eff168c 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandler.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandler.java
@@ -20,14 +20,12 @@ import java.io.File;
import java.util.List;
import java.util.Properties;
-import ch.systemsx.cisd.cina.dss.bundle.BundleDataSetHelper.BundleRegistrationGlobalState;
-import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
+import ch.systemsx.cisd.cina.dss.bundle.registrators.BundleRegistrationState;
+import ch.systemsx.cisd.cina.dss.bundle.registrators.GridPreparationRegistrator;
import ch.systemsx.cisd.etlserver.IDataSetHandler;
import ch.systemsx.cisd.etlserver.IDataSetHandlerRpc;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
/**
* CINA registers data in the form of a bundle. A bundle contains several different kinds data sets.
@@ -84,23 +82,30 @@ public class CinaBundleDataSetHandler implements IDataSetHandler
{
private final IDataSetHandler delegator;
- private final BundleRegistrationGlobalState bundleRegistrationState;
+ private final BundleRegistrationState bundleRegistrationState;
public CinaBundleDataSetHandler(Properties parentProperties, IDataSetHandler delegator,
IEncapsulatedOpenBISService openbisService)
{
this.delegator = delegator;
- this.bundleRegistrationState = createBundleRegistrationState(delegator, openbisService);
+ if (delegator instanceof IDataSetHandlerRpc)
+ {
+ this.bundleRegistrationState =
+ createBundleRegistrationState((IDataSetHandlerRpc) delegator, openbisService);
+ } else
+ {
+ this.bundleRegistrationState = null;
+ }
}
public List<DataSetInformation> handleDataSet(File dataSet)
{
- BundleDataSetHelper helper;
if (delegator instanceof IDataSetHandlerRpc)
{
- helper = new BundleDataSetHelperRpc(bundleRegistrationState, dataSet);
- helper.process();
- return helper.getDataSetInformation();
+ GridPreparationRegistrator registrator =
+ new GridPreparationRegistrator(bundleRegistrationState, dataSet);
+ registrator.register();
+ return registrator.getDataSetInformation();
} else
{
// We are not being invoked from the command line, so we don't have enough contextual
@@ -110,14 +115,9 @@ public class CinaBundleDataSetHandler implements IDataSetHandler
}
}
- private static BundleRegistrationGlobalState createBundleRegistrationState(
- IDataSetHandler delegator, IEncapsulatedOpenBISService openbisService)
+ private static BundleRegistrationState createBundleRegistrationState(
+ IDataSetHandlerRpc delegator, IEncapsulatedOpenBISService openbisService)
{
- SampleType replicaSampleType =
- openbisService.getSampleType(CinaConstants.REPLICA_SAMPLE_TYPE_CODE);
- DataSetTypeWithVocabularyTerms imageDataSetType =
- openbisService.getDataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
- return new BundleRegistrationGlobalState(delegator, openbisService, replicaSampleType,
- imageDataSetType);
+ return new BundleRegistrationState(delegator, openbisService);
}
}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java
index 629a79f086bda173f6b8d3cc2d7ad3aa154bd8ae..af8432098a5fd31bab01cad806886e1eaf1efbca 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java
@@ -17,104 +17,66 @@
package ch.systemsx.cisd.cina.dss.bundle;
import java.io.File;
-import java.io.IOException;
-import java.util.Collections;
import java.util.Properties;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
-import ch.systemsx.cisd.etlserver.IDataSetHandlerRpc;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
+import ch.systemsx.cisd.cina.dss.bundle.registrators.CinaBundleRegistrationTest;
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class CinaBundleDataSetHandlerTest extends AbstractFileSystemTestCase
+public class CinaBundleDataSetHandlerTest extends CinaBundleRegistrationTest
{
- private Mockery context;
-
- private IEncapsulatedOpenBISService openbisService;
-
private CinaBundleDataSetHandler handler;
- private IDataSetHandlerRpc delegator;
-
- private ExternalData externalData;
-
- @Override
- @BeforeMethod
- public void setUp() throws IOException
+ /**
+ * First set up expectations for the case that the entities do not exist, then set up the
+ * expectations for existing entities to simulate registering new entities.
+ */
+ @Test
+ public void testHandlingWithCreationOfNewEntities()
{
- super.setUp();
-
- context = new Mockery();
- openbisService = context.mock(IEncapsulatedOpenBISService.class);
setupOpenBisExpectations();
+ setupSessionContextExpectations();
+ setupCallerDataSetInfoExpectations();
- delegator = context.mock(IDataSetHandlerRpc.class);
+ File dataSetFile =
+ new File("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/");
+
+ setupNewEntititesExpectations();
+
+ setupExistingGridPrepExpectations();
+ setupExistingReplicaExpectations();
+ setupHandleRawDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/RawData/ReplicTest");
+ setupHandleReplicaMetadataDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/Annotations/ReplicTest");
+ setupHandleBundleMetadataDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/BundleMetadata.xml");
initializeDataSetHandler();
- }
+ handler.handleDataSet(dataSetFile);
- @AfterMethod
- public void tearDown()
- {
context.assertIsSatisfied();
}
- // TODO: Changing the code used by this test; once finished, I'll fix the test to match the new
- // code.
- @Test(groups = "broken")
- public void testHandling()
+ /**
+ * Set up the expectations for existing entities to simulate registering updating entities.
+ */
+ @Test
+ public void testRegistratorForExistingEntities()
{
+ setupOpenBisExpectations();
+ setupSessionContextExpectations();
+ setupCallerDataSetInfoExpectations();
+
File dataSetFile =
new File("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/");
- setupDataSetHandlerExpectations(dataSetFile);
-
- context.checking(new Expectations()
- {
- private long uniqueId = 1;
-
- private void delegatorHandleDataSetExpectation(final String path)
- {
- final DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setDataSetCode("Derived");
- dataSetInformation.setSampleCode("" + uniqueId++);
- dataSetInformation.setSpaceCode("Space");
- dataSetInformation.setInstanceCode("Test");
-
- allowing(delegator).linkAndHandleDataSet(with(new File(path)),
- with(any(DataSetInformation.class)));
- will(returnValue(Collections.singletonList(dataSetInformation)));
- }
-
- {
- allowing(openbisService).drawANewUniqueID();
- will(returnValue(uniqueId++));
- allowing(openbisService).registerSample(with(any(NewSample.class)),
- with("test"));
- will(returnValue(new Long(1)));
- delegatorHandleDataSetExpectation("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/Annotations/Replica for MRC files/MRC for Thomas/test20090422_BacklashRef.mrc");
- delegatorHandleDataSetExpectation("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/Annotations/Replica for MRC files/MRC for Thomas/test20090424_TrackAtZeroRef.mrc");
- delegatorHandleDataSetExpectation("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/Annotations/Replica for STEM files/STEM/stem_134588_1.imag");
- }
- });
+ setupExistingGridPrepExpectations();
+ setupExistingReplicaExpectations();
+ setupHandleReplicaMetadataDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/Annotations/ReplicTest");
+ setupHandleBundleMetadataDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/BundleMetadata.xml");
+
+ initializeDataSetHandler();
handler.handleDataSet(dataSetFile);
context.assertIsSatisfied();
@@ -131,68 +93,4 @@ public class CinaBundleDataSetHandlerTest extends AbstractFileSystemTestCase
handler = new CinaBundleDataSetHandler(props, delegator, openbisService);
}
- private void setupOpenBisExpectations()
- {
- final SampleType sampleType = new SampleType();
- sampleType.setCode(CinaConstants.REPLICA_SAMPLE_TYPE_CODE);
- sampleType.setAutoGeneratedCode(true);
- sampleType.setGeneratedCodePrefix("Replica-");
-
- DataSetType dataSetType = new DataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
- final DataSetTypeWithVocabularyTerms dataSetTypeWithTerms =
- new DataSetTypeWithVocabularyTerms();
- dataSetTypeWithTerms.setDataSetType(dataSetType);
-
- externalData = new ExternalData();
- externalData.setCode("1");
-
- // set up the expectations
- context.checking(new Expectations()
- {
- {
- one(openbisService).getSampleType(CinaConstants.REPLICA_SAMPLE_TYPE_CODE);
- will(returnValue(sampleType));
- one(openbisService).getDataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
- will(returnValue(dataSetTypeWithTerms));
- one(openbisService).tryGetDataSet("session-token", externalData.getCode());
- will(returnValue(externalData));
- }
- });
- }
-
- private void setupDataSetHandlerExpectations(final File dataSet)
- {
- final DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setDataSetCode(externalData.getCode());
- dataSetInformation.setSampleCode("GRID-1");
- dataSetInformation.setSpaceCode("Space");
- dataSetInformation.setInstanceCode("Test");
-
- final Sample sample = new Sample();
- Experiment exp = new Experiment();
- exp.setIdentifier("/Space/Exp-1");
- sample.setExperiment(exp);
- sample.setIdentifier(dataSetInformation.getSampleIdentifier().toString());
-
- final SessionContextDTO sessionContext = new SessionContextDTO();
- sessionContext.setSessionToken("session-token");
- sessionContext.setUserEmail("test@test.bar");
- sessionContext.setUserName("test");
-
- // set up the expectations
- context.checking(new Expectations()
- {
- {
- one(delegator).handleDataSet(dataSet);
- will(returnValue(Collections.singletonList(dataSetInformation)));
- allowing(delegator).getSessionContext();
- will(returnValue(sessionContext));
- one(delegator).getFileForExternalData(externalData);
- will(returnValue(dataSet.getParentFile()));
- allowing(openbisService).tryGetSampleWithExperiment(
- dataSetInformation.getSampleIdentifier());
- will(returnValue(sample));
- }
- });
- }
}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..7b2f0d325e449aaa6a87c4b1fe42fb0e7f6d4a7c
--- /dev/null
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java
@@ -0,0 +1,475 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.cina.dss.bundle.registrators;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Collections;
+
+import org.hamcrest.BaseMatcher;
+import org.hamcrest.Description;
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
+import ch.systemsx.cisd.etlserver.IDataSetHandlerRpc;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestCase
+{
+
+ protected static final String TEST_USER_NAME = "test";
+
+ private static final String SESSION_TOKEN = "session-token";
+
+ private static final String RAW_IMAGES_DATA_SET_CODE = "RAW_IMAGES_DATA_SET_CODE";
+
+ private static final String METADATA_DATA_SET_CODE = "METADATA_DATA_SET_CODE";
+
+ private static final String DB_CODE = "DB";
+
+ private static final String SPACE_CODE = "SPACE";
+
+ protected static final String EXPERIMENT_IDENTIFIER = DB_CODE + ":/" + SPACE_CODE
+ + "/PROJECT/EXP-1";
+
+ private static final String GRID_SAMPLE_CODE = "GRID-CODE";
+
+ protected static final String GRID_SAMPLE_IDENTIFIER = DB_CODE + ":/" + SPACE_CODE + "/"
+ + GRID_SAMPLE_CODE;
+
+ private static final String REPLICA_SAMPLE_CODE = "REPLICA-CODE";
+
+ protected static final String REPLICA_SAMPLE_IDENTIFIER = DB_CODE + ":/" + SPACE_CODE + "/"
+ + REPLICA_SAMPLE_CODE;
+
+ private static final String BUNDLE_METADATA_DATA_SET_CODE = null;
+
+ public static abstract class MatcherNoDesc<T> extends BaseMatcher<T>
+ {
+
+ public void describeTo(Description description)
+ {
+
+ }
+
+ }
+
+ protected Mockery context;
+
+ protected IEncapsulatedOpenBISService openbisService;
+
+ protected IDataSetHandlerRpc delegator;
+
+ private ExternalData externalData;
+
+ private DataSetTypeWithVocabularyTerms rawImagesDataSetTypeWithTerms;
+
+ private DataSetTypeWithVocabularyTerms metadataDataSetTypeWithTerms;
+
+ private DataSetTypeWithVocabularyTerms imageDataSetTypeWithTerms;
+
+ /**
+ *
+ *
+ */
+ public CinaBundleRegistrationTest()
+ {
+ super();
+ }
+
+ /**
+ * @param cleanAfterMethod
+ */
+ public CinaBundleRegistrationTest(boolean cleanAfterMethod)
+ {
+ super(cleanAfterMethod);
+ }
+
+ @Override
+ @BeforeMethod
+ public void setUp() throws IOException
+ {
+ super.setUp();
+
+ context = new Mockery();
+ openbisService = context.mock(IEncapsulatedOpenBISService.class);
+ delegator = context.mock(IDataSetHandlerRpc.class);
+ }
+
+ @AfterMethod
+ public void tearDown()
+ {
+ context.assertIsSatisfied();
+ }
+
+ protected void setupOpenBisExpectations()
+ {
+ final SampleType gridPrepSampleType = new SampleType();
+ gridPrepSampleType.setCode(CinaConstants.GRID_PREP_SAMPLE_TYPE_CODE);
+ gridPrepSampleType.setAutoGeneratedCode(true);
+ gridPrepSampleType.setGeneratedCodePrefix("GridPrep-");
+
+ final SampleType replicaSampleType = new SampleType();
+ replicaSampleType.setCode(CinaConstants.REPLICA_SAMPLE_TYPE_CODE);
+ replicaSampleType.setAutoGeneratedCode(true);
+ replicaSampleType.setGeneratedCodePrefix("Replica-");
+
+ DataSetType dataSetType = new DataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
+ rawImagesDataSetTypeWithTerms = new DataSetTypeWithVocabularyTerms();
+ rawImagesDataSetTypeWithTerms.setDataSetType(dataSetType);
+
+ dataSetType = new DataSetType(CinaConstants.METADATA_DATA_SET_TYPE_CODE);
+ metadataDataSetTypeWithTerms = new DataSetTypeWithVocabularyTerms();
+ metadataDataSetTypeWithTerms.setDataSetType(dataSetType);
+
+ dataSetType = new DataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
+ imageDataSetTypeWithTerms = new DataSetTypeWithVocabularyTerms();
+ imageDataSetTypeWithTerms.setDataSetType(dataSetType);
+
+ externalData = new ExternalData();
+ externalData.setCode("1");
+
+ // set up the expectations
+ context.checking(new Expectations()
+ {
+ {
+ one(openbisService).getSampleType(CinaConstants.GRID_PREP_SAMPLE_TYPE_CODE);
+ will(returnValue(gridPrepSampleType));
+ one(openbisService).getSampleType(CinaConstants.REPLICA_SAMPLE_TYPE_CODE);
+ will(returnValue(replicaSampleType));
+ one(openbisService).getDataSetType(CinaConstants.RAW_IMAGES_DATA_SET_TYPE_CODE);
+ will(returnValue(rawImagesDataSetTypeWithTerms));
+ one(openbisService).getDataSetType(CinaConstants.METADATA_DATA_SET_TYPE_CODE);
+ will(returnValue(metadataDataSetTypeWithTerms));
+ one(openbisService).getDataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
+ will(returnValue(imageDataSetTypeWithTerms));
+ // one(openbisService).tryGetDataSet("session-token", externalData.getCode());
+ // will(returnValue(externalData));
+ }
+ });
+ }
+
+ protected void setupExistingGridPrepExpectations()
+ {
+ final Sample sample = new Sample();
+ Experiment exp = new Experiment();
+ exp.setIdentifier(EXPERIMENT_IDENTIFIER);
+ sample.setExperiment(exp);
+ sample.setIdentifier(GRID_SAMPLE_IDENTIFIER);
+
+ // set up the expectations
+ context.checking(new Expectations()
+ {
+ {
+ one(openbisService).tryGetSampleWithExperiment(
+ with(new SampleIdentifierFactory(GRID_SAMPLE_IDENTIFIER)
+ .createIdentifier()));
+ will(returnValue(sample));
+ }
+ });
+ }
+
+ protected void setupExistingReplicaExpectations()
+ {
+ final Sample sample = new Sample();
+ Experiment exp = new Experiment();
+ exp.setIdentifier(EXPERIMENT_IDENTIFIER);
+ sample.setExperiment(exp);
+ sample.setIdentifier(REPLICA_SAMPLE_IDENTIFIER);
+
+ // set up the expectations
+ context.checking(new Expectations()
+ {
+ {
+ one(openbisService).tryGetSampleWithExperiment(
+ with(new SampleIdentifierFactory(REPLICA_SAMPLE_IDENTIFIER)
+ .createIdentifier()));
+ will(returnValue(sample));
+ }
+ });
+ }
+
+ protected void setupHandleRawDataSetExpectations(final String path)
+ {
+ // Create the Raw Images Data Set
+ final DataSetInformation dataSetInformation = new DataSetInformation();
+ dataSetInformation.setDataSetCode(RAW_IMAGES_DATA_SET_CODE);
+ dataSetInformation.setSampleCode(REPLICA_SAMPLE_CODE);
+ dataSetInformation.setSpaceCode(SPACE_CODE);
+ dataSetInformation.setInstanceCode(DB_CODE);
+
+ // set up the expectations
+ context.checking(new Expectations()
+ {
+ {
+ one(delegator).handleDataSet(with(new File(path)),
+ with(new MatcherNoDesc<DataSetInformation>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof DataSetInformation)
+ {
+ DataSetInformation dataSetInfo =
+ (DataSetInformation) item;
+ assertEquals(
+ rawImagesDataSetTypeWithTerms.getDataSetType(),
+ dataSetInfo.getDataSetType());
+ assertEquals(REPLICA_SAMPLE_CODE,
+ dataSetInfo.getSampleCode());
+ return true;
+ }
+ return false;
+ }
+ }));
+ will(returnValue(Collections.singletonList(dataSetInformation)));
+ }
+ });
+ }
+
+ protected void setupHandleReplicaMetadataDataSetExpectations(final String path)
+ {
+ // Create the Raw Images Data Set
+ final DataSetInformation dataSetInformation = new DataSetInformation();
+ dataSetInformation.setDataSetCode(METADATA_DATA_SET_CODE);
+ dataSetInformation.setSampleCode(REPLICA_SAMPLE_CODE);
+ dataSetInformation.setSpaceCode(SPACE_CODE);
+ dataSetInformation.setInstanceCode(DB_CODE);
+
+ externalData = new ExternalData();
+ externalData.setCode(METADATA_DATA_SET_CODE);
+
+ final File dataSetFile = new File(path);
+ final File imageDataSetFile = new File(dataSetFile, "stem_134629_1.imag");
+
+ // set up the expectations
+ context.checking(new Expectations()
+ {
+ {
+ // Register the metadata data set
+ one(delegator).handleDataSet(with(dataSetFile),
+ with(new MatcherNoDesc<DataSetInformation>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof DataSetInformation)
+ {
+ DataSetInformation dataSetInfo =
+ (DataSetInformation) item;
+ assertEquals(
+ metadataDataSetTypeWithTerms.getDataSetType(),
+ dataSetInfo.getDataSetType());
+ assertEquals(REPLICA_SAMPLE_CODE,
+ dataSetInfo.getSampleCode());
+ return true;
+ }
+ return false;
+ }
+ }));
+ will(returnValue(Collections.singletonList(dataSetInformation)));
+
+ // Retrieve the registered data set from openBIS
+ one(openbisService).tryGetDataSet(SESSION_TOKEN, METADATA_DATA_SET_CODE);
+ will(returnValue(externalData));
+ // Retrieve the registered data set from the store
+ one(delegator).getFileForExternalData(externalData);
+ will(returnValue(dataSetFile.getParentFile()));
+
+ // Register the images data set
+ one(delegator).linkAndHandleDataSet(with(imageDataSetFile),
+ with(new MatcherNoDesc<DataSetInformation>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof DataSetInformation)
+ {
+ DataSetInformation dataSetInfo =
+ (DataSetInformation) item;
+ assertEquals(
+ imageDataSetTypeWithTerms.getDataSetType(),
+ dataSetInfo.getDataSetType());
+ assertEquals(REPLICA_SAMPLE_CODE,
+ dataSetInfo.getSampleCode());
+ return true;
+ }
+ return false;
+ }
+ }));
+ will(returnValue(Collections.singletonList(dataSetInformation)));
+ }
+ });
+ }
+
+ protected void setupHandleBundleMetadataDataSetExpectations(final String path)
+ {
+ // Create the Raw Images Data Set
+ final DataSetInformation dataSetInformation = new DataSetInformation();
+ dataSetInformation.setDataSetCode(BUNDLE_METADATA_DATA_SET_CODE);
+ dataSetInformation.setSampleCode(GRID_SAMPLE_CODE);
+ dataSetInformation.setSpaceCode(SPACE_CODE);
+ dataSetInformation.setInstanceCode(DB_CODE);
+
+ final File dataSetFile = new File(path);
+
+ // set up the expectations
+ context.checking(new Expectations()
+ {
+ {
+ // Register the metadata data set
+ one(delegator).handleDataSet(with(dataSetFile),
+ with(new MatcherNoDesc<DataSetInformation>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof DataSetInformation)
+ {
+ DataSetInformation dataSetInfo =
+ (DataSetInformation) item;
+ assertEquals(
+ metadataDataSetTypeWithTerms.getDataSetType(),
+ dataSetInfo.getDataSetType());
+ assertEquals(GRID_SAMPLE_CODE,
+ dataSetInfo.getSampleCode());
+ return true;
+ }
+ return false;
+ }
+ }));
+ will(returnValue(Collections.singletonList(dataSetInformation)));
+ }
+ });
+ }
+
+ protected void setupCallerDataSetInfoExpectations()
+ {
+
+ final DataSetInformation callerDataSetInfo = new DataSetInformation();
+ callerDataSetInfo.setSpaceCode(SPACE_CODE);
+ callerDataSetInfo.setInstanceCode(DB_CODE);
+ callerDataSetInfo.setExperimentIdentifier(new ExperimentIdentifierFactory(
+ EXPERIMENT_IDENTIFIER).createIdentifier());
+
+ // set up the expectations
+ context.checking(new Expectations()
+ {
+ {
+ one(delegator).getCallerDataSetInformation();
+ will(returnValue(callerDataSetInfo));
+ }
+ });
+ }
+
+ protected void setupSessionContextExpectations()
+ {
+ final SessionContextDTO sessionContext = new SessionContextDTO();
+ sessionContext.setSessionToken(SESSION_TOKEN);
+ sessionContext.setUserEmail("test@test.bar");
+ sessionContext.setUserName(TEST_USER_NAME);
+
+ // set up the expectations
+ context.checking(new Expectations()
+ {
+ {
+ one(delegator).getSessionContext();
+ will(returnValue(sessionContext));
+ }
+ });
+
+ }
+
+ protected void setupNewEntititesExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ // The Grid Prep does not yet exist
+ one(openbisService).tryGetSampleWithExperiment(
+ with(new SampleIdentifierFactory(GRID_SAMPLE_IDENTIFIER)
+ .createIdentifier()));
+ will(returnValue(null));
+
+ // Create the Grid Prep
+ one(openbisService).registerSample(with(new BaseMatcher<NewSample>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof NewSample)
+ {
+ NewSample newSample = (NewSample) item;
+ assertEquals(GRID_SAMPLE_IDENTIFIER, newSample.getIdentifier());
+ assertEquals(EXPERIMENT_IDENTIFIER.toString(),
+ newSample.getExperimentIdentifier());
+ assertEquals(null, newSample.getParentIdentifier());
+ return true;
+ }
+ return false;
+ }
+
+ public void describeTo(Description description)
+ {
+ }
+ }), with(TEST_USER_NAME));
+ will(returnValue(new Long(1)));
+
+ // The Replica does not yet exist
+ one(openbisService).tryGetSampleWithExperiment(
+ with(new SampleIdentifierFactory(REPLICA_SAMPLE_IDENTIFIER)
+ .createIdentifier()));
+ will(returnValue(null));
+
+ // Create the Replica
+ one(openbisService).registerSample(with(new MatcherNoDesc<NewSample>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof NewSample)
+ {
+ NewSample newSample = (NewSample) item;
+ assertEquals(REPLICA_SAMPLE_IDENTIFIER,
+ newSample.getIdentifier());
+ assertEquals(EXPERIMENT_IDENTIFIER.toString(),
+ newSample.getExperimentIdentifier());
+ assertEquals(GRID_SAMPLE_IDENTIFIER,
+ newSample.getParentIdentifier());
+ return true;
+ }
+ return false;
+ }
+ }), with(TEST_USER_NAME));
+ will(returnValue(new Long(2)));
+ }
+ });
+ }
+
+}
\ No newline at end of file
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java
index ea7ed9072b1f95ae3df7a045b324f45c53623192..408e41bc8966937a1e8280e8338c730910c25fad 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java
@@ -17,108 +17,18 @@
package ch.systemsx.cisd.cina.dss.bundle.registrators;
import java.io.File;
-import java.io.IOException;
-import java.util.Collections;
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
-import ch.systemsx.cisd.etlserver.IDataSetHandlerRpc;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
+public class GridPreparationRegistratorTest extends CinaBundleRegistrationTest
{
- private static final String TEST_USER_NAME = "test";
-
- private static final String SESSION_TOKEN = "session-token";
-
- private static final String RAW_IMAGES_DATA_SET_CODE = "RAW_IMAGES_DATA_SET_CODE";
-
- private static final String METADATA_DATA_SET_CODE = "METADATA_DATA_SET_CODE";
-
- // Constants used in the test
- private static final String DB_CODE = "DB";
-
- private static final String SPACE_CODE = "SPACE";
-
- private static final String EXPERIMENT_IDENTIFIER = DB_CODE + ":/" + SPACE_CODE
- + "/PROJECT/EXP-1";
-
- private static final String GRID_SAMPLE_CODE = "GRID-CODE";
-
- private static final String GRID_SAMPLE_IDENTIFIER = DB_CODE + ":/" + SPACE_CODE + "/"
- + GRID_SAMPLE_CODE;
-
- private static final String REPLICA_SAMPLE_CODE = "REPLICA-CODE";
-
- private static final String REPLICA_SAMPLE_IDENTIFIER = DB_CODE + ":/" + SPACE_CODE + "/"
- + REPLICA_SAMPLE_CODE;
-
- private static final String BUNDLE_METADATA_DATA_SET_CODE = null;
-
- private static abstract class MatcherNoDesc<T> extends BaseMatcher<T>
- {
-
- public void describeTo(Description description)
- {
-
- }
-
- }
-
- private Mockery context;
-
- private IEncapsulatedOpenBISService openbisService;
-
- private IDataSetHandlerRpc delegator;
-
- private ExternalData externalData;
-
- private GridPreparationRegistrator registrator;
-
- private DataSetTypeWithVocabularyTerms rawImagesDataSetTypeWithTerms;
-
- private DataSetTypeWithVocabularyTerms metadataDataSetTypeWithTerms;
-
- private DataSetTypeWithVocabularyTerms imageDataSetTypeWithTerms;
-
- @Override
- @BeforeMethod
- public void setUp() throws IOException
- {
- super.setUp();
-
- context = new Mockery();
- openbisService = context.mock(IEncapsulatedOpenBISService.class);
- delegator = context.mock(IDataSetHandlerRpc.class);
- }
-
- @AfterMethod
- public void tearDown()
- {
- context.assertIsSatisfied();
- }
+ protected GridPreparationRegistrator registrator;
@Test(expectedExceptions =
{ AssertionError.class })
@@ -160,66 +70,7 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
File dataSetFile =
new File("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/");
- context.checking(new Expectations()
- {
- {
- // The Grid Prep does not yet exist
- one(openbisService).tryGetSampleWithExperiment(
- with(new SampleIdentifierFactory(GRID_SAMPLE_IDENTIFIER)
- .createIdentifier()));
- will(returnValue(null));
-
- // Create the Grid Prep
- one(openbisService).registerSample(with(new BaseMatcher<NewSample>()
- {
- public boolean matches(Object item)
- {
- if (item instanceof NewSample)
- {
- NewSample newSample = (NewSample) item;
- assertEquals(GRID_SAMPLE_IDENTIFIER, newSample.getIdentifier());
- assertEquals(EXPERIMENT_IDENTIFIER.toString(),
- newSample.getExperimentIdentifier());
- assertEquals(null, newSample.getParentIdentifier());
- return true;
- }
- return false;
- }
-
- public void describeTo(Description description)
- {
- }
- }), with(TEST_USER_NAME));
- will(returnValue(new Long(1)));
-
- // The Replica does not yet exist
- one(openbisService).tryGetSampleWithExperiment(
- with(new SampleIdentifierFactory(REPLICA_SAMPLE_IDENTIFIER)
- .createIdentifier()));
- will(returnValue(null));
-
- // Create the Replica
- one(openbisService).registerSample(with(new MatcherNoDesc<NewSample>()
- {
- public boolean matches(Object item)
- {
- if (item instanceof NewSample)
- {
- NewSample newSample = (NewSample) item;
- assertEquals(REPLICA_SAMPLE_IDENTIFIER,
- newSample.getIdentifier());
- assertEquals(EXPERIMENT_IDENTIFIER.toString(),
- newSample.getExperimentIdentifier());
- assertEquals(GRID_SAMPLE_IDENTIFIER,
- newSample.getParentIdentifier());
- return true;
- }
- return false;
- }
- }), with(TEST_USER_NAME));
- will(returnValue(new Long(2)));
- }
- });
+ setupNewEntititesExpectations();
setupExistingGridPrepExpectations();
setupExistingReplicaExpectations();
@@ -233,241 +84,28 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
context.assertIsSatisfied();
}
- private void setupOpenBisExpectations()
- {
- final SampleType gridPrepSampleType = new SampleType();
- gridPrepSampleType.setCode(CinaConstants.GRID_PREP_SAMPLE_TYPE_CODE);
- gridPrepSampleType.setAutoGeneratedCode(true);
- gridPrepSampleType.setGeneratedCodePrefix("GridPrep-");
-
- final SampleType replicaSampleType = new SampleType();
- replicaSampleType.setCode(CinaConstants.REPLICA_SAMPLE_TYPE_CODE);
- replicaSampleType.setAutoGeneratedCode(true);
- replicaSampleType.setGeneratedCodePrefix("Replica-");
-
- DataSetType dataSetType = new DataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
- rawImagesDataSetTypeWithTerms = new DataSetTypeWithVocabularyTerms();
- rawImagesDataSetTypeWithTerms.setDataSetType(dataSetType);
-
- dataSetType = new DataSetType(CinaConstants.METADATA_DATA_SET_TYPE_CODE);
- metadataDataSetTypeWithTerms = new DataSetTypeWithVocabularyTerms();
- metadataDataSetTypeWithTerms.setDataSetType(dataSetType);
-
- dataSetType = new DataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
- imageDataSetTypeWithTerms = new DataSetTypeWithVocabularyTerms();
- imageDataSetTypeWithTerms.setDataSetType(dataSetType);
-
- externalData = new ExternalData();
- externalData.setCode("1");
-
- // set up the expectations
- context.checking(new Expectations()
- {
- {
- one(openbisService).getSampleType(CinaConstants.GRID_PREP_SAMPLE_TYPE_CODE);
- will(returnValue(gridPrepSampleType));
- one(openbisService).getSampleType(CinaConstants.REPLICA_SAMPLE_TYPE_CODE);
- will(returnValue(replicaSampleType));
- one(openbisService).getDataSetType(CinaConstants.RAW_IMAGES_DATA_SET_TYPE_CODE);
- will(returnValue(rawImagesDataSetTypeWithTerms));
- one(openbisService).getDataSetType(CinaConstants.METADATA_DATA_SET_TYPE_CODE);
- will(returnValue(metadataDataSetTypeWithTerms));
- one(openbisService).getDataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
- will(returnValue(imageDataSetTypeWithTerms));
- // one(openbisService).tryGetDataSet("session-token", externalData.getCode());
- // will(returnValue(externalData));
- }
- });
- }
-
- private void setupExistingGridPrepExpectations()
- {
- final Sample sample = new Sample();
- Experiment exp = new Experiment();
- exp.setIdentifier(EXPERIMENT_IDENTIFIER);
- sample.setExperiment(exp);
- sample.setIdentifier(GRID_SAMPLE_IDENTIFIER);
-
- // set up the expectations
- context.checking(new Expectations()
- {
- {
- one(openbisService).tryGetSampleWithExperiment(
- with(new SampleIdentifierFactory(GRID_SAMPLE_IDENTIFIER)
- .createIdentifier()));
- will(returnValue(sample));
- }
- });
- }
-
- private void setupExistingReplicaExpectations()
- {
- final Sample sample = new Sample();
- Experiment exp = new Experiment();
- exp.setIdentifier(EXPERIMENT_IDENTIFIER);
- sample.setExperiment(exp);
- sample.setIdentifier(REPLICA_SAMPLE_IDENTIFIER);
-
- // set up the expectations
- context.checking(new Expectations()
- {
- {
- one(openbisService).tryGetSampleWithExperiment(
- with(new SampleIdentifierFactory(REPLICA_SAMPLE_IDENTIFIER)
- .createIdentifier()));
- will(returnValue(sample));
- }
- });
- }
-
- private void setupHandleRawDataSetExpectations(final String path)
- {
- // Create the Raw Images Data Set
- final DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setDataSetCode(RAW_IMAGES_DATA_SET_CODE);
- dataSetInformation.setSampleCode(REPLICA_SAMPLE_CODE);
- dataSetInformation.setSpaceCode(SPACE_CODE);
- dataSetInformation.setInstanceCode(DB_CODE);
-
- // set up the expectations
- context.checking(new Expectations()
- {
- {
- one(delegator).handleDataSet(with(new File(path)),
- with(new MatcherNoDesc<DataSetInformation>()
- {
- public boolean matches(Object item)
- {
- if (item instanceof DataSetInformation)
- {
- DataSetInformation dataSetInfo =
- (DataSetInformation) item;
- assertEquals(
- rawImagesDataSetTypeWithTerms.getDataSetType(),
- dataSetInfo.getDataSetType());
- assertEquals(REPLICA_SAMPLE_CODE,
- dataSetInfo.getSampleCode());
- return true;
- }
- return false;
- }
- }));
- will(returnValue(Collections.singletonList(dataSetInformation)));
- }
- });
- }
-
- private void setupHandleReplicaMetadataDataSetExpectations(final String path)
+ /**
+ * Set up the expectations for existing entities to simulate registering updating entities.
+ */
+ @Test
+ public void testRegistratorForExistingEntities()
{
- // Create the Raw Images Data Set
- final DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setDataSetCode(METADATA_DATA_SET_CODE);
- dataSetInformation.setSampleCode(REPLICA_SAMPLE_CODE);
- dataSetInformation.setSpaceCode(SPACE_CODE);
- dataSetInformation.setInstanceCode(DB_CODE);
-
- externalData = new ExternalData();
- externalData.setCode(METADATA_DATA_SET_CODE);
-
- final File dataSetFile = new File(path);
- final File imageDataSetFile = new File(dataSetFile, "stem_134629_1.imag");
-
- // set up the expectations
- context.checking(new Expectations()
- {
- {
- // Register the metadata data set
- one(delegator).handleDataSet(with(dataSetFile),
- with(new MatcherNoDesc<DataSetInformation>()
- {
- public boolean matches(Object item)
- {
- if (item instanceof DataSetInformation)
- {
- DataSetInformation dataSetInfo =
- (DataSetInformation) item;
- assertEquals(
- metadataDataSetTypeWithTerms.getDataSetType(),
- dataSetInfo.getDataSetType());
- assertEquals(REPLICA_SAMPLE_CODE,
- dataSetInfo.getSampleCode());
- return true;
- }
- return false;
- }
- }));
- will(returnValue(Collections.singletonList(dataSetInformation)));
-
- // Retrieve the registered data set from openBIS
- one(openbisService).tryGetDataSet(SESSION_TOKEN, METADATA_DATA_SET_CODE);
- will(returnValue(externalData));
- // Retrieve the registered data set from the store
- one(delegator).getFileForExternalData(externalData);
- will(returnValue(dataSetFile.getParentFile()));
+ setupOpenBisExpectations();
+ setupSessionContextExpectations();
+ setupCallerDataSetInfoExpectations();
- // Register the images data set
- one(delegator).linkAndHandleDataSet(with(imageDataSetFile),
- with(new MatcherNoDesc<DataSetInformation>()
- {
- public boolean matches(Object item)
- {
- if (item instanceof DataSetInformation)
- {
- DataSetInformation dataSetInfo =
- (DataSetInformation) item;
- assertEquals(
- imageDataSetTypeWithTerms.getDataSetType(),
- dataSetInfo.getDataSetType());
- assertEquals(REPLICA_SAMPLE_CODE,
- dataSetInfo.getSampleCode());
- return true;
- }
- return false;
- }
- }));
- will(returnValue(Collections.singletonList(dataSetInformation)));
- }
- });
- }
+ File dataSetFile =
+ new File("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/");
- private void setupHandleBundleMetadataDataSetExpectations(final String path)
- {
- // Create the Raw Images Data Set
- final DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setDataSetCode(BUNDLE_METADATA_DATA_SET_CODE);
- dataSetInformation.setSampleCode(GRID_SAMPLE_CODE);
- dataSetInformation.setSpaceCode(SPACE_CODE);
- dataSetInformation.setInstanceCode(DB_CODE);
+ setupExistingGridPrepExpectations();
+ setupExistingReplicaExpectations();
+ setupHandleReplicaMetadataDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/Annotations/ReplicTest");
+ setupHandleBundleMetadataDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/BundleMetadata.xml");
- final File dataSetFile = new File(path);
+ createRegistrator(dataSetFile);
+ registrator.register();
- // set up the expectations
- context.checking(new Expectations()
- {
- {
- // Register the metadata data set
- one(delegator).handleDataSet(with(dataSetFile),
- with(new MatcherNoDesc<DataSetInformation>()
- {
- public boolean matches(Object item)
- {
- if (item instanceof DataSetInformation)
- {
- DataSetInformation dataSetInfo =
- (DataSetInformation) item;
- assertEquals(
- metadataDataSetTypeWithTerms.getDataSetType(),
- dataSetInfo.getDataSetType());
- assertEquals(GRID_SAMPLE_CODE,
- dataSetInfo.getSampleCode());
- return true;
- }
- return false;
- }
- }));
- will(returnValue(Collections.singletonList(dataSetInformation)));
- }
- });
+ context.assertIsSatisfied();
}
private void createRegistrator(final File dataSet)
@@ -475,46 +113,8 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
registrator = new GridPreparationRegistrator(createBundleRegistrationState(), dataSet);
}
- private void setupCallerDataSetInfoExpectations()
- {
-
- final DataSetInformation callerDataSetInfo = new DataSetInformation();
- callerDataSetInfo.setSpaceCode(SPACE_CODE);
- callerDataSetInfo.setInstanceCode(DB_CODE);
- callerDataSetInfo.setExperimentIdentifier(new ExperimentIdentifierFactory(
- EXPERIMENT_IDENTIFIER).createIdentifier());
-
- // set up the expectations
- context.checking(new Expectations()
- {
- {
- one(delegator).getCallerDataSetInformation();
- will(returnValue(callerDataSetInfo));
- }
- });
- }
-
- private void setupSessionContextExpectations()
- {
- final SessionContextDTO sessionContext = new SessionContextDTO();
- sessionContext.setSessionToken(SESSION_TOKEN);
- sessionContext.setUserEmail("test@test.bar");
- sessionContext.setUserName(TEST_USER_NAME);
-
- // set up the expectations
- context.checking(new Expectations()
- {
- {
- one(delegator).getSessionContext();
- will(returnValue(sessionContext));
- }
- });
-
- }
-
private BundleRegistrationState createBundleRegistrationState()
{
return new BundleRegistrationState(delegator, openbisService);
}
-
}