From 5b6345e89c9342a6649b6238be031e3ba7ff286d Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 13 Oct 2010 09:08:19 +0000
Subject: [PATCH] LMS-1811 Implementation of new handlers for CINA.
SVN: 18284
---
.../registrators/BundleDataSetHelper.java | 99 ++++-------------
.../registrators/BundleRegistrationState.java | 101 ++++++++++++++++++
.../GridPreparationRegistrator.java | 26 ++++-
.../ReplicaAnnotatedImagesRegistrator.java | 14 ++-
.../registrators/ReplicaRegistrator.java | 4 +-
.../BundleStructureConstants.java | 2 +-
.../GridPreparationRegistratorTest.java | 98 +++++++++++++++--
7 files changed, 246 insertions(+), 98 deletions(-)
create mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleRegistrationState.java
rename rtd_cina/source/java/ch/systemsx/cisd/cina/shared/{metadata => constants}/BundleStructureConstants.java (97%)
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleDataSetHelper.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleDataSetHelper.java
index bf184665e60..5fc0b59ec5a 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleDataSetHelper.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleDataSetHelper.java
@@ -20,14 +20,11 @@ import java.io.File;
import java.util.ArrayList;
import java.util.List;
-import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
import ch.systemsx.cisd.cina.shared.metadata.IMetadataExtractor;
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.PropertyTypeWithVocabulary;
-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;
@@ -40,83 +37,6 @@ abstract class BundleDataSetHelper
{
private static final String MISC_DATA_SET_PROPERTY_CODE = "MISC";
- static class BundleRegistrationState
- {
- private final IDataSetHandlerRpc delegator;
-
- private final SessionContextDTO sessionContext;
-
- private final IEncapsulatedOpenBISService openbisService;
-
- private final SampleType gridPrepSampleType;
-
- private final SampleType replicaSampleType;
-
- private final DataSetTypeWithVocabularyTerms rawImagesDataSetType;
-
- private final DataSetTypeWithVocabularyTerms metadataDataSetType;
-
- private final DataSetTypeWithVocabularyTerms imageDataSetType;
-
- BundleRegistrationState(IDataSetHandlerRpc delegator,
- IEncapsulatedOpenBISService openbisService)
- {
- this.delegator = delegator;
- sessionContext = delegator.getSessionContext();
- this.openbisService = openbisService;
- this.gridPrepSampleType =
- openbisService.getSampleType(CinaConstants.GRID_PREP_SAMPLE_TYPE_CODE);
- this.replicaSampleType =
- openbisService.getSampleType(CinaConstants.REPLICA_SAMPLE_TYPE_CODE);
- this.rawImagesDataSetType =
- openbisService.getDataSetType(CinaConstants.RAW_IMAGES_DATA_SET_TYPE_CODE);
- this.metadataDataSetType =
- openbisService.getDataSetType(CinaConstants.METADATA_DATA_SET_TYPE_CODE);
- this.imageDataSetType =
- openbisService.getDataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
- }
-
- IDataSetHandlerRpc getDelegator()
- {
- return delegator;
- }
-
- SessionContextDTO getSessionContext()
- {
- return sessionContext;
- }
-
- IEncapsulatedOpenBISService getOpenbisService()
- {
- return openbisService;
- }
-
- SampleType getGridPrepSampleType()
- {
- return gridPrepSampleType;
- }
-
- SampleType getReplicaSampleType()
- {
- return replicaSampleType;
- }
-
- DataSetTypeWithVocabularyTerms getRawImagesDataSetType()
- {
- return rawImagesDataSetType;
- }
-
- DataSetTypeWithVocabularyTerms getMetadataDataSetType()
- {
- return metadataDataSetType;
- }
-
- DataSetTypeWithVocabularyTerms getImageDataSetType()
- {
- return imageDataSetType;
- }
- }
-
protected final BundleRegistrationState globalState;
protected final File dataSet;
@@ -155,6 +75,25 @@ abstract class BundleDataSetHelper
return bigDataSet;
}
+ /**
+ * Register a file which is already in the store as a data set and add it to the
+ * dataSetInformation collection.
+ * <p>
+ * Since the file is already in the store, the new data set contains a (hard) link to it.
+ *
+ * @param dataSetFile A file which is already in the store
+ * @return A collection of data set information objects for each data set just registered
+ */
+ protected List<DataSetInformation> registerLinkedDataSet(File dataSetFile,
+ DataSetInformation dataSetInfo)
+ {
+ // Register the given file
+ List<DataSetInformation> bigDataSet =
+ getDelegator().linkAndHandleDataSet(dataSetFile, dataSetInfo);
+ registeredDataSets.addAll(bigDataSet);
+ return bigDataSet;
+ }
+
protected IEncapsulatedOpenBISService getOpenbisService()
{
return globalState.getOpenbisService();
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleRegistrationState.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleRegistrationState.java
new file mode 100644
index 00000000000..b1c069fd711
--- /dev/null
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/BundleRegistrationState.java
@@ -0,0 +1,101 @@
+/*
+ * 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 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.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
+
+public class BundleRegistrationState
+{
+ private final IDataSetHandlerRpc delegator;
+
+ private final SessionContextDTO sessionContext;
+
+ private final IEncapsulatedOpenBISService openbisService;
+
+ private final SampleType gridPrepSampleType;
+
+ private final SampleType replicaSampleType;
+
+ private final DataSetTypeWithVocabularyTerms rawImagesDataSetType;
+
+ private final DataSetTypeWithVocabularyTerms metadataDataSetType;
+
+ private final DataSetTypeWithVocabularyTerms imageDataSetType;
+
+ public BundleRegistrationState(IDataSetHandlerRpc delegator,
+ IEncapsulatedOpenBISService openbisService)
+ {
+ this.delegator = delegator;
+ sessionContext = delegator.getSessionContext();
+ this.openbisService = openbisService;
+ this.gridPrepSampleType =
+ openbisService.getSampleType(CinaConstants.GRID_PREP_SAMPLE_TYPE_CODE);
+ this.replicaSampleType =
+ openbisService.getSampleType(CinaConstants.REPLICA_SAMPLE_TYPE_CODE);
+ this.rawImagesDataSetType =
+ openbisService.getDataSetType(CinaConstants.RAW_IMAGES_DATA_SET_TYPE_CODE);
+ this.metadataDataSetType =
+ openbisService.getDataSetType(CinaConstants.METADATA_DATA_SET_TYPE_CODE);
+ this.imageDataSetType =
+ openbisService.getDataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
+ }
+
+ IDataSetHandlerRpc getDelegator()
+ {
+ return delegator;
+ }
+
+ SessionContextDTO getSessionContext()
+ {
+ return sessionContext;
+ }
+
+ IEncapsulatedOpenBISService getOpenbisService()
+ {
+ return openbisService;
+ }
+
+ SampleType getGridPrepSampleType()
+ {
+ return gridPrepSampleType;
+ }
+
+ SampleType getReplicaSampleType()
+ {
+ return replicaSampleType;
+ }
+
+ DataSetTypeWithVocabularyTerms getRawImagesDataSetType()
+ {
+ return rawImagesDataSetType;
+ }
+
+ DataSetTypeWithVocabularyTerms getMetadataDataSetType()
+ {
+ return metadataDataSetType;
+ }
+
+ DataSetTypeWithVocabularyTerms getImageDataSetType()
+ {
+ return imageDataSetType;
+ }
+}
\ No newline at end of file
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistrator.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistrator.java
index 0d0fa3feab4..7942d64b873 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistrator.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistrator.java
@@ -17,7 +17,9 @@
package ch.systemsx.cisd.cina.dss.bundle.registrators;
import java.io.File;
+import java.util.List;
+import ch.systemsx.cisd.cina.shared.constants.BundleStructureConstants;
import ch.systemsx.cisd.cina.shared.metadata.BundleMetadataExtractor;
import ch.systemsx.cisd.cina.shared.metadata.ReplicaMetadataExtractor;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -70,10 +72,17 @@ public class GridPreparationRegistrator extends BundleDataSetHelper
for (ReplicaMetadataExtractor replicaMetadataExtractor : bundleMetadataExtractor
.getReplicaMetadataExtractors())
{
- new ReplicaRegistrator(globalState, replicaMetadataExtractor, gridPrepSample,
- gridPrepSampleId, dataSet).register();
+ List<DataSetInformation> childRegisteredDataSets =
+ new ReplicaRegistrator(globalState, replicaMetadataExtractor, gridPrepSample,
+ gridPrepSampleId, dataSet).register();
+ getDataSetInformation().addAll(childRegisteredDataSets);
}
- // getDataSetInformation\
+
+ // Create a DataSetInformation
+ DataSetInformation metadataDataSetInfo = createDataSetInformation();
+
+ File metadataFile = new File(dataSet, BundleStructureConstants.BUNDLE_METADATA_FILE_NAME);
+ registerDataSet(metadataFile, metadataDataSetInfo);
}
private void retrieveOrCreateGridPrepSample()
@@ -105,4 +114,15 @@ public class GridPreparationRegistrator extends BundleDataSetHelper
assert gridPrepSample != null;
}
+
+ private DataSetInformation createDataSetInformation()
+ {
+ DataSetInformation metadataDataSetInfo = new DataSetInformation();
+ metadataDataSetInfo.setSampleCode(gridPrepSampleId.getSampleCode());
+ metadataDataSetInfo.setSpaceCode(gridPrepSampleId.getSpaceLevel().getSpaceCode());
+ metadataDataSetInfo.setInstanceCode(gridPrepSampleId.getSpaceLevel()
+ .getDatabaseInstanceCode());
+ metadataDataSetInfo.setDataSetType(globalState.getMetadataDataSetType().getDataSetType());
+ return metadataDataSetInfo;
+ }
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaAnnotatedImagesRegistrator.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaAnnotatedImagesRegistrator.java
index 5553a4bb188..adc6e7829d5 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaAnnotatedImagesRegistrator.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaAnnotatedImagesRegistrator.java
@@ -26,7 +26,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
- * Registers annotated image data sets.
+ * Registers annotated image data sets. The annotated image data sets refer to files that are
+ * already in the store.
*
* @author Chandrasekhar Ramakrishnan
*/
@@ -36,6 +37,15 @@ public class ReplicaAnnotatedImagesRegistrator extends BundleDataSetHelper
private final SampleIdentifier replicaSampleId;
+ /**
+ * Constructor.
+ *
+ * @param globalState The registration state
+ * @param imageMetadataExtractor An image metadata extractor referring to a file that is already
+ * in the store
+ * @param replicaSample The owning sample of the data set
+ * @param replicaSampleId The owning sample id
+ */
ReplicaAnnotatedImagesRegistrator(BundleRegistrationState globalState,
ImageMetadataExtractor imageMetadataExtractor, Sample replicaSample,
SampleIdentifier replicaSampleId)
@@ -53,7 +63,7 @@ public class ReplicaAnnotatedImagesRegistrator extends BundleDataSetHelper
// Import the metadata
ArrayList<NewProperty> properties = createDataSetProperties(imageMetadataExtractor);
metadataDataSetInfo.setDataSetProperties(properties);
- registerDataSet(dataSet, metadataDataSetInfo);
+ registerLinkedDataSet(dataSet, metadataDataSetInfo);
return getDataSetInformation();
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java
index d06500e51a3..0278c672018 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java
@@ -73,7 +73,8 @@ public class ReplicaRegistrator extends BundleDataSetHelper
{
registerRawImages();
}
- registerMetadata();
+ File registeredDataSetFile = registerMetadata();
+ registerAnnotatedImages(registeredDataSetFile);
return getDataSetInformation();
}
@@ -129,7 +130,6 @@ public class ReplicaRegistrator extends BundleDataSetHelper
return registrator.getMetadataDataSetFile();
}
- @SuppressWarnings("unused")
private void registerAnnotatedImages(File registeredMetadataFile)
{
// Create a metadata extractor on the data set in the store (the ivar is a replica metadata
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/BundleStructureConstants.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/BundleStructureConstants.java
similarity index 97%
rename from rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/BundleStructureConstants.java
rename to rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/BundleStructureConstants.java
index 2ddf9d74d5a..2715427c755 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/BundleStructureConstants.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/BundleStructureConstants.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.cina.shared.metadata;
+package ch.systemsx.cisd.cina.shared.constants;
/**
* Constants that describe the structure fo the CINA bundle files.
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 2feeca594d1..ea7ed9072b1 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
@@ -29,7 +29,6 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.cina.dss.bundle.registrators.BundleDataSetHelper.BundleRegistrationState;
import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
import ch.systemsx.cisd.etlserver.IDataSetHandlerRpc;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
@@ -76,6 +75,8 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
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>
{
@@ -96,6 +97,12 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
private GridPreparationRegistrator registrator;
+ private DataSetTypeWithVocabularyTerms rawImagesDataSetTypeWithTerms;
+
+ private DataSetTypeWithVocabularyTerms metadataDataSetTypeWithTerms;
+
+ private DataSetTypeWithVocabularyTerms imageDataSetTypeWithTerms;
+
@Override
@BeforeMethod
public void setUp() throws IOException
@@ -217,7 +224,8 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
setupExistingGridPrepExpectations();
setupExistingReplicaExpectations();
setupHandleRawDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/RawData/ReplicTest");
- setupHandleMetadataDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/Annotations/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");
createRegistrator(dataSetFile);
registrator.register();
@@ -238,18 +246,15 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
replicaSampleType.setGeneratedCodePrefix("Replica-");
DataSetType dataSetType = new DataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
- final DataSetTypeWithVocabularyTerms rawImagesDataSetTypeWithTerms =
- new DataSetTypeWithVocabularyTerms();
+ rawImagesDataSetTypeWithTerms = new DataSetTypeWithVocabularyTerms();
rawImagesDataSetTypeWithTerms.setDataSetType(dataSetType);
dataSetType = new DataSetType(CinaConstants.METADATA_DATA_SET_TYPE_CODE);
- final DataSetTypeWithVocabularyTerms metadataDataSetTypeWithTerms =
- new DataSetTypeWithVocabularyTerms();
+ metadataDataSetTypeWithTerms = new DataSetTypeWithVocabularyTerms();
metadataDataSetTypeWithTerms.setDataSetType(dataSetType);
dataSetType = new DataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
- final DataSetTypeWithVocabularyTerms imageDataSetTypeWithTerms =
- new DataSetTypeWithVocabularyTerms();
+ imageDataSetTypeWithTerms = new DataSetTypeWithVocabularyTerms();
imageDataSetTypeWithTerms.setDataSetType(dataSetType);
externalData = new ExternalData();
@@ -337,6 +342,9 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
{
DataSetInformation dataSetInfo =
(DataSetInformation) item;
+ assertEquals(
+ rawImagesDataSetTypeWithTerms.getDataSetType(),
+ dataSetInfo.getDataSetType());
assertEquals(REPLICA_SAMPLE_CODE,
dataSetInfo.getSampleCode());
return true;
@@ -349,7 +357,7 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
});
}
- private void setupHandleMetadataDataSetExpectations(final String path)
+ private void setupHandleReplicaMetadataDataSetExpectations(final String path)
{
// Create the Raw Images Data Set
final DataSetInformation dataSetInformation = new DataSetInformation();
@@ -359,14 +367,16 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
dataSetInformation.setInstanceCode(DB_CODE);
externalData = new ExternalData();
- externalData.setCode("1");
+ 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>()
{
@@ -376,6 +386,9 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
{
DataSetInformation dataSetInfo =
(DataSetInformation) item;
+ assertEquals(
+ metadataDataSetTypeWithTerms.getDataSetType(),
+ dataSetInfo.getDataSetType());
assertEquals(REPLICA_SAMPLE_CODE,
dataSetInfo.getSampleCode());
return true;
@@ -384,10 +397,75 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
}
}));
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)));
+ }
+ });
+ }
+
+ 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);
+
+ 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)));
}
});
}
--
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