From e8a738f96f249c8d69f6b9749c5f7776fa7a6ed4 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 13 Oct 2010 08:11:26 +0000
Subject: [PATCH] LMS-1811 Implementation of new handlers for CINA.
SVN: 18280
---
rtd_cina/resource/db/cina_metadata.sql | 12 +-
.../dss/bundle/CinaBundleDataSetHandler.java | 4 +-
.../registrators/BundleDataSetHelper.java | 83 +++++--
.../GridPreparationRegistrator.java | 2 +-
.../ReplicaAnnotatedImagesRegistrator.java | 48 +++-
.../ReplicaMetadataRegistrator.java | 71 +++++-
.../ReplicaRawImagesRegistrator.java | 72 ++++++
.../registrators/ReplicaRegistrator.java | 77 ++++++-
.../cina/shared/constants/CinaConstants.java | 6 +
.../metadata/BundleStructureConstants.java | 69 ++++++
.../metadata/IMetadataExtractor.java} | 19 +-
.../metadata/ImageMetadataExtractor.java | 2 +-
.../metadata/ReplicaMetadataExtractor.java | 8 +-
.../GridPreparationRegistratorTest.java | 205 ++++++++++++------
14 files changed, 545 insertions(+), 133 deletions(-)
create mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRawImagesRegistrator.java
create mode 100644 rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/BundleStructureConstants.java
rename rtd_cina/source/java/ch/systemsx/cisd/cina/{dss/bundle/registrators/ReplicaOriginalImagesRegistrator.java => shared/metadata/IMetadataExtractor.java} (60%)
diff --git a/rtd_cina/resource/db/cina_metadata.sql b/rtd_cina/resource/db/cina_metadata.sql
index 9f8e6fd3bfb..8248f296549 100644
--- a/rtd_cina/resource/db/cina_metadata.sql
+++ b/rtd_cina/resource/db/cina_metadata.sql
@@ -18,7 +18,7 @@ SET search_path = public, pg_catalog;
-- Dependencies: 1704
-- Data for Name: experiment_types; Type: TABLE DATA; Schema: public; Owner: cramakri
--
-INSERT INTO experiment_types (id, code, description, dbin_id, modification_timestamp) VALUES (1, 'CINA_EXP_TYPE', 'CINA Generic Experiment Type', 1, '2010-03-18 08:37:38.173356+01');
+INSERT INTO experiment_types (id, code, description, dbin_id, modification_timestamp) VALUES (1, 'CINA_EXP_TYPE', 'Generic Experiment Type', 1, '2010-03-18 08:37:38.173356+01');
-- Completed on 2010-08-18 10:19:08 CEST
--
@@ -27,8 +27,8 @@ INSERT INTO experiment_types (id, code, description, dbin_id, modification_times
-- Data for Name: sample_types; Type: TABLE DATA; Schema: public; Owner: cramakri
--
INSERT INTO sample_types (id, code, description, dbin_id, is_listable, generated_from_depth, part_of_depth, modification_timestamp, is_auto_generated_code, generated_code_prefix, is_subcode_unique) VALUES (1, 'ORIGINAL', 'The sample for an experiment', 1, true, 1, 0, '2010-03-18 10:09:48.073644+01', false, 'ORIGINAL', false);
+INSERT INTO sample_types (id, code, description, dbin_id, is_listable, generated_from_depth, part_of_depth, modification_timestamp, is_auto_generated_code, generated_code_prefix, is_subcode_unique) VALUES (2, 'GRID_PREP', 'Grid biochemistry and preparation', 1, true, 1, 0, '2010-06-04 14:44:53.706263+02', false, 'EM-PREP', false);
INSERT INTO sample_types (id, code, description, dbin_id, is_listable, generated_from_depth, part_of_depth, modification_timestamp, is_auto_generated_code, generated_code_prefix, is_subcode_unique) VALUES (3, 'GRID_REPLICA', 'A replica of a grid template', 1, true, 1, 0, '2010-06-04 14:46:38.886039+02', false, 'REPLICA', false);
-INSERT INTO sample_types (id, code, description, dbin_id, is_listable, generated_from_depth, part_of_depth, modification_timestamp, is_auto_generated_code, generated_code_prefix, is_subcode_unique) VALUES (2, 'GRID_TEMPLATE', 'Grid biochemistry and preparation', 1, true, 1, 0, '2010-06-04 14:44:53.706263+02', false, 'EM-PREP', false);
-- Completed on 2010-08-18 10:13:10 CEST
--
@@ -37,9 +37,11 @@ INSERT INTO sample_types (id, code, description, dbin_id, is_listable, generated
-- Data for Name: data_set_types; Type: TABLE DATA; Schema: public; Owner: cramakri
--
INSERT INTO data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) VALUES (1, 'UNKNOWN', 'Unknown', 1, '2010-03-18 08:33:32.470674+01', NULL, NULL);
-INSERT INTO data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) VALUES (3, 'BUNDLE', 'CINA Bundle Data Set', 1, '2010-06-04 15:40:58.882161+02', '.*.bundle', NULL);
-INSERT INTO data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) VALUES (5, 'ANALYSIS', 'CINA Analysis', 1, '2010-06-04 16:07:04.556718+02', NULL, NULL);
-INSERT INTO data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) VALUES (4, 'IMAGE', 'CINA Image', 1, '2010-06-04 16:06:40.980157+02', '.*.png', 'original/Representations');
+INSERT INTO data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) VALUES (2, 'BUNDLE', 'Bundle Data Set', 1, '2010-06-04 15:40:58.882161+02', '.*.bundle', NULL);
+INSERT INTO data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) VALUES (3, 'RAW_IMAGES', 'Raw Images', 1, '2010-06-04 16:08:40.980157+02', NULL, NULL);
+INSERT INTO data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) VALUES (4, 'METADATA', 'Metadata', 1, '2010-06-04 16:08:40.980157+02', 'metadata.xml', 'original');
+INSERT INTO data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) VALUES (5, 'IMAGE', 'Image', 1, '2010-06-04 16:06:40.980157+02', '.*.png', 'original/Representations');
+INSERT INTO data_set_types (id, code, description, dbin_id, modification_timestamp, main_ds_pattern, main_ds_path) VALUES (6, 'ANALYSIS', 'Analysis', 1, '2010-06-04 16:07:04.556718+02', NULL, NULL);
-- Completed on 2010-08-18 10:19:39 CEST
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 a3312a48e3c..fe4ce92f5d6 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
@@ -58,7 +58,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
* <li>Individual Image Thumbnails</li>
* </ul>
* </li>
- * <li>Replica Original Images</li>
+ * <li>Replica Raw Images</li>
* </ul>
* </li>
* </ul>
@@ -68,7 +68,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
* <li>Create a grid preparation sample if one does not exist</li>
* <li>For each replica:
* <ul>
- * <li>If the replica sample does not exist, create it and register an original images data set</li>
+ * <li>If the replica sample does not exist, create it and register a raw images data set</li>
* <li>Create a metadata data set and associate it with the replica; update the replica's metadata</li>
* <li>Create datasets for each of the annotated images in the data set</li>
* </ul>
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 e3fa02d22d4..bf184665e60 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
@@ -20,11 +20,15 @@ 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;
/**
@@ -34,6 +38,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
*/
abstract class BundleDataSetHelper
{
+ private static final String MISC_DATA_SET_PROPERTY_CODE = "MISC";
+
static class BundleRegistrationState
{
private final IDataSetHandlerRpc delegator;
@@ -42,19 +48,32 @@ abstract class BundleDataSetHelper
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, SampleType replicaSampleType,
- DataSetTypeWithVocabularyTerms imageDataSetType)
+ IEncapsulatedOpenBISService openbisService)
{
this.delegator = delegator;
sessionContext = delegator.getSessionContext();
this.openbisService = openbisService;
- this.replicaSampleType = replicaSampleType;
- this.imageDataSetType = imageDataSetType;
+ 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()
@@ -72,11 +91,26 @@ abstract class BundleDataSetHelper
return openbisService;
}
+ SampleType getGridPrepSampleType()
+ {
+ return gridPrepSampleType;
+ }
+
SampleType getReplicaSampleType()
{
return replicaSampleType;
}
+ DataSetTypeWithVocabularyTerms getRawImagesDataSetType()
+ {
+ return rawImagesDataSetType;
+ }
+
+ DataSetTypeWithVocabularyTerms getMetadataDataSetType()
+ {
+ return metadataDataSetType;
+ }
+
DataSetTypeWithVocabularyTerms getImageDataSetType()
{
return imageDataSetType;
@@ -96,16 +130,27 @@ abstract class BundleDataSetHelper
this.registeredDataSets = new ArrayList<DataSetInformation>();
}
+ /**
+ * Get all the data set information that has been created as a result of
+ * {@link #registerDataSet}. Only makes sense to invoke after registerDataSet has been called
+ */
+ public ArrayList<DataSetInformation> getDataSetInformation()
+ {
+ return registeredDataSets;
+ }
+
/**
* Register the provided file as a data set and add it to the dataSetInformation collection.
*
* @param dataSetFile The file to register as a data set
* @return A collection of data set information objects for each data set just registered
*/
- public List<DataSetInformation> registerDataSet(File dataSetFile)
+ protected List<DataSetInformation> registerDataSet(File dataSetFile,
+ DataSetInformation dataSetInfo)
{
// Register the given file
- List<DataSetInformation> bigDataSet = getDelegator().handleDataSet(dataSetFile);
+ List<DataSetInformation> bigDataSet =
+ getDelegator().handleDataSet(dataSetFile, dataSetInfo);
registeredDataSets.addAll(bigDataSet);
return bigDataSet;
}
@@ -125,13 +170,25 @@ abstract class BundleDataSetHelper
return globalState.getSessionContext();
}
- /**
- * Get all the data set information that has been created as a result of
- * {@link #registerDataSet}. Only makes sense to invoke after registerDataSet has been called
- */
- public ArrayList<DataSetInformation> getDataSetInformation()
+ protected ArrayList<NewProperty> createDataSetProperties(IMetadataExtractor metadata)
{
- return registeredDataSets;
- }
+ List<PropertyTypeWithVocabulary> propertyTypes =
+ globalState.getImageDataSetType().getPropertyTypes();
+ ArrayList<NewProperty> properties = new ArrayList<NewProperty>();
+ for (PropertyTypeWithVocabulary propertyType : propertyTypes)
+ {
+ String value = metadata.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, metadata.getMetadataMap()
+ .toString()));
+ return properties;
+ }
}
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 d080c5723e0..0d0fa3feab4 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
@@ -95,7 +95,7 @@ public class GridPreparationRegistrator extends BundleDataSetHelper
{
NewSample newSample =
NewSample.createWithParent(gridPrepSampleId.toString(),
- globalState.getReplicaSampleType(), null, null);
+ globalState.getGridPrepSampleType(), null, null);
newSample.setExperimentIdentifier(expId.toString());
String userId = getSessionContext().getUserName();
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 d4d7668768f..5553a4bb188 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
@@ -16,7 +16,14 @@
package ch.systemsx.cisd.cina.dss.bundle.registrators;
-import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.cina.shared.metadata.ImageMetadataExtractor;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
* Registers annotated image data sets.
@@ -25,15 +32,40 @@ import java.io.File;
*/
public class ReplicaAnnotatedImagesRegistrator extends BundleDataSetHelper
{
+ private final ImageMetadataExtractor imageMetadataExtractor;
+
+ private final SampleIdentifier replicaSampleId;
- /**
- * @param globalState
- * @param dataSet
- */
- ReplicaAnnotatedImagesRegistrator(BundleRegistrationState globalState, File dataSet)
+ ReplicaAnnotatedImagesRegistrator(BundleRegistrationState globalState,
+ ImageMetadataExtractor imageMetadataExtractor, Sample replicaSample,
+ SampleIdentifier replicaSampleId)
{
- super(globalState, dataSet);
- // TODO Auto-generated constructor stub
+ super(globalState, imageMetadataExtractor.getFolder());
+ this.imageMetadataExtractor = imageMetadataExtractor;
+ this.replicaSampleId = replicaSampleId;
}
+ public List<DataSetInformation> register()
+ {
+ // Create a DataSetInformation
+ DataSetInformation metadataDataSetInfo = createDataSetInformation();
+
+ // Import the metadata
+ ArrayList<NewProperty> properties = createDataSetProperties(imageMetadataExtractor);
+ metadataDataSetInfo.setDataSetProperties(properties);
+ registerDataSet(dataSet, metadataDataSetInfo);
+
+ return getDataSetInformation();
+ }
+
+ private DataSetInformation createDataSetInformation()
+ {
+ DataSetInformation metadataDataSetInfo = new DataSetInformation();
+ metadataDataSetInfo.setSampleCode(replicaSampleId.getSampleCode());
+ metadataDataSetInfo.setSpaceCode(replicaSampleId.getSpaceLevel().getSpaceCode());
+ metadataDataSetInfo.setInstanceCode(replicaSampleId.getSpaceLevel()
+ .getDatabaseInstanceCode());
+ metadataDataSetInfo.setDataSetType(globalState.getImageDataSetType().getDataSetType());
+ return metadataDataSetInfo;
+ }
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaMetadataRegistrator.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaMetadataRegistrator.java
index ed3ec060c2a..f3120000b60 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaMetadataRegistrator.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaMetadataRegistrator.java
@@ -17,6 +17,15 @@
package ch.systemsx.cisd.cina.dss.bundle.registrators;
import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.cina.shared.metadata.ReplicaMetadataExtractor;
+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.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
* Registers a metadata data set.
@@ -25,15 +34,67 @@ import java.io.File;
*/
public class ReplicaMetadataRegistrator extends BundleDataSetHelper
{
+ private final ReplicaMetadataExtractor replicaMetadataExtractor;
+
+ private final SampleIdentifier replicaSampleId;
+
+ private File metadataDataSetFile = null;
+
+ ReplicaMetadataRegistrator(BundleRegistrationState globalState,
+ ReplicaMetadataExtractor replicaMetadataExtractor, Sample replicaSample,
+ SampleIdentifier replicaSampleId)
+ {
+ super(globalState, replicaMetadataExtractor.getFolder());
+ this.replicaMetadataExtractor = replicaMetadataExtractor;
+ this.replicaSampleId = replicaSampleId;
+ }
/**
- * @param globalState
- * @param dataSet
+ * Register the metadata data set. Initialize the file object for the data set in the store.
*/
- ReplicaMetadataRegistrator(BundleRegistrationState globalState, File dataSet)
+ public List<DataSetInformation> register()
+ {
+ String dataSetFileName = dataSet.getName();
+
+ // Create a DataSetInformation
+ DataSetInformation metadataDataSetInfo = createDataSetInformation();
+
+ // Import the metadata
+ ArrayList<NewProperty> properties = createDataSetProperties(replicaMetadataExtractor);
+ metadataDataSetInfo.setDataSetProperties(properties);
+ registerDataSet(dataSet, metadataDataSetInfo);
+
+ // Get the data set information for the data set we just registered
+ DataSetInformation registeredDataSetInformation = getDataSetInformation().get(0);
+ initializeMetadataDataSetFile(registeredDataSetInformation, dataSetFileName);
+
+ return getDataSetInformation();
+ }
+
+ public File getMetadataDataSetFile()
{
- super(globalState, dataSet);
- // TODO Auto-generated constructor stub
+ assert metadataDataSetFile != null : "Can get metadataDataSetFile only after calling register";
+ return metadataDataSetFile;
}
+ private DataSetInformation createDataSetInformation()
+ {
+ DataSetInformation metadataDataSetInfo = new DataSetInformation();
+ metadataDataSetInfo.setSampleCode(replicaSampleId.getSampleCode());
+ metadataDataSetInfo.setSpaceCode(replicaSampleId.getSpaceLevel().getSpaceCode());
+ metadataDataSetInfo.setInstanceCode(replicaSampleId.getSpaceLevel()
+ .getDatabaseInstanceCode());
+ metadataDataSetInfo.setDataSetType(globalState.getMetadataDataSetType().getDataSetType());
+ return metadataDataSetInfo;
+ }
+
+ private void initializeMetadataDataSetFile(DataSetInformation registeredDataSetInformation,
+ String dataSetFileName)
+ {
+ ExternalData metadataExternalData =
+ getOpenbisService().tryGetDataSet(getSessionContext().getSessionToken(),
+ registeredDataSetInformation.getDataSetCode());
+ File containerFile = getDelegator().getFileForExternalData(metadataExternalData);
+ metadataDataSetFile = new File(containerFile, dataSetFileName);
+ }
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRawImagesRegistrator.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRawImagesRegistrator.java
new file mode 100644
index 00000000000..0c5361aa6f6
--- /dev/null
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRawImagesRegistrator.java
@@ -0,0 +1,72 @@
+/*
+ * 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.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.cina.shared.metadata.ReplicaMetadataExtractor;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+
+/**
+ * Registers a replica's raw image data set.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ReplicaRawImagesRegistrator extends BundleDataSetHelper
+{
+ private final ReplicaMetadataExtractor replicaMetadataExtractor;
+
+ private final SampleIdentifier replicaSampleId;
+
+ ReplicaRawImagesRegistrator(BundleRegistrationState globalState,
+ ReplicaMetadataExtractor replicaMetadataExtractor, Sample replicaSample,
+ SampleIdentifier replicaSampleId, File dataSet)
+ {
+ super(globalState, dataSet);
+ this.replicaMetadataExtractor = replicaMetadataExtractor;
+ this.replicaSampleId = replicaSampleId;
+ }
+
+ public List<DataSetInformation> register()
+ {
+ // Create a DataSetInformation
+ DataSetInformation imagesDataSetInfo = createDataSetInformation();
+
+ // Import the metadata
+ ArrayList<NewProperty> properties = createDataSetProperties(replicaMetadataExtractor);
+ imagesDataSetInfo.setDataSetProperties(properties);
+ registerDataSet(dataSet, imagesDataSetInfo);
+
+ return getDataSetInformation();
+ }
+
+ private DataSetInformation createDataSetInformation()
+ {
+ DataSetInformation imagesDataSetInfo = new DataSetInformation();
+ imagesDataSetInfo.setSampleCode(replicaSampleId.getSampleCode());
+ imagesDataSetInfo.setSpaceCode(replicaSampleId.getSpaceLevel().getSpaceCode());
+ imagesDataSetInfo
+ .setInstanceCode(replicaSampleId.getSpaceLevel().getDatabaseInstanceCode());
+ imagesDataSetInfo.setDataSetType(globalState.getRawImagesDataSetType().getDataSetType());
+ return imagesDataSetInfo;
+ }
+}
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 b45fdb329d2..d06500e51a3 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
@@ -17,19 +17,24 @@
package ch.systemsx.cisd.cina.dss.bundle.registrators;
import java.io.File;
+import java.util.List;
+import ch.systemsx.cisd.cina.shared.metadata.ImageMetadataExtractor;
import ch.systemsx.cisd.cina.shared.metadata.ReplicaMetadataExtractor;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
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.dto.identifier.SampleIdentifier;
/**
- * Registers/Updates a replica, its metadata, the original images and the annotated images.
+ * Registers/Updates a replica, its metadata, the raw images and the annotated images.
*
* @author Chandrasekhar Ramakrishnan
*/
public class ReplicaRegistrator extends BundleDataSetHelper
{
+ private static final String RAW_IMAGES_FOLDER_NAME = "RawData";
+
private final ReplicaMetadataExtractor replicaMetadataExtractor;
private final Sample gridPrepSample;
@@ -41,10 +46,8 @@ public class ReplicaRegistrator extends BundleDataSetHelper
private Sample replicaSample;
- /**
- * @param globalState
- * @param dataSet
- */
+ private boolean didCreateSample = false;
+
ReplicaRegistrator(BundleRegistrationState globalState,
ReplicaMetadataExtractor replicaMetadataExtractor, Sample gridPrepSample,
SampleIdentifier gridPrepSampleId, File dataSet)
@@ -60,17 +63,27 @@ public class ReplicaRegistrator extends BundleDataSetHelper
* Create the replica sample (if necessary). Register the original images (if the replica sample
* did not exist), register the metadata dataset, and update the sample metadata, register the
* annotated images.
+ *
+ * @return DataSetInformation objects for each of the data sets registered
*/
- public void register()
+ public List<DataSetInformation> register()
{
- retrieveOrCreateGridPrepSample();
+ retrieveOrCreateReplicaSample();
+ if (didCreateSample)
+ {
+ registerRawImages();
+ }
+ registerMetadata();
+
+ return getDataSetInformation();
}
- private void retrieveOrCreateGridPrepSample()
+ private void retrieveOrCreateReplicaSample()
{
String sampleCode = replicaMetadataExtractor.tryReplicaSampleCode();
replicaSampleId = new SampleIdentifier(gridPrepSampleId.getSpaceLevel(), sampleCode);
replicaSample = getOpenbisService().tryGetSampleWithExperiment(replicaSampleId);
+ didCreateSample = false;
// Sample doesn't exist, create it
if (replicaSample == null)
@@ -83,8 +96,56 @@ public class ReplicaRegistrator extends BundleDataSetHelper
String userId = getSessionContext().getUserName();
getOpenbisService().registerSample(newSample, userId);
replicaSample = getOpenbisService().tryGetSampleWithExperiment(replicaSampleId);
+ didCreateSample = true;
}
assert replicaSample != null;
}
+
+ private void registerRawImages()
+ {
+ String replicaName = replicaMetadataExtractor.getFolder().getName();
+ File replicaOriginalImages =
+ new File(new File(dataSet, RAW_IMAGES_FOLDER_NAME), replicaName);
+ ReplicaRawImagesRegistrator registrator =
+ new ReplicaRawImagesRegistrator(globalState, replicaMetadataExtractor,
+ replicaSample, replicaSampleId, replicaOriginalImages);
+ List<DataSetInformation> registeredDataSetInfos = registrator.register();
+ getDataSetInformation().addAll(registeredDataSetInfos);
+ }
+
+ /**
+ * Register the metadata data set and return the File object for the registered data set.
+ *
+ * @return The File object for the registered data set
+ */
+ private File registerMetadata()
+ {
+ ReplicaMetadataRegistrator registrator =
+ new ReplicaMetadataRegistrator(globalState, replicaMetadataExtractor,
+ replicaSample, replicaSampleId);
+ List<DataSetInformation> registeredDataSetInfos = registrator.register();
+ getDataSetInformation().addAll(registeredDataSetInfos);
+ 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
+ // extractor on the data set in the incoming directory, so the paths it has are not
+ // persistent)
+ ReplicaMetadataExtractor storeReplicaMetadataExtractor =
+ new ReplicaMetadataExtractor(registeredMetadataFile);
+ storeReplicaMetadataExtractor.prepare();
+ for (ImageMetadataExtractor imageMetadataExtractor : storeReplicaMetadataExtractor
+ .getImageMetadataExtractors())
+ {
+ ReplicaAnnotatedImagesRegistrator registrator =
+ new ReplicaAnnotatedImagesRegistrator(globalState, imageMetadataExtractor,
+ replicaSample, replicaSampleId);
+ List<DataSetInformation> registeredDataSetInfos = registrator.register();
+ getDataSetInformation().addAll(registeredDataSetInfos);
+ }
+ }
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java
index ffdc760ba7b..1c64a8a40f3 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java
@@ -23,8 +23,14 @@ public class CinaConstants
{
public static final String BUNDLE_DATA_SET_TYPE_CODE = "BUNDLE";
+ public static final String RAW_IMAGES_DATA_SET_TYPE_CODE = "RAW_IMAGES";
+
+ public static final String METADATA_DATA_SET_TYPE_CODE = "METADATA";
+
public static final String IMAGE_DATA_SET_TYPE_CODE = "IMAGE";
+ public static final String GRID_PREP_SAMPLE_TYPE_CODE = "GRID_PREP";
+
public final static String REPLICA_SAMPLE_TYPE_CODE = "GRID_REPLICA";
public static final String DIMENSION_PREFIX = "Dimension";
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/metadata/BundleStructureConstants.java
new file mode 100644
index 00000000000..2ddf9d74d5a
--- /dev/null
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/BundleStructureConstants.java
@@ -0,0 +1,69 @@
+/*
+ * 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.shared.metadata;
+
+/**
+ * Constants that describe the structure fo the CINA bundle files.
+ * <p>
+ * Root.bundle/
+ * <ul>
+ * <li>BUNDLE_METADATA_FILE_NAME</li>
+ * <li>METADATA_FOLDER_NAME
+ * <ul>
+ * <li>Replica Folder
+ * <ul>
+ * <li>REPLICA_METADATA_FILE_NAME</li>
+ * <li>ANNOTATED_IMAGES_FOLDER_NAME
+ * <ul>
+ * <li>IMAGE_METADATA_FILE_NAME</li>
+ * </ul>
+ * </li>
+ * </ul>
+ * </li>
+ * </ul>
+ * </li>
+ * <li>RAW_IMAGES_FOLDER_NAME</li>
+ * </ul>
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class BundleStructureConstants
+{
+ public static final String METADATA_FOLDER_NAME = "Annotations";
+
+ public static final String RAW_IMAGES_FOLDER_NAME = "RawData";
+
+ public static final String ANNOTATED_IMAGES_FOLDER_NAME = "Representations";
+
+ public static final String BUNDLE_METADATA_FILE_NAME = "BundleMetadata.xml";
+
+ public static final String REPLICA_METADATA_FILE_NAME = "ReplicaMetadata.xml";
+
+ public final static String IMAGE_METADATA_FILE_NAME = "metadata.xml";
+
+ public static final String GRID_PREP_SAMPLE_CODE_KEY = "database link information";
+
+ public static final String REPLICA_SAMPLE_CODE_KEY = "database id (replica)";
+
+ /**
+ * No reason to instantiate this class.
+ */
+ private BundleStructureConstants()
+ {
+
+ }
+}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaOriginalImagesRegistrator.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/IMetadataExtractor.java
similarity index 60%
rename from rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaOriginalImagesRegistrator.java
rename to rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/IMetadataExtractor.java
index 22c8f354930..8dfeef4a94a 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaOriginalImagesRegistrator.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/IMetadataExtractor.java
@@ -14,26 +14,17 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.cina.dss.bundle.registrators;
+package ch.systemsx.cisd.cina.shared.metadata;
-import java.io.File;
+import java.util.Map;
/**
- * Registers a replica's original image data set.
- *
* @author Chandrasekhar Ramakrishnan
*/
-public class ReplicaOriginalImagesRegistrator extends BundleDataSetHelper
+public interface IMetadataExtractor
{
-
/**
- * @param globalState
- * @param dataSet
+ * Get the metadata extracted from the file in the form of a map.
*/
- ReplicaOriginalImagesRegistrator(BundleRegistrationState globalState, File dataSet)
- {
- super(globalState, dataSet);
- // TODO Auto-generated constructor stub
- }
-
+ public Map<String, String> getMetadataMap();
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ImageMetadataExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ImageMetadataExtractor.java
index 96c8934c9e3..1a3254c4a13 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ImageMetadataExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ImageMetadataExtractor.java
@@ -29,7 +29,7 @@ import ch.systemsx.cisd.cina.shared.labview.LVDataParser;
*
* @author Chandrasekhar Ramakrishnan
*/
-public class ImageMetadataExtractor
+public class ImageMetadataExtractor implements IMetadataExtractor
{
private final HashMap<String, String> metadataMap;
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ReplicaMetadataExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ReplicaMetadataExtractor.java
index 6c34c2ee7b2..efad5ad7500 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ReplicaMetadataExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ReplicaMetadataExtractor.java
@@ -28,9 +28,9 @@ import ch.systemsx.cisd.cina.shared.labview.LVDataParser;
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class ReplicaMetadataExtractor
+public class ReplicaMetadataExtractor implements IMetadataExtractor
{
- private static final String METADATA_FILE_NAME = "ReplicaMetadata.xml";
+ private static final String REPLICA_METADATA_FILE_NAME = "ReplicaMetadata.xml";
private static final String REPLICA_SAMPLE_CODE_KEY = "database id (replica)";
@@ -44,7 +44,7 @@ public class ReplicaMetadataExtractor
public static boolean doesFolderContainReplicaMetadata(File folder)
{
- File metadataFile = new File(folder, METADATA_FILE_NAME);
+ File metadataFile = new File(folder, REPLICA_METADATA_FILE_NAME);
return metadataFile.exists();
}
@@ -67,7 +67,7 @@ public class ReplicaMetadataExtractor
}
// First parse the metadata for the replica
- File metadataFile = new File(folder, METADATA_FILE_NAME);
+ File metadataFile = new File(folder, REPLICA_METADATA_FILE_NAME);
lvdata = LVDataParser.parse(metadataFile);
if (null == lvdata)
{
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 6b7a50e8297..2feeca594d1 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
@@ -18,6 +18,7 @@ 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;
@@ -49,6 +50,14 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
*/
public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
{
+ 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";
@@ -67,6 +76,16 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
private static final String REPLICA_SAMPLE_IDENTIFIER = DB_CODE + ":/" + SPACE_CODE + "/"
+ REPLICA_SAMPLE_CODE;
+ private static abstract class MatcherNoDesc<T> extends BaseMatcher<T>
+ {
+
+ public void describeTo(Description description)
+ {
+
+ }
+
+ }
+
private Mockery context;
private IEncapsulatedOpenBISService openbisService;
@@ -136,21 +155,6 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
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_CODE);
- // dataSetInformation.setInstanceCode("Test");
- //
- // allowing(delegator).linkAndHandleDataSet(with(new File(path)),
- // with(any(DataSetInformation.class)));
- // will(returnValue(Collections.singletonList(dataSetInformation)));
- // }
-
{
// The Grid Prep does not yet exist
one(openbisService).tryGetSampleWithExperiment(
@@ -178,7 +182,7 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
public void describeTo(Description description)
{
}
- }), with("test"));
+ }), with(TEST_USER_NAME));
will(returnValue(new Long(1)));
// The Replica does not yet exist
@@ -188,7 +192,7 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
will(returnValue(null));
// Create the Replica
- one(openbisService).registerSample(with(new BaseMatcher<NewSample>()
+ one(openbisService).registerSample(with(new MatcherNoDesc<NewSample>()
{
public boolean matches(Object item)
{
@@ -205,21 +209,15 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
}
return false;
}
-
- public void describeTo(Description description)
- {
- }
- }), with("test"));
+ }), with(TEST_USER_NAME));
will(returnValue(new Long(2)));
-
- // 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();
+ 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");
createRegistrator(dataSetFile);
registrator.register();
@@ -229,15 +227,30 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
private void setupOpenBisExpectations()
{
- final SampleType sampleType = new SampleType();
- sampleType.setCode(CinaConstants.REPLICA_SAMPLE_TYPE_CODE);
- sampleType.setAutoGeneratedCode(true);
- sampleType.setGeneratedCodePrefix("Replica-");
+ 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);
- final DataSetTypeWithVocabularyTerms dataSetTypeWithTerms =
+ final DataSetTypeWithVocabularyTerms rawImagesDataSetTypeWithTerms =
+ new DataSetTypeWithVocabularyTerms();
+ rawImagesDataSetTypeWithTerms.setDataSetType(dataSetType);
+
+ dataSetType = new DataSetType(CinaConstants.METADATA_DATA_SET_TYPE_CODE);
+ final DataSetTypeWithVocabularyTerms metadataDataSetTypeWithTerms =
+ new DataSetTypeWithVocabularyTerms();
+ metadataDataSetTypeWithTerms.setDataSetType(dataSetType);
+
+ dataSetType = new DataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
+ final DataSetTypeWithVocabularyTerms imageDataSetTypeWithTerms =
new DataSetTypeWithVocabularyTerms();
- dataSetTypeWithTerms.setDataSetType(dataSetType);
+ imageDataSetTypeWithTerms.setDataSetType(dataSetType);
externalData = new ExternalData();
externalData.setCode("1");
@@ -246,10 +259,16 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
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(sampleType));
+ 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(dataSetTypeWithTerms));
+ will(returnValue(imageDataSetTypeWithTerms));
// one(openbisService).tryGetDataSet("session-token", externalData.getCode());
// will(returnValue(externalData));
}
@@ -296,41 +315,88 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
});
}
+ 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(REPLICA_SAMPLE_CODE,
+ dataSetInfo.getSampleCode());
+ return true;
+ }
+ return false;
+ }
+ }));
+ will(returnValue(Collections.singletonList(dataSetInformation)));
+ }
+ });
+ }
+
+ private void setupHandleMetadataDataSetExpectations(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("1");
+
+ final File dataSetFile = new File(path);
+
+ // set up the expectations
+ context.checking(new Expectations()
+ {
+ {
+ one(delegator).handleDataSet(with(dataSetFile),
+ with(new MatcherNoDesc<DataSetInformation>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof DataSetInformation)
+ {
+ DataSetInformation dataSetInfo =
+ (DataSetInformation) item;
+ assertEquals(REPLICA_SAMPLE_CODE,
+ dataSetInfo.getSampleCode());
+ return true;
+ }
+ return false;
+ }
+ }));
+ will(returnValue(Collections.singletonList(dataSetInformation)));
+ one(openbisService).tryGetDataSet(SESSION_TOKEN, METADATA_DATA_SET_CODE);
+ will(returnValue(externalData));
+ one(delegator).getFileForExternalData(externalData);
+ will(returnValue(dataSetFile.getParentFile()));
+ }
+ });
+ }
+
private void createRegistrator(final File dataSet)
{
registrator = new GridPreparationRegistrator(createBundleRegistrationState(), dataSet);
}
- // private void setupNewSampleExpectations(final File dataSet)
- // {
- // setupSessionContextExpectations();
- //
- // final DataSetInformation dataSetInformation = new DataSetInformation();
- // dataSetInformation.setDataSetCode(externalData.getCode());
- // dataSetInformation.setSampleCode("GRID-1");
- // dataSetInformation.setSpaceCode(SPACE_CODE);
- // 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());
- //
- // // set up the expectations
- // context.checking(new Expectations()
- // {
- // {
- // one(delegator).handleDataSet(dataSet);
- // will(returnValue(Collections.singletonList(dataSetInformation)));
- // one(delegator).getFileForExternalData(externalData);
- // will(returnValue(dataSet.getParentFile()));
- // }
- // });
- //
- // createRegistrator(dataSet);
- // }
-
private void setupCallerDataSetInfoExpectations()
{
@@ -353,9 +419,9 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
private void setupSessionContextExpectations()
{
final SessionContextDTO sessionContext = new SessionContextDTO();
- sessionContext.setSessionToken("session-token");
+ sessionContext.setSessionToken(SESSION_TOKEN);
sessionContext.setUserEmail("test@test.bar");
- sessionContext.setUserName("test");
+ sessionContext.setUserName(TEST_USER_NAME);
// set up the expectations
context.checking(new Expectations()
@@ -370,12 +436,7 @@ public class GridPreparationRegistratorTest extends AbstractFileSystemTestCase
private BundleRegistrationState createBundleRegistrationState()
{
- SampleType replicaSampleType =
- openbisService.getSampleType(CinaConstants.REPLICA_SAMPLE_TYPE_CODE);
- DataSetTypeWithVocabularyTerms imageDataSetType =
- openbisService.getDataSetType(CinaConstants.IMAGE_DATA_SET_TYPE_CODE);
- return new BundleRegistrationState(delegator, openbisService, replicaSampleType,
- imageDataSetType);
+ return new BundleRegistrationState(delegator, openbisService);
}
}
--
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