diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/StorageProcessor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/StorageProcessor.java
index 49407936743429cdbbf7ed0883d3e152292a41bf..69a7c600f35589443dacaaf7085cea30073e9020 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/StorageProcessor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/StorageProcessor.java
@@ -19,7 +19,6 @@ package ch.systemsx.cisd.cina.dss;
import java.io.File;
import java.util.Properties;
-import ch.systemsx.cisd.cina.dss.info.EntityRegistrationSuccessEmail;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.etlserver.AbstractDelegatingStorageProcessor;
import ch.systemsx.cisd.etlserver.IStorageProcessor;
@@ -35,18 +34,9 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
*/
public class StorageProcessor extends AbstractDelegatingStorageProcessor
{
- private String defaultEmailAddress = "root@localhost";
-
- private static final String DEFAULT_EMAIL_ADDRESS_KEY = "default-email";
-
public StorageProcessor(Properties properties)
{
super(properties);
-
- if (properties.containsKey(DEFAULT_EMAIL_ADDRESS_KEY))
- {
- defaultEmailAddress = properties.getProperty(DEFAULT_EMAIL_ADDRESS_KEY);
- }
}
public StorageProcessor(IStorageProcessor delegatedProcessor)
@@ -59,25 +49,10 @@ public class StorageProcessor extends AbstractDelegatingStorageProcessor
final ITypeExtractor typeExtractor, final IMailClient mailClient,
final File incomingDataSetDirectory, final File rootDir)
{
- // Create the email first because the email looks into the directory to determine its
- // content.
- EntityRegistrationSuccessEmail successEmail =
- new EntityRegistrationSuccessEmail(dataSetInformation, incomingDataSetDirectory);
-
File answer =
super.storeData(dataSetInformation, typeExtractor, mailClient,
incomingDataSetDirectory, rootDir);
- String emailAddress = dataSetInformation.tryGetUploadingUserEmail();
- if (emailAddress == null)
- {
- emailAddress = defaultEmailAddress;
- }
-
- mailClient.sendMessageWithAttachment(successEmail.getSubject(), successEmail
- .getContentMimeText(), successEmail.getContentMimeAttachmentFileName(),
- successEmail.getContentMimeAttachmentContent(), null, null, emailAddress);
-
return answer;
}
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
new file mode 100644
index 0000000000000000000000000000000000000000..5dd523fbb1b6e5745dbe4bb26653cf523d53a728
--- /dev/null
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/BundleDataSetHelper.java
@@ -0,0 +1,177 @@
+/*
+ * 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.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.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.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+
+/**
+ * Helper class for processing bundle data sets.
+ *
+ * @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;
+ }
+ }
+
+ private final BundleRegistrationGlobalState globalState;
+
+ // Invocation-specific State
+ private final String sessionOwnerUserId;
+
+ private final File dataSet;
+
+ private final ArrayList<DataSetInformation> dataSetInformation;
+
+ BundleDataSetHelper(BundleRegistrationGlobalState globalState, String sessionOwnerUserId,
+ File dataSet)
+ {
+ this.globalState = globalState;
+ this.sessionOwnerUserId = sessionOwnerUserId;
+ 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);
+ if (dataSetInformation.isEmpty())
+ {
+ return;
+ }
+
+ BundleMetadataExtractor bundleMetadata = new BundleMetadataExtractor(dataSet);
+ for (ReplicaMetadataExtractor replicaMetadata : bundleMetadata.getMetadataExtractors())
+ {
+ handleDerivedDataSets(replicaMetadata);
+ }
+ }
+
+ /**
+ * 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;
+ }
+
+ private void handleDerivedDataSets(ReplicaMetadataExtractor replicaMetadata)
+ {
+ SampleType replicaSampleType = globalState.getReplicaSampleType();
+ long sampleCodeSuffix = getOpenbisService().drawANewUniqueID();
+ String sampleCode =
+ String.format("%s%d", replicaSampleType.getGeneratedCodePrefix(), sampleCodeSuffix);
+ SampleIdentifier parentIdentifier = getBigDataSetInformation().getSampleIdentifier();
+
+ // Register a sample with this ID of type GRID_REPLICA, derived from the GRID_TEMPLATE
+ // registered by the client
+ SampleIdentifier identifier =
+ new SampleIdentifier(parentIdentifier.getSpaceLevel(), sampleCode);
+ NewSample sample =
+ new NewSample(identifier.toString(), replicaSampleType,
+ parentIdentifier.toString(), "");
+ getOpenbisService().registerSample(sample, sessionOwnerUserId);
+
+ // Register all the data sets derived from this sample
+ for (ImageMetadataExtractor imageMetadata : replicaMetadata.getMetadataExtractors())
+ {
+ handleDerivedDataSet(identifier.toString(), imageMetadata);
+ }
+ }
+
+ private void handleDerivedDataSet(String sampleId, ImageMetadataExtractor imageMetadata)
+ {
+ // Register a data set for the image
+
+ }
+
+ /**
+ * 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);
+ }
+
+ private IDataSetHandler getDelegator()
+ {
+ return globalState.getDelegator();
+ }
+
+ private IEncapsulatedOpenBISService getOpenbisService()
+ {
+ return globalState.getOpenbisService();
+ }
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..ed4a7ea77045b6de1e3d8111b674781360c2bf34
--- /dev/null
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandler.java
@@ -0,0 +1,67 @@
+/*
+ * 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.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.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;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class CinaBundleDataSetHandler implements IDataSetHandler
+{
+ private final IDataSetHandler delegator;
+
+ private final IEncapsulatedOpenBISService openbisService;
+
+ private final BundleRegistrationGlobalState bundleRegistrationGlobalState;
+
+ public CinaBundleDataSetHandler(Properties parentProperties, IDataSetHandler delegator,
+ IEncapsulatedOpenBISService openbisService)
+ {
+ this.delegator = delegator;
+ this.openbisService = openbisService;
+ this.bundleRegistrationGlobalState = createBundleRegistrationGlobalState();
+ }
+
+ public List<DataSetInformation> handleDataSet(File dataSet)
+ {
+ BundleDataSetHelper helper =
+ new BundleDataSetHelper(bundleRegistrationGlobalState, null, dataSet);
+ helper.process();
+ return helper.getDataSetInformation();
+ }
+
+ private BundleRegistrationGlobalState createBundleRegistrationGlobalState()
+ {
+ 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);
+ }
+}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaDataSetInfoExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetInfoExtractor.java
similarity index 82%
rename from rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaDataSetInfoExtractor.java
rename to rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetInfoExtractor.java
index 058b8d0ff31c0370cb19f924cc9cb8973eacaa4b..f4cf67236ec655df0594b1bcc85a88cacdbeae11 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaDataSetInfoExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetInfoExtractor.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.cina.dss.bundle;
import java.io.File;
+import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -29,14 +30,19 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
*
* @author Chandrasekhar Ramakrishnan
*/
-public class CinaDataSetInfoExtractor implements IDataSetInfoExtractor
+public class CinaBundleDataSetInfoExtractor implements IDataSetInfoExtractor
{
+ public CinaBundleDataSetInfoExtractor(final Properties globalProperties)
+ {
+
+ }
public DataSetInformation getDataSetInformation(File incomingDataSetPath,
IEncapsulatedOpenBISService openbisService) throws UserFailureException,
EnvironmentFailureException
{
- return new DataSetInformation();
- }
+ DataSetInformation result = new DataSetInformation();
+ return result;
+ }
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaTypeExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleTypeExtractor.java
similarity index 83%
rename from rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaTypeExtractor.java
rename to rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleTypeExtractor.java
index c0aae4be07f608a9d05a883a1a5bba82ad642b96..cbf21e7c10f37396e9fa7f4a91794ea6d505b2aa 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaTypeExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleTypeExtractor.java
@@ -17,7 +17,9 @@
package ch.systemsx.cisd.cina.dss.bundle;
import java.io.File;
+import java.util.Properties;
+import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
@@ -26,13 +28,16 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class CinaTypeExtractor implements ITypeExtractor
+public class CinaBundleTypeExtractor implements ITypeExtractor
{
- private static final String BUNDLE_DATA_SET_TYPE = "BUNDLE";
+ public CinaBundleTypeExtractor(final Properties properties)
+ {
+
+ }
public DataSetType getDataSetType(File incomingDataSetPath)
{
- return new DataSetType(BUNDLE_DATA_SET_TYPE);
+ return new DataSetType(CinaConstants.BUNDLE_DATA_SET_TYPE_CODE);
}
public FileFormatType getFileFormatType(File incomingDataSetPath)
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java
index 31d7f5c8d1115dd9504e5014a50d20f99990a3df..6f9752cfcc7288cdd8685a83244f28c5aa87a849 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/info/CinaDataSetInfoExtractor.java
@@ -36,7 +36,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
/**
* CINA uses the data store server to register experiments and samples in addition to data sets. The
- * CinaDataSetInfoExtractor follows the conventions agreed to by the CINA project to determine if
+ * CinaBundleDataSetInfoExtractor follows the conventions agreed to by the CINA project to determine if
* the file represents an experiment, sample, or data set and takes according action.
* <p>
* In the case of data representing experiments and samples, the extractor may need to register the
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
new file mode 100644
index 0000000000000000000000000000000000000000..ffdc760ba7b4387864f71795e1ea4bd17563a348
--- /dev/null
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java
@@ -0,0 +1,39 @@
+/*
+ * 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.constants;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class CinaConstants
+{
+ public static final String BUNDLE_DATA_SET_TYPE_CODE = "BUNDLE";
+
+ public static final String IMAGE_DATA_SET_TYPE_CODE = "IMAGE";
+
+ public final static String REPLICA_SAMPLE_TYPE_CODE = "GRID_REPLICA";
+
+ public static final String DIMENSION_PREFIX = "Dimension";
+
+ public static final String SIZE_PREFIX = "Size";
+
+ // No need to instantiate this class
+ private CinaConstants()
+ {
+
+ }
+}
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 b0383e3b7894d269fc078ce0be41b8c893306e08..96c8934c9e3e4d9608a37970aa6f454fd3d5f25e 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
@@ -20,6 +20,7 @@ import java.io.File;
import java.util.HashMap;
import java.util.Map;
+import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
import ch.systemsx.cisd.cina.shared.labview.LVData;
import ch.systemsx.cisd.cina.shared.labview.LVDataParser;
@@ -36,14 +37,14 @@ public class ImageMetadataExtractor
private LVData lvdata;
- private static final String METADATA_FILE_NAME = "metadata.xml";
+ private final static String METADATA_FILE_NAME = "metadata.xml";
- private static final HashMap<String, String> prefixMap;
+ private final static HashMap<String, String> prefixMap;
static
{
prefixMap = new HashMap<String, String>();
- prefixMap.put("Pixelsize (nm)", "Size");
- prefixMap.put("Image dimension (px)", "Dimension");
+ prefixMap.put("Pixelsize (nm)", CinaConstants.SIZE_PREFIX);
+ prefixMap.put("Image dimension (px)", CinaConstants.DIMENSION_PREFIX);
}
public static boolean doesFolderContainImageMetadata(File folder)
@@ -108,6 +109,11 @@ public class ImageMetadataExtractor
return metadataMap;
}
+ public File getFolder()
+ {
+ return folder;
+ }
+
private void checkPrepared()
{
assert lvdata != null;
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 378c7e38bd757a540ee93afea366b7ab8b718fab..938d6c561ae3f9a7dca01efbeb9201f3f8bfce29 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
@@ -118,6 +118,11 @@ public class ReplicaMetadataExtractor
return metadataExtractors;
}
+ public File getFolder()
+ {
+ return folder;
+ }
+
private void checkPrepared()
{
assert lvdata != null;