From b5fedbae6a4e27ab4a6dba2511ed5d55b7b38cbc Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Tue, 20 Sep 2011 21:40:14 +0000
Subject: [PATCH] [LMS-2508] verify some more IStorageProcessorTransaction
implementations are Serializable
SVN: 23006
---
...AbstractStrorageProcessorWithUploader.java | 94 +++++++------
.../cisd/etlserver/CifexStorageProcessor.java | 30 +++--
.../etlserver/DefaultStorageProcessor.java | 2 +-
...DelegatingStorageProcessorWithDropbox.java | 19 ++-
.../ExceptionThrowingStorageProcessor.java | 4 +-
.../plasmid/dss/PlasmidStorageProcessor.java | 127 ++++++++++--------
.../yeastx/etl/QuantMLStorageProcessor.java | 121 +++++++++--------
.../biozentrum/LinkingStorageProcessor.java | 113 +++++++++-------
.../FeatureVectorStorageProcessor.java | 16 ++-
.../etl/genedata/FeatureStorageProcessor.java | 125 +++++++++--------
10 files changed, 362 insertions(+), 289 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStrorageProcessorWithUploader.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStrorageProcessorWithUploader.java
index cd1ab42481e..e30493079ff 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStrorageProcessorWithUploader.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStrorageProcessorWithUploader.java
@@ -57,54 +57,68 @@ public abstract class AbstractStrorageProcessorWithUploader extends
IStorageProcessorTransaction nestedTransaction =
super.createTransaction(transactionParameters);
- return new AbstractDelegatingStorageProcessorTransaction(transactionParameters,
- nestedTransaction)
- {
+ return new StorageProcessorWithUploaderTransaction(transactionParameters,
+ nestedTransaction, this);
+ }
- private static final long serialVersionUID = 1L;
+ static class StorageProcessorWithUploaderTransaction extends
+ AbstractDelegatingStorageProcessorTransaction
+ {
- @Override
- protected File executeStoreData(ITypeExtractor typeExtractor, IMailClient mailClient)
- {
+ private static final long serialVersionUID = 1L;
- nestedTransaction
- .storeData(typeExtractor, mailClient, incomingDataSetDirectory);
- File storeData = nestedTransaction.getStoredDataDirectory();
- File originalData = nestedTransaction.tryGetProprietaryData();
- if (originalData == null)
- {
- throw new ConfigurationFailureException(
- "The original data is no longer available by the wrapped storage processor. "
- + "Another storage processor should be used.");
- }
- uploader.upload(originalData, dataSetInformation);
- return storeData;
- }
+ private final transient AbstractStrorageProcessorWithUploader processor;
+
+ StorageProcessorWithUploaderTransaction(StorageProcessorTransactionParameters parameters, IStorageProcessorTransaction nestedTransaction, AbstractStrorageProcessorWithUploader processor) {
+ super(parameters, nestedTransaction);
+ this.processor = processor;
+ }
+
+ @Override
+ protected File executeStoreData(ITypeExtractor typeExtractor, IMailClient mailClient)
+ {
- @Override
- public UnstoreDataAction executeRollback(Throwable exception)
+ nestedTransaction.storeData(typeExtractor, mailClient, incomingDataSetDirectory);
+ File storeData = nestedTransaction.getStoredDataDirectory();
+ File originalData = nestedTransaction.tryGetProprietaryData();
+ if (originalData == null)
{
- try
- {
- nestedTransaction.rollback(exception);
- } finally
- {
- uploader.rollback();
- }
- logDataSetFileError(incomingDataSetDirectory, exception);
- return UnstoreDataAction.LEAVE_UNTOUCHED;
+ throw new ConfigurationFailureException(
+ "The original data is no longer available by the wrapped storage processor. "
+ + "Another storage processor should be used.");
}
-
- @Override
- public void executeCommit()
+ processor.uploader.upload(originalData, dataSetInformation);
+ return storeData;
+ }
+
+ @Override
+ public UnstoreDataAction executeRollback(Throwable exception)
+ {
+ try
+ {
+ nestedTransaction.rollback(exception);
+ } finally
+ {
+ if (processor != null)
{
- nestedTransaction.commit();
- uploader.commit();
+ processor.uploader.rollback();
}
-
- };
-
- }
+ }
+ if (processor != null)
+ {
+ processor.logDataSetFileError(incomingDataSetDirectory, exception);
+ }
+ return UnstoreDataAction.LEAVE_UNTOUCHED;
+ }
+
+ @Override
+ public void executeCommit()
+ {
+ nestedTransaction.commit();
+ processor.uploader.commit();
+ }
+
+ }
/**
* Logs an error for the specified data set and exception.
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java
index c8f083f88ed..2e5fb32ee92 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java
@@ -74,24 +74,33 @@ public class CifexStorageProcessor extends AbstractDelegatingStorageProcessor
{
IStorageProcessorTransaction superTransaction = super.createTransaction(parameters);
- return new CifexStorageProcessorTransaction(parameters, superTransaction);
+ return new CifexStorageProcessorTransaction(parameters, superTransaction, keepFileRegex,
+ moveToErrorFolder);
}
- private final class CifexStorageProcessorTransaction extends
+ private static final class CifexStorageProcessorTransaction extends
AbstractDelegatingStorageProcessorTransaction
{
private static final long serialVersionUID = 1L;
- private File dirToRestore;
+ private final String keepFileRegex;
- private File fileToMove;
+ private final boolean moveToErrorFolder;
+
+ private transient File dirToRestore;
+
+ private transient File fileToMove;
+
+ private transient boolean dirDeleted = false;
- private boolean dirDeleted = false;
private CifexStorageProcessorTransaction(StorageProcessorTransactionParameters parameters,
- IStorageProcessorTransaction transaction)
+ IStorageProcessorTransaction transaction, String keepFileRegex,
+ boolean moveErrorToFolder)
{
super(parameters, transaction);
+ this.keepFileRegex = keepFileRegex;
+ this.moveToErrorFolder = moveErrorToFolder;
}
@Override
@@ -100,7 +109,8 @@ public class CifexStorageProcessor extends AbstractDelegatingStorageProcessor
File newIncomingDataSetDirectory = incomingDataSetDirectory;
if (StringUtils.isBlank(keepFileRegex) == false)
{
- newIncomingDataSetDirectory = clean(incomingDataSetDirectory, keepFileRegex);
+ newIncomingDataSetDirectory =
+ clean(incomingDataSetDirectory, keepFileRegex);
}
nestedTransaction.storeData(typeExtractor, mailClient, newIncomingDataSetDirectory);
@@ -201,10 +211,4 @@ public class CifexStorageProcessor extends AbstractDelegatingStorageProcessor
}
}
-
- @Override
- public UnstoreDataAction getDefaultUnstoreDataAction(Throwable exception)
- {
- return moveToErrorFolder ? UnstoreDataAction.MOVE_TO_ERROR : UnstoreDataAction.DELETE;
- }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java
index 915a4c22ae9..42217f41c43 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java
@@ -84,7 +84,7 @@ public class DefaultStorageProcessor extends AbstractStorageProcessor
private final boolean deleteUnzipped;
- private final UnstoreDataAction unstoreDataAction;
+ protected final UnstoreDataAction unstoreDataAction;
public DefaultStorageProcessorTransaction(StorageProcessorTransactionParameters parameters,
DefaultStorageProcessor processor)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DelegatingStorageProcessorWithDropbox.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DelegatingStorageProcessorWithDropbox.java
index 50cc3e9198e..4b64cd0db06 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DelegatingStorageProcessorWithDropbox.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DelegatingStorageProcessorWithDropbox.java
@@ -73,22 +73,26 @@ public abstract class DelegatingStorageProcessorWithDropbox extends
StorageProcessorTransactionParameters parameters)
{
final IStorageProcessorTransaction superTransaction = super.createTransaction(parameters);
- return new StorageProcessorWithDropboxTransaction(parameters, superTransaction);
+ final IPostRegistrationDatasetHandler dropboxHandler =
+ createPostRegistrationDataSetHandler();
+ return new StorageProcessorWithDropboxTransaction(parameters, superTransaction,
+ dropboxHandler);
}
- public final class StorageProcessorWithDropboxTransaction extends
+ public static final class StorageProcessorWithDropboxTransaction extends
AbstractDelegatingStorageProcessorTransaction
{
private static final long serialVersionUID = 1L;
- private final IPostRegistrationDatasetHandler dropboxHandler =
- createPostRegistrationDataSetHandler();
+ private final transient IPostRegistrationDatasetHandler dropboxHandler;
private StorageProcessorWithDropboxTransaction(
StorageProcessorTransactionParameters parameters,
- IStorageProcessorTransaction transaction)
+ IStorageProcessorTransaction transaction,
+ IPostRegistrationDatasetHandler dropboxHandler)
{
super(parameters, transaction);
+ this.dropboxHandler = dropboxHandler;
}
@Override
@@ -109,7 +113,10 @@ public abstract class DelegatingStorageProcessorWithDropbox extends
@Override
protected UnstoreDataAction executeRollback(Throwable ex)
{
- dropboxHandler.undoLastOperation();
+ if (dropboxHandler != null)
+ {
+ dropboxHandler.undoLastOperation();
+ }
return nestedTransaction.rollback(ex);
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExceptionThrowingStorageProcessor.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExceptionThrowingStorageProcessor.java
index 656b5d4770a..720c4cd8ab5 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExceptionThrowingStorageProcessor.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExceptionThrowingStorageProcessor.java
@@ -48,7 +48,7 @@ public class ExceptionThrowingStorageProcessor extends DefaultStorageProcessor
return new ExceptionThrowingStorageProcessorTransaction(parameters, this);
}
- private class ExceptionThrowingStorageProcessorTransaction extends
+ private static class ExceptionThrowingStorageProcessorTransaction extends
DefaultStorageProcessorTransaction
{
@@ -103,7 +103,7 @@ public class ExceptionThrowingStorageProcessor extends DefaultStorageProcessor
// directory structure will persist. Right now, we consider this is fine as these empty
// directories will not disturb the running application.
FileRenamer.renameAndLog(targetFile, incomingDataSetDirectory);
- return getDefaultUnstoreDataAction(ex);
+ return unstoreDataAction;
}
}
diff --git a/plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/PlasmidStorageProcessor.java b/plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/PlasmidStorageProcessor.java
index e38a5e81ec8..dbbcd489793 100644
--- a/plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/PlasmidStorageProcessor.java
+++ b/plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/PlasmidStorageProcessor.java
@@ -96,64 +96,8 @@ public class PlasmidStorageProcessor extends AbstractDelegatingStorageProcessor
public IStorageProcessorTransaction createTransaction(
StorageProcessorTransactionParameters parameters)
{
- return new AbstractDelegatingStorageProcessorTransaction(parameters,
- super.createTransaction(parameters))
- {
-
- private static final long serialVersionUID = 1L;
-
- @Override
- protected File executeStoreData(ITypeExtractor typeExtractor, IMailClient mailClient)
- {
- nestedTransaction
- .storeData(typeExtractor, mailClient, incomingDataSetDirectory);
- File answer = nestedTransaction.getStoredDataDirectory();
-
- if (typeExtractor.getDataSetType(incomingDataSetDirectory).getCode()
- .equals(DataSetTypeOracle.DataSetTypeInfo.SEQ_FILE.name()))
- {
- File originalDir = new File(answer, ORIGINAL_DIR);
- File[] files = originalDir.listFiles();
- assert files.length == 1;
- File seqFile = files[0];
-
- String baseFileName = FilenameUtils.getBaseName(seqFile.getName());
- String svgFileName = baseFileName + SVG_FILE_EXTENSION;
- String gbFileName = baseFileName + GB_FILE_EXTENSION;
-
- File generatedDir = new File(answer, GENERATED_DIR);
- if (generatedDir.mkdir())
- {
- final File svgFileDest = new File(generatedDir, svgFileName);
- final File gbFileDest = new File(generatedDir, gbFileName);
-
- operationLog.info("Uploading '" + seqFile.getName()
- + "' to PlasMapper.");
- uploadAndCopyGeneratedFile(seqFile, PlasMapperService.GRAPHIC_MAP,
- svgFileDest);
- uploadAndCopyGeneratedFile(seqFile, PlasMapperService.GENEBANK_OUTPUT,
- gbFileDest);
- } else
- {
- throw new EnvironmentFailureException("Couldn't create directory '"
- + generatedDir + "'.");
- }
- }
- return answer;
- }
-
- @Override
- protected UnstoreDataAction executeRollback(Throwable ex)
- {
- return nestedTransaction.rollback(ex);
- }
-
- @Override
- protected void executeCommit()
- {
- nestedTransaction.commit();
- }
- };
+ return new PlasmidStorageProcessorTransaction(parameters,
+ super.createTransaction(parameters), this);
}
// WORKAROUND cannot move the file because it is on a different filesystem
@@ -181,4 +125,71 @@ public class PlasmidStorageProcessor extends AbstractDelegatingStorageProcessor
}
}
+ static class PlasmidStorageProcessorTransaction extends
+ AbstractDelegatingStorageProcessorTransaction
+ {
+
+ private static final long serialVersionUID = 1L;
+
+ private final transient PlasmidStorageProcessor processor;
+
+ public PlasmidStorageProcessorTransaction(StorageProcessorTransactionParameters parameters,
+ IStorageProcessorTransaction superTransaction, PlasmidStorageProcessor processor)
+ {
+ super(parameters, superTransaction);
+ this.processor = processor;
+ }
+
+ @Override
+ protected File executeStoreData(ITypeExtractor typeExtractor, IMailClient mailClient)
+ {
+ nestedTransaction.storeData(typeExtractor, mailClient, incomingDataSetDirectory);
+ File answer = nestedTransaction.getStoredDataDirectory();
+
+ if (typeExtractor.getDataSetType(incomingDataSetDirectory).getCode()
+ .equals(DataSetTypeOracle.DataSetTypeInfo.SEQ_FILE.name()))
+ {
+ File originalDir = new File(answer, ORIGINAL_DIR);
+ File[] files = originalDir.listFiles();
+ assert files.length == 1;
+ File seqFile = files[0];
+
+ String baseFileName = FilenameUtils.getBaseName(seqFile.getName());
+ String svgFileName = baseFileName + SVG_FILE_EXTENSION;
+ String gbFileName = baseFileName + GB_FILE_EXTENSION;
+
+ File generatedDir = new File(answer, GENERATED_DIR);
+ if (generatedDir.mkdir())
+ {
+ final File svgFileDest = new File(generatedDir, svgFileName);
+ final File gbFileDest = new File(generatedDir, gbFileName);
+
+ operationLog.info("Uploading '" + seqFile.getName() + "' to PlasMapper.");
+ processor.uploadAndCopyGeneratedFile(seqFile, PlasMapperService.GRAPHIC_MAP,
+ svgFileDest);
+ processor.uploadAndCopyGeneratedFile(seqFile,
+ PlasMapperService.GENEBANK_OUTPUT,
+ gbFileDest);
+ } else
+ {
+ throw new EnvironmentFailureException("Couldn't create directory '"
+ + generatedDir + "'.");
+ }
+ }
+ return answer;
+ }
+
+ @Override
+ protected UnstoreDataAction executeRollback(Throwable ex)
+ {
+ return nestedTransaction.rollback(ex);
+ }
+
+ @Override
+ protected void executeCommit()
+ {
+ nestedTransaction.commit();
+ }
+ }
+
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/QuantMLStorageProcessor.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/QuantMLStorageProcessor.java
index aed3f7ec513..eb0571fd39d 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/QuantMLStorageProcessor.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/QuantMLStorageProcessor.java
@@ -57,51 +57,33 @@ public class QuantMLStorageProcessor extends AbstractDelegatingStorageProcessor
public IStorageProcessorTransaction createTransaction(
StorageProcessorTransactionParameters parameters)
{
- return new AbstractDelegatingStorageProcessorTransaction(parameters,
- super.createTransaction(parameters))
- {
-
- private static final long serialVersionUID = 1L;
+ return new QuantMLStorageProcessorTransaction(parameters,
+ super.createTransaction(parameters), this);
- @Override
- protected File executeStoreData(ITypeExtractor typeExtractor, IMailClient mailClient)
- {
- ensureUploadableFileExists(incomingDataSetDirectory);
- acquireWriteAccess(incomingDataSetDirectory);
- nestedTransaction
- .storeData(typeExtractor, mailClient, incomingDataSetDirectory);
- File originalData = nestedTransaction.tryGetProprietaryData();
- File quantML = findFile(originalData, mlFileExtension);
- databaseUploader.upload(quantML, dataSetInformation);
- return nestedTransaction.getStoredDataDirectory();
- }
+ }
- @Override
- protected void executeCommit()
- {
- nestedTransaction.commit();
- databaseUploader.commit();
- }
- @Override
- protected UnstoreDataAction executeRollback(Throwable ex)
- {
- try
- {
- nestedTransaction.rollback(ex);
- } finally
- {
- if (databaseUploader != null)
- {
- databaseUploader.rollback();
- }
- }
- return UnstoreDataAction.LEAVE_UNTOUCHED;
- }
- };
+ // returns the only file with the specified extension or throws an exceptions if none or more
+ // than one is found.
+ public static File findFile(File incomingItem, String fileExtension)
+ {
+ if (incomingItem.isFile()
+ && FilenameUtils.isExtension(incomingItem.getName(), fileExtension))
+ {
+ return incomingItem;
+ }
+ List<File> files = FileOperations.getInstance().listFiles(incomingItem, new String[]
+ { fileExtension }, false);
+ if (files.size() != 1)
+ {
+ throw UserFailureException.fromTemplate(
+ "There should be exactly one file with '%s' extension"
+ + " in '%s' directory, but %d have been found.", fileExtension,
+ incomingItem.getPath(), files.size());
+ }
+ return files.get(0);
}
-
private void acquireWriteAccess(final File incomingDataSetDirectory)
{
String incomingName = incomingDataSetDirectory.getName();
@@ -118,24 +100,55 @@ public class QuantMLStorageProcessor extends AbstractDelegatingStorageProcessor
findFile(incomingDataSetDirectory, mlFileExtension);
}
- // returns the only file with the specified extension or throws an exceptions if none or more
- // than one is found.
- public static File findFile(File incomingItem, String fileExtension)
+ private static class QuantMLStorageProcessorTransaction extends
+ AbstractDelegatingStorageProcessorTransaction
{
- if (incomingItem.isFile()
- && FilenameUtils.isExtension(incomingItem.getName(), fileExtension))
+
+ private static final long serialVersionUID = 1L;
+
+ private transient QuantMLStorageProcessor processor;
+
+ public QuantMLStorageProcessorTransaction(StorageProcessorTransactionParameters parameters,
+ IStorageProcessorTransaction nestedTransaction,
+ QuantMLStorageProcessor quantMLStorageProcessor)
{
- return incomingItem;
+ super(parameters, nestedTransaction);
+ this.processor = quantMLStorageProcessor;
}
- List<File> files = FileOperations.getInstance().listFiles(incomingItem, new String[]
- { fileExtension }, false);
- if (files.size() != 1)
+
+ @Override
+ protected File executeStoreData(ITypeExtractor typeExtractor, IMailClient mailClient)
{
- throw UserFailureException.fromTemplate(
- "There should be exactly one file with '%s' extension"
- + " in '%s' directory, but %d have been found.", fileExtension,
- incomingItem.getPath(), files.size());
+ processor.ensureUploadableFileExists(incomingDataSetDirectory);
+ processor.acquireWriteAccess(incomingDataSetDirectory);
+ nestedTransaction.storeData(typeExtractor, mailClient, incomingDataSetDirectory);
+ File originalData = nestedTransaction.tryGetProprietaryData();
+ File quantML = findFile(originalData, processor.mlFileExtension);
+ processor.databaseUploader.upload(quantML, dataSetInformation);
+ return nestedTransaction.getStoredDataDirectory();
+ }
+
+ @Override
+ protected void executeCommit()
+ {
+ nestedTransaction.commit();
+ processor.databaseUploader.commit();
+ }
+
+ @Override
+ protected UnstoreDataAction executeRollback(Throwable ex)
+ {
+ try
+ {
+ nestedTransaction.rollback(ex);
+ } finally
+ {
+ if (processor != null && processor.databaseUploader != null)
+ {
+ processor.databaseUploader.rollback();
+ }
+ }
+ return UnstoreDataAction.LEAVE_UNTOUCHED;
}
- return files.get(0);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/LinkingStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/LinkingStorageProcessor.java
index cec38e24d4a..433db90086e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/LinkingStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/LinkingStorageProcessor.java
@@ -70,58 +70,67 @@ public class LinkingStorageProcessor extends AbstractDelegatingStorageProcessor
StorageProcessorTransactionParameters parameters)
{
final IStorageProcessorTransaction superTransaction = super.createTransaction(parameters);
- return new AbstractDelegatingStorageProcessorTransaction(parameters, superTransaction)
- {
-
- private static final long serialVersionUID = 1L;
-
- private File symbolicLink;
-
- private File markerFile;
-
- @Override
- protected File executeStoreData(ITypeExtractor typeExtractor, IMailClient mailClient)
- {
-
- nestedTransaction
- .storeData(typeExtractor, mailClient, incomingDataSetDirectory);
- File source = nestedTransaction.tryGetProprietaryData();
- boolean success = SoftLinkMaker.createSymbolicLink(source, targetDir);
- if (success)
- {
- symbolicLink = new File(targetDir, source.getName());
- markerFile =
- new File(targetDir, Constants.IS_FINISHED_PREFIX + source.getName());
- FileUtilities.writeToFile(markerFile, dataSetInformation.getDataSetCode());
- } else
- {
- throw EnvironmentFailureException.fromTemplate(
- "Can not create symbolic link to '%s' in '%s'.", source.getPath(),
- targetDir.getPath());
- }
- return nestedTransaction.getStoredDataDirectory();
- }
-
- @Override
- protected UnstoreDataAction executeRollback(Throwable ex)
- {
- if (symbolicLink != null)
- {
- FileUtilities.deleteRecursively(symbolicLink);
- }
- if (markerFile != null)
- {
- FileUtilities.delete(markerFile);
- }
- return nestedTransaction.rollback(ex);
- }
-
- @Override
- protected void executeCommit()
- {
- nestedTransaction.commit();
- }
- };
+ return new LinkingStorageProcessorTransaction(parameters, superTransaction, targetDir);
}
+ private static class LinkingStorageProcessorTransaction extends
+ AbstractDelegatingStorageProcessorTransaction
+ {
+
+ private static final long serialVersionUID = 1L;
+
+ private final File targetDir;
+
+ private transient File symbolicLink;
+
+ private transient File markerFile;
+
+ public LinkingStorageProcessorTransaction(StorageProcessorTransactionParameters parameters,
+ IStorageProcessorTransaction superTransaction, File targetDir)
+ {
+ super(parameters, superTransaction);
+ this.targetDir = targetDir;
+ }
+
+ @Override
+ protected File executeStoreData(ITypeExtractor typeExtractor, IMailClient mailClient)
+ {
+
+ nestedTransaction.storeData(typeExtractor, mailClient, incomingDataSetDirectory);
+ File source = nestedTransaction.tryGetProprietaryData();
+ boolean success = SoftLinkMaker.createSymbolicLink(source, targetDir);
+ if (success)
+ {
+ symbolicLink = new File(targetDir, source.getName());
+ markerFile = new File(targetDir, Constants.IS_FINISHED_PREFIX + source.getName());
+ FileUtilities.writeToFile(markerFile, dataSetInformation.getDataSetCode());
+ } else
+ {
+ throw EnvironmentFailureException.fromTemplate(
+ "Can not create symbolic link to '%s' in '%s'.", source.getPath(),
+ targetDir.getPath());
+ }
+ return nestedTransaction.getStoredDataDirectory();
+ }
+
+ @Override
+ protected UnstoreDataAction executeRollback(Throwable ex)
+ {
+ if (symbolicLink != null)
+ {
+ FileUtilities.deleteRecursively(symbolicLink);
+ }
+ if (markerFile != null)
+ {
+ FileUtilities.delete(markerFile);
+ }
+ return nestedTransaction.rollback(ex);
+ }
+
+ @Override
+ protected void executeCommit()
+ {
+ nestedTransaction.commit();
+ }
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java
index eeabd48d7ef..0ae11404a55 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java
@@ -85,22 +85,24 @@ public class FeatureVectorStorageProcessor extends AbstractDelegatingStorageProc
StorageProcessorTransactionParameters parameters)
{
final IStorageProcessorTransaction superTransaction = super.createTransaction(parameters);
- return new FeatureVectorStorageProcessorTransaction(parameters,
- superTransaction);
+ return new FeatureVectorStorageProcessorTransaction(parameters, superTransaction, this);
}
- private final class FeatureVectorStorageProcessorTransaction extends
+ private static final class FeatureVectorStorageProcessorTransaction extends
AbstractDelegatingStorageProcessorTransaction
{
private static final long serialVersionUID = 1L;
- private IImagingQueryDAO dataAccessObject = null;
+ private transient IImagingQueryDAO dataAccessObject = null;
+
+ private final transient FeatureVectorStorageProcessor processor;
private FeatureVectorStorageProcessorTransaction(
StorageProcessorTransactionParameters parameters,
- IStorageProcessorTransaction transaction)
+ IStorageProcessorTransaction transaction, FeatureVectorStorageProcessor processor)
{
super(parameters, transaction);
+ this.processor = processor;
}
@Override
@@ -108,12 +110,12 @@ public class FeatureVectorStorageProcessor extends AbstractDelegatingStorageProc
{
nestedTransaction.storeData(typeExtractor, mailClient, incomingDataSetDirectory);
- dataAccessObject = createDAO();
+ dataAccessObject = processor.createDAO();
File parent = new File(nestedTransaction.getStoredDataDirectory(), ORIGINAL_DIR);
File dataSet = new File(parent, incomingDataSetDirectory.getName());
try
{
- loadDataSetIntoDatabase(dataAccessObject, dataSet, dataSetInformation);
+ processor.loadDataSetIntoDatabase(dataAccessObject, dataSet, dataSetInformation);
} catch (IOException ex)
{
throw new IOExceptionUnchecked(ex);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessor.java
index 1f2c1a55cf0..2b0bcc844de 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessor.java
@@ -172,62 +172,7 @@ public class FeatureStorageProcessor extends AbstractDelegatingStorageProcessor
StorageProcessorTransactionParameters parameters)
{
final IStorageProcessorTransaction superTransaction = super.createTransaction(parameters);
- return new AbstractDelegatingStorageProcessorTransaction(parameters, superTransaction)
- {
- private static final long serialVersionUID = 1L;
-
- private IImagingQueryDAO dataAccessObject = null;
-
- @Override
- protected File executeStoreData(ITypeExtractor typeExtractor, IMailClient mailClient)
- {
- nestedTransaction
- .storeData(typeExtractor, mailClient, incomingDataSetDirectory);
-
- dataAccessObject = createDAO();
- File storedDataSet = nestedTransaction.getStoredDataDirectory();
- File originalDir = DefaultStorageProcessor.getOriginalDirectory(storedDataSet);
- File targetFile =
- new File(originalDir, incomingDataSetDirectory.getName());
- transform(dataAccessObject, targetFile, storedDataSet, dataSetInformation);
- return nestedTransaction.getStoredDataDirectory();
- }
-
- @Override
- protected void executeCommit()
- {
- nestedTransaction.commit();
-
- if (null == dataAccessObject)
- {
- return;
- }
- dataAccessObject.commit();
- closeDataAccessObject();
- }
-
- @Override
- protected UnstoreDataAction executeRollback(Throwable ex)
- {
- // Delete the data from the database
- if (null != dataAccessObject)
- {
- dataAccessObject.rollback();
- closeDataAccessObject();
- }
-
- return nestedTransaction.rollback(ex);
- }
-
- /**
- * Close the DAO and set it to null to make clear that it is not initialized.
- */
- private void closeDataAccessObject()
- {
- dataAccessObject.close();
- dataAccessObject = null;
- }
- };
+ return new FeatureStorageProcessorTransaction(parameters, superTransaction, this);
}
protected void transform(IImagingQueryDAO dataAccessObject, File originalDataSet,
@@ -387,5 +332,73 @@ public class FeatureStorageProcessor extends AbstractDelegatingStorageProcessor
return new UserFailureException("Error in line " + lineIndex + 1 + ": " + reason + ": "
+ line);
}
+
+ private static class FeatureStorageProcessorTransaction extends
+ AbstractDelegatingStorageProcessorTransaction
+ {
+ private static final long serialVersionUID = 1L;
+
+ private transient final FeatureStorageProcessor processor;
+
+ private transient IImagingQueryDAO dataAccessObject = null;
+
+ FeatureStorageProcessorTransaction(StorageProcessorTransactionParameters parameters,
+ IStorageProcessorTransaction nestedTransaction, FeatureStorageProcessor processor)
+ {
+ super(parameters, nestedTransaction);
+ this.processor = processor;
+ }
+
+ @Override
+ protected File executeStoreData(ITypeExtractor typeExtractor, IMailClient mailClient)
+ {
+ nestedTransaction
+ .storeData(typeExtractor, mailClient, incomingDataSetDirectory);
+
+ dataAccessObject = processor.createDAO();
+ File storedDataSet = nestedTransaction.getStoredDataDirectory();
+ File originalDir = DefaultStorageProcessor.getOriginalDirectory(storedDataSet);
+ File targetFile =
+ new File(originalDir, incomingDataSetDirectory.getName());
+ processor.transform(dataAccessObject, targetFile, storedDataSet, dataSetInformation);
+ return nestedTransaction.getStoredDataDirectory();
+ }
+
+ @Override
+ protected void executeCommit()
+ {
+ nestedTransaction.commit();
+
+ if (null == dataAccessObject)
+ {
+ return;
+ }
+ dataAccessObject.commit();
+ closeDataAccessObject();
+ }
+
+ @Override
+ protected UnstoreDataAction executeRollback(Throwable ex)
+ {
+ // Delete the data from the database
+ if (null != dataAccessObject)
+ {
+ dataAccessObject.rollback();
+ closeDataAccessObject();
+ }
+
+ return nestedTransaction.rollback(ex);
+ }
+
+ /**
+ * Close the DAO and set it to null to make clear that it is not initialized.
+ */
+ private void closeDataAccessObject()
+ {
+ dataAccessObject.close();
+ dataAccessObject = null;
+ }
+ }
+
}
--
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