diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
index 2351fd7d447937f36f5c22cdb59faaaf7a2d146c..9ad70f4b99a20d21594d4e2a3da0f2e1e574b7ef 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
@@ -61,6 +61,16 @@ public class DataSetRegistrationAlgorithm
public void rollback(DataSetRegistrationAlgorithm algorithm, Throwable ex);
}
+ /**
+ * Interface for code that is run to register a new data set.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+ public static interface IDataSetInApplicationServerRegistrator
+ {
+ public void registerDataSetInApplicationServer(NewExternalData data) throws Throwable;
+ }
+
/**
* Object for holding the state necessary for registring a data set.
*
@@ -150,75 +160,10 @@ public class DataSetRegistrationAlgorithm
this.emailSubjectTemplate = EMAIL_SUBJECT_TEMPLATE;
}
- public String getErrorMessageTemplate()
- {
- return defaultErrorMessageTemplate;
- }
-
public File getIncomingDataSetFile()
{
return incomingDataSetFile;
}
-
- public IEncapsulatedOpenBISService getOpenBisService()
- {
- return openBisService;
- }
-
- public IDelegatedActionWithResult<Boolean> getCleanAftrewardsAction()
- {
- return cleanAfterwardsAction;
- }
-
- public IPreRegistrationAction getPreRegistrationAction()
- {
- return preRegistrationAction;
- }
-
- public IPostRegistrationAction getPostRegistrationAction()
- {
- return postRegistrationAction;
- }
-
- public DataSetInformation getDataSetInformation()
- {
- return dataSetInformation;
- }
-
- public IDataStoreStrategy getDataStoreStrategy()
- {
- return dataStoreStrategy;
- }
-
- public ITypeExtractor getTypeExtractor()
- {
- return typeExtractor;
- }
-
- public IStorageProcessor getStorageProcessor()
- {
- return storageProcessor;
- }
-
- public DataSetType getDataSetType()
- {
- return dataSetType;
- }
-
- public File getStoreRoot()
- {
- return storeRoot;
- }
-
- public IMailClient getMailClient()
- {
- return mailClient;
- }
-
- public Lock getRegistrationLock()
- {
- return registrationLock;
- }
}
static private final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY,
@@ -239,6 +184,8 @@ public class DataSetRegistrationAlgorithm
// Immutable State
private final DataSetRegistrationAlgorithmState state;
+ private final IDataSetInApplicationServerRegistrator applicationServerRegistrator;
+
private final IRollbackDelegate rollbackDelegate;
private final File incomingDataSetFile;
@@ -250,14 +197,21 @@ public class DataSetRegistrationAlgorithm
private String errorMessageTemplate;
- public DataSetRegistrationAlgorithm(DataSetRegistrationAlgorithmState state,
+ public DataSetRegistrationAlgorithm(final DataSetRegistrationAlgorithmState state,
IRollbackDelegate rollbackDelegate)
+ {
+ this(state, rollbackDelegate, new DefaultApplicationServerRegistrator(state));
+ }
+
+ public DataSetRegistrationAlgorithm(DataSetRegistrationAlgorithmState state,
+ IRollbackDelegate rollbackDelegate, IDataSetInApplicationServerRegistrator applicationServerRegistrator)
{
this.state = state;
this.rollbackDelegate = rollbackDelegate;
incomingDataSetFile = state.incomingDataSetFile;
dataSetInformation = state.dataSetInformation;
- errorMessageTemplate = state.getErrorMessageTemplate();
+ errorMessageTemplate = state.defaultErrorMessageTemplate;
+ this.applicationServerRegistrator = applicationServerRegistrator;
}
/**
@@ -307,11 +261,9 @@ public class DataSetRegistrationAlgorithm
final String errorMessage =
"Error when trying to register data set '" + incomingDataSetFile.getName()
+ "'.";
- state.getMailClient()
- .sendMessage(
- String.format(errorMessage, dataSetInformation
- .getExperimentIdentifier().getExperimentCode()),
- ex.getMessage(), null, null, userEmailOrNull);
+ state.mailClient.sendMessage(String.format(errorMessage, dataSetInformation
+ .getExperimentIdentifier().getExperimentCode()), ex.getMessage(), null,
+ null, userEmailOrNull);
if (state.shouldDeleteUnidentified)
{
deleted = removeAndLog(errorMessage + " [" + ex.getMessage() + "]");
@@ -329,6 +281,21 @@ public class DataSetRegistrationAlgorithm
}
}
+ /**
+ * This method is only ever called for unidentified data sets.
+ */
+ public final void dealWithUnidentifiedDataSet()
+ {
+ final boolean ok =
+ state.shouldDeleteUnidentified ? (removeAndLog(incomingDataSetFile.getName()
+ + " could not be identified.")) : FileRenamer.renameAndLog(
+ incomingDataSetFile, getBaseDirectoryHolder().getTargetFile());
+ if (ok)
+ {
+ clean();
+ }
+ }
+
public final File createBaseDirectory(final IDataStoreStrategy strategy, final File baseDir,
final DataSetInformation dataSetInfo)
{
@@ -366,7 +333,7 @@ public class DataSetRegistrationAlgorithm
public File getStoreRoot()
{
- return state.getStoreRoot();
+ return state.storeRoot;
}
/**
@@ -385,14 +352,33 @@ public class DataSetRegistrationAlgorithm
return state.cleanAfterwardsAction.execute();
}
+ private static class DefaultApplicationServerRegistrator implements IDataSetInApplicationServerRegistrator
+ {
+ private final IEncapsulatedOpenBISService openBisService;
+
+ private final DataSetInformation dataSetInformation;
+
+ DefaultApplicationServerRegistrator(DataSetRegistrationAlgorithmState state)
+ {
+ openBisService = state.openBisService;
+ dataSetInformation = state.dataSetInformation;
+ }
+
+ public void registerDataSetInApplicationServer(NewExternalData data) throws Throwable
+ {
+ openBisService.registerDataSet(dataSetInformation, data);
+ }
+
+ }
+
/**
- * Contact openBis and register the data set there. Subclasses may override.
+ * Use the applicationServerRegistrator to register the data set with the app server.
*
* @throws Throwable
*/
- protected void registerDataSetInApplicationServer(NewExternalData data) throws Throwable
+ private void registerDataSetInApplicationServer(NewExternalData data) throws Throwable
{
- state.getOpenBisService().registerDataSet(dataSetInformation, data);
+ applicationServerRegistrator.registerDataSetInApplicationServer(data);
}
private void rollback(Throwable ex)
@@ -421,7 +407,7 @@ public class DataSetRegistrationAlgorithm
incomingDataSetFile.getAbsolutePath());
File dataFile =
getStorageProcessor().storeData(dataSetInformation, getTypeExtractor(),
- state.getMailClient(), incomingDataSetFile,
+ state.mailClient, incomingDataSetFile,
baseDirectoryHolder.getBaseDirectory());
if (getOperationLog().isInfoEnabled())
{
@@ -438,7 +424,7 @@ public class DataSetRegistrationAlgorithm
final BooleanOrUnknown isCompleteFlag = dataSetInformation.getIsCompleteFlag();
// Ensure that we either register the data set and initiate the processing copy or
// do none of both.
- state.getRegistrationLock().lock();
+ state.registrationLock.lock();
try
{
errorMessageTemplate = DATA_SET_REGISTRATION_FAILURE_TEMPLATE;
@@ -447,7 +433,7 @@ public class DataSetRegistrationAlgorithm
clean();
} finally
{
- state.getRegistrationLock().unlock();
+ state.registrationLock.unlock();
}
getStorageProcessor().commit(incomingDataSetFile,
baseDirectoryHolder.getBaseDirectory());
@@ -491,10 +477,9 @@ public class DataSetRegistrationAlgorithm
}
if (StringUtils.isBlank(email) == false)
{
- state.getMailClient().sendMessage(
- String.format(state.emailSubjectTemplate, dataSetInformation
- .getExperimentIdentifier().getExperimentCode()), msg, null, null,
- email);
+ state.mailClient.sendMessage(String.format(state.emailSubjectTemplate,
+ dataSetInformation.getExperimentIdentifier().getExperimentCode()), msg,
+ null, null, email);
}
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmRunner.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmRunner.java
index 166572320f251c385da84fe9e3409254a02c0911..79c175c3ed05270d9898ad3fc1e912cac1c455fe 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmRunner.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmRunner.java
@@ -22,6 +22,8 @@ import java.util.List;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
/**
+ * Runs DataSetRegistrationAlgorithm objects.
+ *
* @author Chandrasekhar Ramakrishnan
*/
public class DataSetRegistrationAlgorithmRunner
@@ -40,32 +42,45 @@ public class DataSetRegistrationAlgorithmRunner
}
- private final TransferredDataSetHandlerDataSetRegistrationAlgorithm registrationHelper;
+ private final DataSetRegistrationAlgorithm registrationAlgorithm;
private final IDataSetRegistrationAlgorithmRunnerDelegate delegate;
- public DataSetRegistrationAlgorithmRunner(TransferredDataSetHandlerDataSetRegistrationAlgorithm registrationAlgorithm)
+ public DataSetRegistrationAlgorithmRunner(
+ TransferredDataSetHandlerDataSetRegistrationAlgorithm registrationHelper)
+ {
+ this(registrationHelper, new NoOpDelegate());
+ }
+
+ public DataSetRegistrationAlgorithmRunner(
+ TransferredDataSetHandlerDataSetRegistrationAlgorithm registrationHelper,
+ IDataSetRegistrationAlgorithmRunnerDelegate delegate)
+ {
+ this(registrationHelper.getRegistrationAlgorithm(), delegate);
+ }
+
+ public DataSetRegistrationAlgorithmRunner(DataSetRegistrationAlgorithm registrationAlgorithm)
{
this(registrationAlgorithm, new NoOpDelegate());
}
- public DataSetRegistrationAlgorithmRunner(TransferredDataSetHandlerDataSetRegistrationAlgorithm registrationAlgorithm,
+ public DataSetRegistrationAlgorithmRunner(DataSetRegistrationAlgorithm registrationAlgorithm,
IDataSetRegistrationAlgorithmRunnerDelegate delegate)
{
- this.registrationHelper = registrationAlgorithm;
+ this.registrationAlgorithm = registrationAlgorithm;
this.delegate = delegate;
}
public List<DataSetInformation> runAlgorithm()
{
- registrationHelper.prepare();
- if (registrationHelper.hasDataSetBeenIdentified())
+ registrationAlgorithm.prepare();
+ if (registrationAlgorithm.hasDataSetBeenIdentified())
{
- return registrationHelper.registerDataSet();
+ return registrationAlgorithm.registerDataSet();
} else
{
delegate.didNotIdentifyDataSet();
- registrationHelper.dealWithUnidentifiedDataSet();
+ registrationAlgorithm.dealWithUnidentifiedDataSet();
return Collections.emptyList();
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IExtensibleDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IExtensibleDataSetHandler.java
index 09e3e449b5fa9751be378317c6f6cd5c91e93926..df33f706bd6fb1c2d438e138d847cf0422bd8d63 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IExtensibleDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IExtensibleDataSetHandler.java
@@ -20,7 +20,6 @@ import java.io.File;
import java.util.List;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
/**
* An interface for data set handlers that give other code a chance to implement the registration of
@@ -30,16 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
*/
public interface IExtensibleDataSetHandler extends IDataSetHandler
{
- /**
- * Interface for code that is run to register a new data set.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- public static interface IDataSetRegistrator
- {
- public void registerDataSetInApplicationServer(NewExternalData data) throws Throwable;
- }
-
public List<DataSetInformation> handleDataSet(final File dataSet,
- DataSetInformation dataSetInformation, IDataSetRegistrator registrator);
+ DataSetInformation dataSetInformation,
+ DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator registrator);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
index 7c6e2a6d4fad06eed2394e9d67dd91f1f7ad493c..6ecf4feea80a5d25d0e0e13ed76dbe0f69f8c322 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
@@ -36,6 +36,7 @@ import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
+import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator;
import ch.systemsx.cisd.etlserver.IStorageProcessor.UnstoreDataAction;
import ch.systemsx.cisd.etlserver.utils.PostRegistrationExecutor;
import ch.systemsx.cisd.etlserver.utils.PreRegistrationExecutor;
@@ -43,7 +44,6 @@ import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
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.DatabaseInstance;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
/**
* The class that handles the incoming data set.
@@ -227,7 +227,8 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
}
public List<DataSetInformation> handleDataSet(final File dataSet,
- DataSetInformation dataSetInformation, IDataSetRegistrator registrator)
+ DataSetInformation dataSetInformation,
+ DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator registrator)
{
dataSetInformation.setInstanceCode(getHomeDatabaseInstance().getCode());
dataSetInformation.setInstanceUUID(getHomeDatabaseInstance().getUuid());
@@ -300,7 +301,8 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
}
private TransferredDataSetHandlerDataSetRegistrationAlgorithm createRegistrationHelper(
- File dataSet, DataSetInformation dataSetInformation, IDataSetRegistrator registrator)
+ File dataSet, DataSetInformation dataSetInformation,
+ DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator registrator)
{
if (useIsFinishedMarkerFile)
{
@@ -315,7 +317,7 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
private TransferredDataSetHandlerDataSetRegistrationAlgorithm createRegistrationHelperWithIsFinishedFile(
final File isFinishedFile, final DataSetInformation dsInfo,
- IDataSetRegistrator registrator)
+ DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator registrator)
{
assert isFinishedFile != null : "Unspecified is-finished file.";
final String name = isFinishedFile.getName();
@@ -353,7 +355,7 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
private TransferredDataSetHandlerDataSetRegistrationAlgorithm createRegistrationHelperWithQuietPeriodFilter(
File incomingDataSetFile, final DataSetInformation dsInfo,
- IDataSetRegistrator registrator)
+ DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator registrator)
{
IDelegatedActionWithResult<Boolean> cleanAftrewardsAction =
new IDelegatedActionWithResult<Boolean>()
@@ -436,12 +438,6 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
private class RegistrationHelper extends TransferredDataSetHandlerDataSetRegistrationAlgorithm
{
- /**
- * @param transferredDataSetHandler
- * @param incomingDataSetFile
- * @param cleanAftrewardsAction
- * @param postRegistrationAction
- */
RegistrationHelper(TransferredDataSetHandler transferredDataSetHandler,
File incomingDataSetFile,
IDelegatedActionWithResult<Boolean> cleanAftrewardsAction,
@@ -452,6 +448,17 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
postRegistrationAction);
}
+ RegistrationHelper(TransferredDataSetHandler transferredDataSetHandler,
+ File incomingDataSetFile,
+ IDelegatedActionWithResult<Boolean> cleanAftrewardsAction,
+ IPreRegistrationAction preRegistrationAction,
+ IPostRegistrationAction postRegistrationAction,
+ IDataSetInApplicationServerRegistrator appServerRegistrator)
+ {
+ super(incomingDataSetFile, cleanAftrewardsAction, preRegistrationAction,
+ postRegistrationAction, appServerRegistrator);
+ }
+
// state accessors
@Override
protected IEncapsulatedOpenBISService getOpenBisService()
@@ -552,12 +559,12 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
Thread.interrupted(); // Ensure the thread's interrupted state is cleared.
getOperationLog().warn(
String.format("Requested to stop registration of data set '%s'",
- algorithm.getDataSetInformation()));
+ registrationAlgorithm.getDataSetInformation()));
} else
{
getNotificationLog().error(
- String.format(algorithm.getErrorMessageTemplate(),
- algorithm.getDataSetInformation()), throwable);
+ String.format(registrationAlgorithm.getErrorMessageTemplate(),
+ registrationAlgorithm.getDataSetInformation()), throwable);
}
// Errors which are not AssertionErrors leave the system in a state that we don't
// know and can't trust. Thus we will not perform any operations any more in this
@@ -566,25 +573,26 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
{
throw (Error) throwable;
}
- UnstoreDataAction action = algorithm.rollbackStorageProcessor(throwable);
+ UnstoreDataAction action = registrationAlgorithm.rollbackStorageProcessor(throwable);
if (stopped == false)
{
if (action == UnstoreDataAction.MOVE_TO_ERROR)
{
final File baseDirectory =
- algorithm.createBaseDirectory(
+ registrationAlgorithm.createBaseDirectory(
TransferredDataSetHandler.ERROR_DATA_STRATEGY,
- algorithm.getStoreRoot(), algorithm.getDataSetInformation());
- algorithm.setBaseDirectoryHolder(new BaseDirectoryHolder(
+ registrationAlgorithm.getStoreRoot(),
+ registrationAlgorithm.getDataSetInformation());
+ registrationAlgorithm.setBaseDirectoryHolder(new BaseDirectoryHolder(
TransferredDataSetHandler.ERROR_DATA_STRATEGY, baseDirectory,
incomingDataSetFile));
boolean moveInCaseOfErrorOk =
- FileRenamer.renameAndLog(incomingDataSetFile, algorithm
+ FileRenamer.renameAndLog(incomingDataSetFile, registrationAlgorithm
.getBaseDirectoryHolder().getTargetFile());
writeThrowable(throwable);
if (moveInCaseOfErrorOk)
{
- algorithm.clean();
+ registrationAlgorithm.clean();
}
} else if (action == UnstoreDataAction.DELETE)
{
@@ -598,8 +606,6 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
private class OverridingRegistrationHelper extends RegistrationHelper
{
- private final IDataSetRegistrator registrator;
-
/**
* @param transferredDataSetHandler
* @param incomingDataSetFile
@@ -610,11 +616,11 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
File incomingDataSetFile,
IDelegatedActionWithResult<Boolean> cleanAftrewardsAction,
IPreRegistrationAction preRegistrationAction,
- IPostRegistrationAction postRegistrationAction, IDataSetRegistrator registrator)
+ IPostRegistrationAction postRegistrationAction,
+ DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator registrator)
{
super(transferredDataSetHandler, incomingDataSetFile, cleanAftrewardsAction,
- preRegistrationAction, postRegistrationAction);
- this.registrator = registrator;
+ preRegistrationAction, postRegistrationAction, registrator);
}
@Override
@@ -628,11 +634,5 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
{
return false;
}
-
- @Override
- protected void registerDataSetInApplicationServer(NewExternalData data) throws Throwable
- {
- registrator.registerDataSetInApplicationServer(data);
- }
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerDataSetRegistrationAlgorithm.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerDataSetRegistrationAlgorithm.java
index af804280d97ef0f32c22084cf5860065faab6c0c..b939c0a01057266e094b430a9bd46a5ba19bea1b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerDataSetRegistrationAlgorithm.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerDataSetRegistrationAlgorithm.java
@@ -34,11 +34,11 @@ import ch.systemsx.cisd.common.filesystem.IFileOperations;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm.DataSetRegistrationAlgorithmState;
+import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator;
import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
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.DatabaseInstance;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
public abstract class TransferredDataSetHandlerDataSetRegistrationAlgorithm implements
DataSetRegistrationAlgorithm.IRollbackDelegate
@@ -61,7 +61,7 @@ public abstract class TransferredDataSetHandlerDataSetRegistrationAlgorithm impl
protected final File incomingDataSetFile;
- protected final DataSetRegistrationAlgorithm algorithm;
+ protected final DataSetRegistrationAlgorithm registrationAlgorithm;
public TransferredDataSetHandlerDataSetRegistrationAlgorithm(File incomingDataSetFile,
IDelegatedActionWithResult<Boolean> cleanAftrewardsAction,
@@ -79,16 +79,42 @@ public abstract class TransferredDataSetHandlerDataSetRegistrationAlgorithm impl
getStorageProcessor(), getFileOperations(), getDataSetValidator(),
getMailClient(), shouldDeleteUnidentified(), getRegistrationLock(),
getDataStoreCode(), shouldNotifySuccessfulRegistration());
- algorithm = new DataSetRegistrationAlgorithm(algorithmState, this);
+ registrationAlgorithm = new DataSetRegistrationAlgorithm(algorithmState, this);
this.incomingDataSetFile = algorithmState.getIncomingDataSetFile();
}
+ public TransferredDataSetHandlerDataSetRegistrationAlgorithm(File incomingDataSetFile,
+ IDelegatedActionWithResult<Boolean> cleanAftrewardsAction,
+ IPreRegistrationAction preRegistrationAction,
+ IPostRegistrationAction postRegistrationAction, IDataSetInApplicationServerRegistrator appServerRegistrator)
+ {
+ DataSetInformation dataSetInformation = extractDataSetInformation(incomingDataSetFile);
+ IDataStoreStrategy dataStoreStrategy =
+ getDataStrategyStore()
+ .getDataStoreStrategy(dataSetInformation, incomingDataSetFile);
+ DataSetRegistrationAlgorithmState algorithmState =
+ new DataSetRegistrationAlgorithmState(incomingDataSetFile, getOpenBisService(),
+ cleanAftrewardsAction, preRegistrationAction, postRegistrationAction,
+ dataSetInformation, dataStoreStrategy, getTypeExtractor(),
+ getStorageProcessor(), getFileOperations(), getDataSetValidator(),
+ getMailClient(), shouldDeleteUnidentified(), getRegistrationLock(),
+ getDataStoreCode(), shouldNotifySuccessfulRegistration());
+ registrationAlgorithm =
+ new DataSetRegistrationAlgorithm(algorithmState, this, appServerRegistrator);
+ this.incomingDataSetFile = algorithmState.getIncomingDataSetFile();
+ }
+
+ public DataSetRegistrationAlgorithm getRegistrationAlgorithm()
+ {
+ return registrationAlgorithm;
+ }
+
/**
* Return the data set information.
*/
public DataSetInformation getDataSetInformation()
{
- return algorithm.getDataSetInformation();
+ return registrationAlgorithm.getDataSetInformation();
}
/**
@@ -96,12 +122,12 @@ public abstract class TransferredDataSetHandlerDataSetRegistrationAlgorithm impl
*/
public final void prepare()
{
- algorithm.prepare();
+ registrationAlgorithm.prepare();
}
public final boolean hasDataSetBeenIdentified()
{
- return algorithm.hasDataSetBeenIdentified();
+ return registrationAlgorithm.hasDataSetBeenIdentified();
}
/**
@@ -109,7 +135,7 @@ public abstract class TransferredDataSetHandlerDataSetRegistrationAlgorithm impl
*/
public final List<DataSetInformation> registerDataSet()
{
- return algorithm.registerDataSet();
+ return registrationAlgorithm.registerDataSet();
}
/**
@@ -117,34 +143,7 @@ public abstract class TransferredDataSetHandlerDataSetRegistrationAlgorithm impl
*/
public final void dealWithUnidentifiedDataSet()
{
- final boolean ok =
- shouldDeleteUnidentified() ? (removeAndLog(incomingDataSetFile.getName()
- + " could not be identified.")) : FileRenamer.renameAndLog(
- incomingDataSetFile, algorithm.getBaseDirectoryHolder().getTargetFile());
- if (ok)
- {
- algorithm.clean();
- }
- }
-
- private boolean removeAndLog(String msg)
- {
- final boolean ok = getFileOperations().removeRecursivelyQueueing(incomingDataSetFile);
- if (getOperationLog().isInfoEnabled())
- {
- getOperationLog().info("Dataset deleted in registration: " + msg);
- }
- return ok;
- }
-
- /**
- * Contact openBis and register the data set there. Subclasses may override.
- *
- * @throws Throwable
- */
- protected void registerDataSetInApplicationServer(NewExternalData data) throws Throwable
- {
- getOpenBisService().registerDataSet(algorithm.getDataSetInformation(), data);
+ registrationAlgorithm.dealWithUnidentifiedDataSet();
}
/**
@@ -193,8 +192,8 @@ public abstract class TransferredDataSetHandlerDataSetRegistrationAlgorithm impl
{
final String fileName = incomingDataSetFile.getName() + ".exception";
final File file =
- new File(algorithm.getBaseDirectoryHolder().getTargetFile().getParentFile(),
- fileName);
+ new File(registrationAlgorithm.getBaseDirectoryHolder().getTargetFile()
+ .getParentFile(), fileName);
FileWriter writer = null;
try
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
index ef1b0c8e2a939d757c7b73b5f4bd8f5b0c2d7992..541ba1dcb106b5c4759ad228bd9992de537bfadb 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
@@ -581,7 +581,7 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
@Override
protected void rollback(Throwable ex)
{
- algorithm.rollbackStorageProcessor(ex);
+ registrationAlgorithm.rollbackStorageProcessor(ex);
if (ex instanceof UserFailureException)
{
throw (UserFailureException) ex;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
index 05efead3dd5ae21fc307336ba77ac73cb35aff30..1bfe32b30fbf40408e036d2ec96e296c01907b3c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
@@ -19,8 +19,8 @@ package ch.systemsx.cisd.etlserver.entityregistration;
import java.io.File;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
import ch.systemsx.cisd.etlserver.IExtensibleDataSetHandler;
-import ch.systemsx.cisd.etlserver.TransferredDataSetHandler;
import ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetControlFileProcessor.ControlFileRegistrationProperties;
import ch.systemsx.cisd.etlserver.entityregistration.SampleDataSetPair.SampleDataSetPairProcessing;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -41,7 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
* @author Chandrasekhar Ramakrishnan
*/
class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor implements
- TransferredDataSetHandler.IDataSetRegistrator
+ DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator
{
private final ControlFileRegistrationProperties properties;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..5c6c29203f11825865628bc585bcc8851563e07b
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmTest.java
@@ -0,0 +1,339 @@
+/*
+ * Copyright 2011 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.etlserver;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.concurrent.locks.Lock;
+
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.jmock.api.Action;
+import org.jmock.api.Invocation;
+import org.jmock.lib.action.CustomAction;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileOperations;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.filesystem.IFileOperations;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
+import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm.DataSetRegistrationAlgorithmState;
+import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator;
+import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm.IRollbackDelegate;
+import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class DataSetRegistrationAlgorithmTest extends AbstractFileSystemTestCase
+{
+
+ private static final String DATA_STORE_CODE = "data-store";
+
+ private static final String DATA_SET_CODE = "data-set-code";
+
+ private static final LocatorType LOCATOR_TYPE = new LocatorType("L1");
+
+ private static final DataSetType DATA_SET_TYPE = new DataSetType("O1");
+
+ private static final FileFormatType FILE_FORMAT_TYPE = new FileFormatType("FF1");
+
+ private static final String EXAMPLE_PROCESSOR_ID = "DATA_ACQUISITION";
+
+ private DataSetRegistrationAlgorithm registrationAlgorithm;
+
+ private Mockery context;
+
+ private IEncapsulatedOpenBISService openBisService;
+
+ private IRollbackDelegate rollbackDelegate;
+
+ private IDataSetInApplicationServerRegistrator appServerRegistrator;
+
+ private IDelegatedActionWithResult<Boolean> cleanAftrewardsAction;
+
+ private IPreRegistrationAction preRegistrationAction;
+
+ private IPostRegistrationAction postRegistrationAction;
+
+ private IDataStoreStrategy dataStoreStrategy;
+
+ private ITypeExtractor typeExtractor;
+
+ private IStorageProcessor storageProcessor;
+
+ private IFileOperations fileOperations;
+
+ private IDataSetValidator dataSetValidator;
+
+ private IMailClient mailClient;
+
+ private Lock registrationLock;
+
+ private RecordingMatcher<Throwable> exceptionMatcher;
+
+ private DataSetInformation dataSetInformation;
+
+ private File incomingDataSetFile;
+
+ private File storedDataSetFile;
+
+ @SuppressWarnings("unchecked")
+ @Override
+ @BeforeMethod
+ public void setUp() throws IOException
+ {
+ super.setUp();
+ context = new Mockery();
+ openBisService = context.mock(IEncapsulatedOpenBISService.class);
+ rollbackDelegate = context.mock(IRollbackDelegate.class);
+ appServerRegistrator = context.mock(IDataSetInApplicationServerRegistrator.class);
+ cleanAftrewardsAction = context.mock(IDelegatedActionWithResult.class);
+ preRegistrationAction = context.mock(IPreRegistrationAction.class);
+ postRegistrationAction = context.mock(IPostRegistrationAction.class);
+
+ dataStoreStrategy = context.mock(IDataStoreStrategy.class);
+ typeExtractor = context.mock(ITypeExtractor.class);
+ storageProcessor = context.mock(IStorageProcessor.class);
+ // fileOperations = context.mock(IFileOperations.class);
+ fileOperations = FileOperations.getInstance();
+ dataSetValidator = context.mock(IDataSetValidator.class);
+ mailClient = context.mock(IMailClient.class);
+ registrationLock = context.mock(Lock.class);
+ exceptionMatcher = new RecordingMatcher<Throwable>();
+
+ dataSetInformation = new DataSetInformation();
+ }
+
+ @Test
+ public void testSuccessfulRegistrationWithoutNotification() throws Throwable
+ {
+ incomingDataSetFile = createDirectory("data_set");
+ storedDataSetFile = createDirectory("stored_data_set");
+
+ FileUtilities.writeToFile(new File(incomingDataSetFile, "read.me"), "hello world");
+ setUpExpectations(incomingDataSetFile);
+
+ createAlgorithmAndState(true, false);
+
+ new DataSetRegistrationAlgorithmRunner(registrationAlgorithm).runAlgorithm();
+
+ for (Throwable ex : exceptionMatcher.getRecordedObjects())
+ {
+ ex.printStackTrace();
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ private void setUpExpectations(final File incomingDataSetFile) throws Throwable
+ {
+ setUpOpenBisExpectations();
+ setUpTypeExtractorExpectations();
+ setUpStorageProcessorExpectations();
+ setUpDataSetValidatorExpectations();
+ setUpDataStoreStrategyExpectations();
+ setUpPreAndPostRegistrationExpectations();
+ setUpLockExpectations();
+ setUpDataSetRegistratorExpectations();
+ setUpCleanAfterwardsExpectations();
+ setUpRollbackExpectations();
+ }
+
+ private void setUpOpenBisExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(openBisService).createDataSetCode();
+ will(returnValue(DATA_SET_CODE));
+ }
+ });
+ }
+
+ private void setUpTypeExtractorExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(typeExtractor).getLocatorType(incomingDataSetFile);
+ will(returnValue(LOCATOR_TYPE));
+
+ one(typeExtractor).getFileFormatType(incomingDataSetFile);
+ will(returnValue(FILE_FORMAT_TYPE));
+
+ one(typeExtractor).getProcessorType(incomingDataSetFile);
+ will(returnValue(EXAMPLE_PROCESSOR_ID));
+
+ one(typeExtractor).isMeasuredData(incomingDataSetFile);
+ will(returnValue(true));
+
+ one(typeExtractor).getDataSetType(incomingDataSetFile);
+ will(returnValue(DATA_SET_TYPE));
+
+ one(typeExtractor).getDataSetType(with(any(File.class)));
+ will(returnValue(DATA_SET_TYPE));
+ }
+ });
+ }
+
+ private void setUpStorageProcessorExpectations()
+ {
+ final Action storeDataAction = new CustomAction("StoreData")
+ {
+
+ public Object invoke(Invocation invocation) throws Throwable
+ {
+ fileOperations.move(incomingDataSetFile, storedDataSetFile);
+ return storedDataSetFile;
+ }
+ };
+
+ context.checking(new Expectations()
+ {
+ {
+ one(storageProcessor).getStoreRootDirectory();
+ will(returnValue(workingDirectory));
+
+ one(storageProcessor).storeData(dataSetInformation, typeExtractor, mailClient,
+ incomingDataSetFile, workingDirectory);
+ will(storeDataAction);
+
+ one(storageProcessor).getStorageFormat();
+ will(returnValue(StorageFormat.PROPRIETARY));
+
+ one(storageProcessor).commit(incomingDataSetFile, workingDirectory);
+ }
+ });
+ }
+
+ private void setUpDataStoreStrategyExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dataStoreStrategy).getBaseDirectory(with(workingDirectory),
+ with(any(DataSetInformation.class)), with(DATA_SET_TYPE));
+ will(returnValue(workingDirectory));
+
+ one(dataStoreStrategy).getKey();
+ will(returnValue(DataStoreStrategyKey.IDENTIFIED));
+ }
+ });
+ }
+
+ private void setUpDataSetValidatorExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE, incomingDataSetFile);
+ }
+ });
+ }
+
+ private void setUpPreAndPostRegistrationExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(preRegistrationAction).execute(DATA_SET_CODE,
+ incomingDataSetFile.getAbsolutePath());
+
+ one(postRegistrationAction).execute(with(DATA_SET_CODE),
+ with(any(String.class)));
+ }
+ });
+ }
+
+ private void setUpLockExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(registrationLock).lock();
+ one(registrationLock).unlock();
+ }
+ });
+ }
+
+ private void setUpDataSetRegistratorExpectations() throws Throwable
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(appServerRegistrator).registerDataSetInApplicationServer(
+ with(any(NewExternalData.class)));
+ }
+ });
+ }
+
+ private void setUpCleanAfterwardsExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(cleanAftrewardsAction).execute();
+ will(returnValue(Boolean.TRUE));
+ }
+ });
+ }
+
+ private void setUpRollbackExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ allowing(rollbackDelegate).rollback(
+ with(any(DataSetRegistrationAlgorithm.class)), with(exceptionMatcher));
+ }
+ });
+ }
+
+ private void createAlgorithmAndState(boolean shouldDeleteUnidentified,
+ boolean shouldNotifySuccessfulRegistration)
+ {
+
+ String dataStoreCode = DATA_STORE_CODE;
+ DataSetRegistrationAlgorithmState state =
+ new DataSetRegistrationAlgorithmState(incomingDataSetFile, openBisService,
+ cleanAftrewardsAction, preRegistrationAction, postRegistrationAction,
+ dataSetInformation, dataStoreStrategy, typeExtractor, storageProcessor,
+ fileOperations, dataSetValidator, mailClient, shouldDeleteUnidentified,
+ registrationLock, dataStoreCode, shouldNotifySuccessfulRegistration);
+ registrationAlgorithm =
+ new DataSetRegistrationAlgorithm(state, rollbackDelegate, appServerRegistrator);
+ }
+
+ private File createDirectory(final String directoryName)
+ {
+ final File file = new File(workingDirectory, directoryName);
+ file.mkdir();
+ return file;
+ }
+}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
index ad4bb0afa9a5f0836627da08f58507a08da3f5c7..4437d9a146e53acb4ae3f69a40c4a7cef6caa751 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
@@ -39,8 +39,8 @@ import ch.systemsx.cisd.common.logging.BufferedAppender;
import ch.systemsx.cisd.common.mail.EMailAddress;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
import ch.systemsx.cisd.etlserver.IExtensibleDataSetHandler;
-import ch.systemsx.cisd.etlserver.IExtensibleDataSetHandler.IDataSetRegistrator;
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.Experiment;
@@ -500,8 +500,8 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
{
{
final RecordingMatcher<File> fileMatcher = new RecordingMatcher<File>();
- final RecordingMatcher<IExtensibleDataSetHandler.IDataSetRegistrator> registratorMatcher =
- new RecordingMatcher<IExtensibleDataSetHandler.IDataSetRegistrator>();
+ final RecordingMatcher<DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator> registratorMatcher =
+ new RecordingMatcher<DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator>();
for (int i = 1; i < 4; ++i)
{
@@ -520,9 +520,9 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
{
public Object invoke(Invocation invocation) throws Throwable
{
- List<IDataSetRegistrator> recordedObjects =
+ List<DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator> recordedObjects =
registratorMatcher.getRecordedObjects();
- IDataSetRegistrator registrator =
+ DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator registrator =
recordedObjects.get(recordedObjects.size() - 1);
fillExternalDataFromInformation(externalData, dataSetInfoMatcher
.getRecordedObjects().get(recordedObjects.size() - 1));