From 88d74ec764ca879b91375d123cf9cf3c695b3792 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 15 Dec 2010 14:29:12 +0000
Subject: [PATCH] LMS-1909 Fill out DataSetInformation better. More robust
error reporting.
SVN: 19154
---
.../AlwaysIdentifiedDataStrategyStore.java | 36 --------
.../DataSetRegistrationAlgorithm.java | 6 +-
.../etlserver/IExtensibleDataSetHandler.java | 2 +-
.../etlserver/TransferredDataSetHandler.java | 9 +-
.../SampleAndDataSetControlFileProcessor.java | 25 +++--
.../SampleAndDataSetFolderProcessor.java | 2 +-
.../SampleAndDataSetRegistrationHandler.java | 2 +-
.../SampleAndDataSetRegistrator.java | 92 ++++++++++++++++---
.../entityregistration/SampleDataSetPair.java | 3 +
9 files changed, 108 insertions(+), 69 deletions(-)
delete mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/AlwaysIdentifiedDataStrategyStore.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AlwaysIdentifiedDataStrategyStore.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AlwaysIdentifiedDataStrategyStore.java
deleted file mode 100644
index 83b2654a3d5..00000000000
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AlwaysIdentifiedDataStrategyStore.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * 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.etlserver;
-
-import java.io.File;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class AlwaysIdentifiedDataStrategyStore implements IDataStrategyStore
-{
- private final IdentifiedDataStrategy identifiedStrategy = new IdentifiedDataStrategy();
-
- public IDataStoreStrategy getDataStoreStrategy(DataSetInformation dataSetInfo,
- File incomingDataSetPath)
- {
- return identifiedStrategy;
- }
-
-}
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 58e80921576..4165183217a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
@@ -205,6 +205,7 @@ public abstract class DataSetRegistrationAlgorithm
* Registers the data set.
*/
private void registerDataSetAndInitiateProcessing(final String procedureTypeCode)
+ throws Throwable
{
final File markerFile = createProcessingMarkerFile();
try
@@ -312,6 +313,7 @@ public abstract class DataSetRegistrationAlgorithm
private final void plainRegisterDataSet(NewExternalData data, final String relativePath,
final StorageFormat storageFormat, final BooleanOrUnknown isCompleteFlag)
+ throws Throwable
{
updateExternalData(data, relativePath, storageFormat, isCompleteFlag);
// Finally: register the data set in the database.
@@ -320,8 +322,10 @@ public abstract class DataSetRegistrationAlgorithm
/**
* Contact openBis and register the data set there. Subclasses may override.
+ *
+ * @throws Throwable
*/
- protected void registerDataSetInApplicationServer(NewExternalData data)
+ protected void registerDataSetInApplicationServer(NewExternalData data) throws Throwable
{
getOpenBisService().registerDataSet(dataSetInformation, data);
}
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 e80c6ce2774..210e8f8ca98 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IExtensibleDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IExtensibleDataSetHandler.java
@@ -29,7 +29,7 @@ public interface IExtensibleDataSetHandler extends IDataSetHandler
{
public static interface IDataSetRegistrator
{
- public void registerDataSetInApplicationServer(NewExternalData data);
+ public void registerDataSetInApplicationServer(NewExternalData data) throws Throwable;
}
public List<DataSetInformation> handleDataSet(final File dataSet,
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 809b0b275d0..9fdb8dcc384 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
@@ -609,16 +609,9 @@ public final class TransferredDataSetHandler implements IPathHandler, ISelfTesta
}
@Override
- protected void registerDataSetInApplicationServer(NewExternalData data)
+ protected void registerDataSetInApplicationServer(NewExternalData data) throws Throwable
{
registrator.registerDataSetInApplicationServer(data);
}
-
- @Override
- protected IDataStrategyStore getDataStrategyStore()
- {
- return new AlwaysIdentifiedDataStrategyStore();
- }
-
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java
index 24403c55957..c73fab86951 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java
@@ -34,6 +34,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.io.DelegatedReader;
import ch.systemsx.cisd.common.mail.EMailAddress;
import ch.systemsx.cisd.common.utilities.UnicodeUtils;
+import ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetRegistrator.RegistrationErrorWrapper;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
@@ -48,8 +49,8 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
{
private final File controlFile;
- private final HashMap<SampleDataSetPair, Exception> errorMap =
- new HashMap<SampleDataSetPair, Exception>();
+ private final HashMap<SampleDataSetPair, RegistrationErrorWrapper> errorMap =
+ new HashMap<SampleDataSetPair, RegistrationErrorWrapper>();
/**
* Utility class for accessing the properties defined in a control file.
@@ -235,12 +236,13 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
List<SampleDataSetPair> loadedSampleDataSetPairs = null;
+ Reader reader = UnicodeUtils.createReader(new FileInputStream(controlFile));
+ DelegatedReader delegatedReader = new DelegatedReader(reader, controlFile.getName());
+
try
{
properties.checkValidity();
- Reader reader = UnicodeUtils.createReader(new FileInputStream(controlFile));
- loadedSampleDataSetPairs =
- controlFileLoader.load(new DelegatedReader(reader, controlFile.getName()));
+ loadedSampleDataSetPairs = controlFileLoader.load(delegatedReader);
} catch (UserFailureException e)
{
// If we don't know which user to send the email to, don't handle this error -- leave it
@@ -252,6 +254,15 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
sendEmailWithErrorMessage(properties, e.getMessage());
return;
+ } finally
+ {
+ try
+ {
+ delegatedReader.close();
+ } catch (IOException ex)
+ {
+ // Ignore this failure
+ }
}
String userId = properties.getUser().getUserId();
@@ -261,7 +272,7 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
sampleDataSet.getDataSetInformation().setUploadingUserId(userId);
SampleAndDataSetRegistrator registrator =
new SampleAndDataSetRegistrator(folder, properties, sampleDataSet);
- Exception resultOrNull = registrator.register();
+ RegistrationErrorWrapper resultOrNull = registrator.register();
if (null != resultOrNull)
{
errorMap.put(sampleDataSet, resultOrNull);
@@ -280,7 +291,7 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
sb.append("Encountered errors in the following lines:\n");
for (SampleDataSetPair pair : errorMap.keySet())
{
- Exception error = errorMap.get(pair);
+ RegistrationErrorWrapper error = errorMap.get(pair);
sb.append("# ");
sb.append(error.getMessage());
sb.append("\n");
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetFolderProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetFolderProcessor.java
index 9e790196c38..5de7a300775 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetFolderProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetFolderProcessor.java
@@ -69,7 +69,7 @@ class SampleAndDataSetFolderProcessor extends AbstractSampleAndDataSetProcessor
new SampleAndDataSetControlFileProcessor(globalState, folder,
controlFile);
controlFileProcessor.register();
- } catch (Exception e)
+ } catch (UserFailureException e)
{
errorMap.put(controlFile, e);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java
index 0378b02fbc4..2020b85929b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java
@@ -145,7 +145,7 @@ public class SampleAndDataSetRegistrationHandler implements IDataSetHandlerWithM
folderProcessor.register();
} catch (Exception ex)
{
- operationLog.error(ex);
+ operationLog.error("Could not register samples / data sets in ", ex);
throw new CheckedExceptionTunnel(ex);
} finally
{
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 b6ce51d9b92..53f5fb60727 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
@@ -18,14 +18,15 @@ package ch.systemsx.cisd.etlserver.entityregistration;
import java.io.File;
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.etlserver.IExtensibleDataSetHandler;
import ch.systemsx.cisd.etlserver.TransferredDataSetHandler;
import ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetControlFileProcessor.ControlFileRegistrationProperties;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
/**
* Utitlity class for registering one sample/dataset combination
@@ -35,6 +36,47 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor implements
TransferredDataSetHandler.IDataSetRegistrator
{
+
+ /**
+ * A wrapper around errors encountered during registration.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+ static class RegistrationErrorWrapper
+ {
+ private final boolean isError;
+
+ private final Throwable errorOrNull;
+
+ RegistrationErrorWrapper(Throwable errorOrNull)
+ {
+ this.errorOrNull = errorOrNull;
+ isError = errorOrNull != null;
+ }
+
+ public boolean isError()
+ {
+ return isError;
+ }
+
+ public Throwable getErrorOrNull()
+ {
+ return errorOrNull;
+ }
+
+ public String getMessage()
+ {
+ if (isError)
+ {
+ return errorOrNull.getMessage();
+ } else
+ {
+ return "Success";
+ }
+ }
+
+ }
+
private final ControlFileRegistrationProperties properties;
private final SampleDataSetPair sampleDataSetPair;
@@ -42,7 +84,7 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
// State that is updated during the registration
private boolean didSucceed = false;
- private Exception failureException = null;
+ private RegistrationErrorWrapper failureException = null;
SampleAndDataSetRegistrator(File folder, ControlFileRegistrationProperties properties,
SampleDataSetPair sampleDataSetPair)
@@ -57,13 +99,16 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
*
* @return An exception if one was encountered, otherwise null.
*/
- public Exception register()
+ public RegistrationErrorWrapper register()
{
File dataSetFile = new File(folder, sampleDataSetPair.getFolderName());
- Exception isEmptyException = checkDataSetFileNotEmpty(dataSetFile);
- if (null != isEmptyException)
+ try
{
- return isEmptyException;
+ checkDataSetFileNotEmpty(dataSetFile);
+ checkExperimentExists();
+ } catch (UserFailureException ex)
+ {
+ return new RegistrationErrorWrapper(ex);
}
if (globalState.getDelegator() instanceof IExtensibleDataSetHandler)
@@ -79,13 +124,30 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
return failureException;
}
- private Exception checkDataSetFileNotEmpty(File dataSetFile)
+ private void checkDataSetFileNotEmpty(File dataSetFile)
{
if (0 == dataSetFile.list().length)
{
- return new UserFailureException("The data set folder cannot be empty");
+ throw new UserFailureException("The data set folder cannot be empty");
}
- return null;
+ }
+
+ private void checkExperimentExists()
+ {
+ ExperimentIdentifier experimentId =
+ sampleDataSetPair.getDataSetInformation().getExperimentIdentifier();
+ if (null == experimentId)
+ {
+ throw new UserFailureException("An experiment identifier must be specified");
+ }
+
+ Experiment experiment = globalState.getOpenbisService().tryToGetExperiment(experimentId);
+ if (null == experiment)
+ {
+ throw new UserFailureException("The experiment with identifier " + experimentId
+ + " does not exist");
+ }
+ sampleDataSetPair.getDataSetInformation().setExperiment(experiment);
}
private void logDataRegistered()
@@ -94,7 +156,7 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
globalState.getOperationLog().info(message);
}
- public void registerDataSetInApplicationServer(NewExternalData data)
+ public void registerDataSetInApplicationServer(NewExternalData data) throws Throwable
{
data.setDataSetType(properties.getDataSetType());
if (null != sampleDataSetPair.getFileFormatTypeCode())
@@ -116,13 +178,15 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
} catch (UserFailureException e)
{
didSucceed = false;
- failureException = e;
+ failureException = new RegistrationErrorWrapper(e);
throw e;
- } catch (Exception e)
+ } catch (Throwable e)
{
+ globalState.getOperationLog().error(
+ "Could not register " + sampleDataSetPair + " in openBIS", e);
didSucceed = false;
- failureException = e;
- throw new CheckedExceptionTunnel(e);
+ failureException = new RegistrationErrorWrapper(e);
+ throw e;
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPair.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPair.java
index b94344a616a..7431b76730c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPair.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPair.java
@@ -26,6 +26,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
/**
* An object that represents a sample/data set pair defined in a file
@@ -106,6 +107,8 @@ public class SampleDataSetPair
public void setSampleExperimentIdentifier(String experimentIdentifier)
{
this.newSample.setExperimentIdentifier(experimentIdentifier);
+ this.dataSetInformation.setExperimentIdentifier(new ExperimentIdentifierFactory(
+ experimentIdentifier).createIdentifier());
}
@BeanProperty(label = DATA_SET_CODE, optional = true)
--
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