From 0a3bd6d87690c36440e64770e934be3de54af60d Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Mon, 30 May 2011 13:24:23 +0000
Subject: [PATCH] LMS-2264 Support for specifying data set code
SVN: 21506
---
.../v1/IDataSetRegistrationTransaction.java | 7 ++-
.../api/v1/impl/AbstractTransactionState.java | 25 +++++++-
.../impl/DataSetRegistrationTransaction.java | 5 ++
.../DataSetRegistrationTransactionTest.java | 59 +++++++++++++++++--
4 files changed, 89 insertions(+), 7 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
index 3957ca09d83..6d5a2c885e6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
@@ -39,10 +39,15 @@ public interface IDataSetRegistrationTransaction
IDataSet createNewDataSet();
/**
- * Create a new data set with the specified code.
+ * Create a new data set with the specified type.
*/
IDataSet createNewDataSet(String dataSetType);
+ /**
+ * Create a new data set with the specified type and code.
+ */
+ IDataSet createNewDataSet(String dataSetType, String dataSetCode);
+
/**
* Get a sample from the openBIS AS. Returns null if the sample does not exist.
*
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
index 56bf8f96f49..c572f792f8d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
@@ -151,15 +151,36 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
return createNewDataSet(registrationDetails);
}
+ public IDataSet createNewDataSet(String dataSetType, String dataSetCode)
+ {
+ // Create registration details for the new data set
+ DataSetRegistrationDetails<T> registrationDetails =
+ registrationDetailsFactory.createDataSetRegistrationDetails();
+ registrationDetails.setDataSetType(dataSetType);
+
+ return createNewDataSet(registrationDetails, dataSetCode);
+ }
+
public IDataSet createNewDataSet(DataSetRegistrationDetails<T> registrationDetails)
{
// Request a code, so we can keep the staging file name and the data set code in sync
- String dataSetCode = registrationDetails.getDataSetInformation().getDataSetCode();
- if (null == dataSetCode)
+ return createNewDataSet(registrationDetails, registrationDetails
+ .getDataSetInformation().getDataSetCode());
+ }
+
+ public IDataSet createNewDataSet(DataSetRegistrationDetails<T> registrationDetails,
+ String specifiedCode)
+ {
+ final String dataSetCode;
+ if (null == specifiedCode)
{
dataSetCode = generateDataSetCode(registrationDetails);
registrationDetails.getDataSetInformation().setDataSetCode(dataSetCode);
+ } else
+ {
+ dataSetCode = specifiedCode.toUpperCase();
}
+ registrationDetails.getDataSetInformation().setDataSetCode(dataSetCode);
// Create a directory for the data set
File stagingFolder = new File(stagingDirectory, dataSetCode);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
index e4506c519ac..e31481806c8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
@@ -192,6 +192,11 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
return getStateAsLiveState().createNewDataSet(dataSetType);
}
+ public IDataSet createNewDataSet(String dataSetType, String dataSetCode)
+ {
+ return getStateAsLiveState().createNewDataSet(dataSetType, dataSetCode);
+ }
+
public IDataSet createNewDataSet(DataSetRegistrationDetails<T> registrationDetails)
{
return getStateAsLiveState().createNewDataSet(registrationDetails);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
index 30281aecaad..b5e052a7079 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
@@ -69,7 +69,7 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
{
private static final String EXPERIMENT_IDENTIFIER = "/SPACE/PROJECT/EXP-CODE";
- private static final String DATA_SET_CODE = "data-set-code";
+ private static final String DATA_SET_CODE = "data-set-code".toUpperCase();
private static final String DATABASE_INSTANCE_UUID = "db-uuid";
@@ -164,6 +164,42 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
context.assertIsSatisfied();
}
+ @Test
+ public void testCommitSpecifyingDataSetCode()
+ {
+ setUpOpenBisExpectations(true, false);
+ setUpDataSetValidatorExpectations("my-data-set-code");
+ createTransaction();
+
+ IDataSet newDataSet = tr.createNewDataSet("UNKNOWN", "my-data-set-code");
+ String dst = tr.moveFile(srcFile.getAbsolutePath(), newDataSet);
+ IExperimentImmutable experiment = tr.getExperiment(EXPERIMENT_IDENTIFIER);
+ newDataSet.setExperiment(experiment);
+ newDataSet.setDataSetType(DATA_SET_TYPE.getCode());
+
+ checkContentsOfFile(new File(dst));
+
+ File[] rollbackQueueFiles = listRollbackQueueFiles();
+ assertEquals(2, rollbackQueueFiles.length);
+
+ tr.commit();
+
+ System.out.println(logAppender.getLogContent());
+
+ assertTrue(logAppender.getLogContent().length() > 0);
+ // Skip this for the moment
+ // new LogMatcher(logAppender,
+ // "Identified that database knows experiment '/SPACE/PROJECT/EXP-CODE'.*",
+ // "Start storing data set for experiment '/SPACE/PROJECT/EXP-CODE'.*",
+ // "Finished storing data set for experiment '/SPACE/PROJECT/EXP-CODE', took .*",
+ // "Successfully registered data set: .+").assertMatches();
+
+ rollbackQueueFiles = listRollbackQueueFiles();
+ assertEquals(0, rollbackQueueFiles.length);
+
+ context.assertIsSatisfied();
+ }
+
@Test
public void testCommitContainerDataSet()
{
@@ -404,13 +440,22 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
}
private void setUpOpenBisExpectations(final boolean willRegister)
+ {
+ setUpOpenBisExpectations(willRegister, true);
+ }
+
+ private void setUpOpenBisExpectations(final boolean willRegister,
+ final boolean createDataSetCode)
{
setUpHomeDataBaseExpectations();
context.checking(new Expectations()
{
{
- oneOf(openBisService).createDataSetCode();
- will(returnValue(DATA_SET_CODE + 1));
+ if (createDataSetCode)
+ {
+ oneOf(openBisService).createDataSetCode();
+ will(returnValue(DATA_SET_CODE + 1));
+ }
if (willRegister)
{
@@ -446,7 +491,13 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
private void setUpDataSetValidatorExpectations()
{
- File dataSetDir = new File(stagingDirectory, DATA_SET_CODE + "1");
+ setUpDataSetValidatorExpectations(DATA_SET_CODE + "1");
+
+ }
+
+ private void setUpDataSetValidatorExpectations(String dataSetCode)
+ {
+ File dataSetDir = new File(stagingDirectory, dataSetCode.toUpperCase());
final File dataSetFile = new File(dataSetDir, srcFile.getName());
context.checking(new Expectations()
{
--
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