From 47ff283c7e2e6f96a03edd5f38da52b7ef4b9f19 Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Tue, 31 Jan 2023 18:19:37 +0100
Subject: [PATCH] SSDM-13365 fixes to server-original-data-store test
---
.../TransferredDataSetHandlerTest.java | 369 +++++++++---------
1 file changed, 186 insertions(+), 183 deletions(-)
diff --git a/server-original-data-store/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java b/server-original-data-store/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
index 91a8a7351c0..b4fcaf9c5d1 100644
--- a/server-original-data-store/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
+++ b/server-original-data-store/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
@@ -83,13 +83,13 @@ import ch.systemsx.cisd.openbis.util.LogRecordingUtils;
/**
* Test cases for corresponding {@link TransferredDataSetHandler} class.
- *
+ *
* @author Franz-Josef Elmer
*/
@Friend(toClasses =
-{ TransferredDataSetHandler.class, DataSetRegistrationHelper.class,
- IdentifiedDataStrategy.class, PluginTaskInfoProvider.class,
- DssPropertyParametersUtil.class })
+ { TransferredDataSetHandler.class, DataSetRegistrationHelper.class,
+ IdentifiedDataStrategy.class, PluginTaskInfoProvider.class,
+ DssPropertyParametersUtil.class })
public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestCase
{
@@ -305,13 +305,13 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
new DataSetStorageRecoveryManager());
context.checking(new Expectations()
+ {
{
- {
- one(storageProcessor).setStoreRootDirectory(workingDirectory);
- allowing(storageProcessor).getStoreRootDirectory();
- will(returnValue(workingDirectory));
- }
- });
+ one(storageProcessor).setStoreRootDirectory(workingDirectory);
+ allowing(storageProcessor).getStoreRootDirectory();
+ will(returnValue(workingDirectory));
+ }
+ });
handler = new TransferredDataSetHandler(globalState, plugin);
@@ -336,7 +336,8 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
targetFolder =
IdentifiedDataStrategy.createBaseDirectory(workingDirectory, dataSetInformation);
targetData1 = createTargetData(data1);
- logRecorder = LogRecordingUtils.createRecorder("%-5p %c - %m%n", Level.INFO, ".*(DataStrategyStore|FileRenamer)");
+ logRecorder = LogRecordingUtils.createRecorder("%-5p %c - %m%n", Level.INFO,
+ ".*(DataStrategyStore|FileRenamer)");
}
private final String createLogMsgOfSuccess(final DataSetInformation dataSet)
@@ -426,22 +427,22 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
private final void prepareForStrategy(final File dataSet, final Sample sample)
{
context.checking(new Expectations()
+ {
{
- {
- one(dataSetInfoExtractor).getDataSetInformation(dataSet, null);
- will(returnValue(dataSetInformation));
+ one(dataSetInfoExtractor).getDataSetInformation(dataSet, null);
+ will(returnValue(dataSetInformation));
- one(limsService).getHomeDatabaseInstance(SESSION_TOKEN);
- will(returnValue(homeDatabaseInstance));
+ one(limsService).getHomeDatabaseInstance(SESSION_TOKEN);
+ will(returnValue(homeDatabaseInstance));
- atLeast(1).of(limsService).tryGetSampleWithExperiment(SESSION_TOKEN,
- dataSetInformation.getSampleIdentifier());
- will(returnValue(sample));
+ atLeast(1).of(limsService).tryGetSampleWithExperiment(SESSION_TOKEN,
+ dataSetInformation.getSampleIdentifier());
+ will(returnValue(sample));
- allowing(typeExtractor).getDataSetType(dataSet);
- will(returnValue(DATA_SET_TYPE));
- }
- });
+ allowing(typeExtractor).getDataSetType(dataSet);
+ will(returnValue(DATA_SET_TYPE));
+ }
+ });
}
private final void prepareForStrategyIDENTIFIED(final File dataSet,
@@ -449,35 +450,35 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
{
prepareForStrategy(dataSet, sample);
context.checking(new Expectations()
+ {
{
- {
- one(limsService).tryGetPropertiesOfSample(SESSION_TOKEN,
- dataSetInformation.getSampleIdentifier());
- will(returnValue(new IEntityProperty[0]));
- }
- });
+ one(limsService).tryGetPropertiesOfSample(SESSION_TOKEN,
+ dataSetInformation.getSampleIdentifier());
+ will(returnValue(new IEntityProperty[0]));
+ }
+ });
}
private final void prepareForRegistration(final File dataSet)
{
context.checking(new Expectations()
+ {
{
- {
- one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE, dataSet);
+ one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE, dataSet);
- one(typeExtractor).getLocatorType(dataSet);
- will(returnValue(LOCATOR_TYPE));
+ one(typeExtractor).getLocatorType(dataSet);
+ will(returnValue(LOCATOR_TYPE));
- one(typeExtractor).getFileFormatType(dataSet);
- will(returnValue(FILE_FORMAT_TYPE));
+ one(typeExtractor).getFileFormatType(dataSet);
+ will(returnValue(FILE_FORMAT_TYPE));
- one(typeExtractor).getProcessorType(dataSet);
- will(returnValue(EXAMPLE_PROCESSOR_ID));
+ one(typeExtractor).getProcessorType(dataSet);
+ will(returnValue(EXAMPLE_PROCESSOR_ID));
- one(typeExtractor).isMeasuredData(dataSet);
- will(returnValue(true));
- }
- });
+ one(typeExtractor).isMeasuredData(dataSet);
+ will(returnValue(true));
+ }
+ });
}
private final String getNotificationEmailContent(final DataSetInformation dataset,
@@ -513,7 +514,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
{
final String normalizedMessage = normalize(e.getMessage());
assertEquals("Error moving path 'data1' from '<wd>' to '<wd>': "
- + "Incoming data set directory '<wd>/data1' is not writable.",
+ + "Incoming data set directory '<wd>/data1' is not writable.",
normalizedMessage);
}
@@ -551,33 +552,33 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
prepareForStrategyIDENTIFIED(data1, targetData1, baseSample);
prepareForRegistration(data1);
context.checking(new Expectations()
+ {
{
- {
- one(limsService).registerDataSet(with(equal(SESSION_TOKEN)),
- with(equal(dataSetInformation.getSampleIdentifier())),
- with(new ExternalDataMatcher(targetData1)));
-
- checkSuccessEmailNotification(this, dataSetInformation, DATA_SET_CODE,
- baseExperiment.getRegistrator().getEmail());
-
- allowing(storageProcessor).getStorageFormat();
- will(returnValue(StorageFormat.BDS_DIRECTORY));
- one(storageProcessor).createTransaction(
- with(any(StorageProcessorTransactionParameters.class)));
- will(returnValue(transaction));
-
- one(transaction).storeData(typeExtractor, mailClient, data1);
- one(transaction).getStoredDataDirectory();
- final File finalDataSetPath = new File(baseDir, DATA1_NAME);
- will(returnValue(finalDataSetPath));
- one(transaction).commit();
-
- one(shareIdManager).setShareId(DATA_SET_CODE, "1");
-
- allowing(limsService).setStorageConfirmed(with(equal(SESSION_TOKEN)),
- with(equal(Collections.singletonList(DATA_SET_CODE))));
- }
- });
+ one(limsService).registerDataSet(with(equal(SESSION_TOKEN)),
+ with(equal(dataSetInformation.getSampleIdentifier())),
+ with(new ExternalDataMatcher(targetData1)));
+
+ checkSuccessEmailNotification(this, dataSetInformation, DATA_SET_CODE,
+ baseExperiment.getRegistrator().getEmail());
+
+ allowing(storageProcessor).getStorageFormat();
+ will(returnValue(StorageFormat.BDS_DIRECTORY));
+ one(storageProcessor).createTransaction(
+ with(any(StorageProcessorTransactionParameters.class)));
+ will(returnValue(transaction));
+
+ one(transaction).storeData(typeExtractor, mailClient, data1);
+ one(transaction).getStoredDataDirectory();
+ final File finalDataSetPath = new File(baseDir, DATA1_NAME);
+ will(returnValue(finalDataSetPath));
+ one(transaction).commit();
+
+ one(shareIdManager).setShareId(DATA_SET_CODE, "1");
+
+ allowing(limsService).setStorageConfirmed(with(equal(SESSION_TOKEN)),
+ with(equal(Collections.singletonList(DATA_SET_CODE))));
+ }
+ });
final LogMonitoringAppender appender =
LogMonitoringAppender.addAppender(LogCategory.OPERATION,
createLogMsgOfSuccess(dataSetInformation));
@@ -602,33 +603,33 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
prepareForStrategyIDENTIFIED(data1, targetData1, baseSample);
prepareForRegistration(data1);
context.checking(new Expectations()
+ {
{
- {
- one(limsService).registerDataSet(with(equal(SESSION_TOKEN)),
- with(equal(dataSetInformation.getSampleIdentifier())),
- with(new ExternalDataMatcher(targetData1)));
-
- checkSuccessEmailNotification(this, dataSetInformation, DATA_SET_CODE,
- baseExperiment.getRegistrator().getEmail());
-
- allowing(storageProcessor).getStorageFormat();
- will(returnValue(StorageFormat.BDS_DIRECTORY));
-
- one(storageProcessor).createTransaction(
- with(any(StorageProcessorTransactionParameters.class)));
- will(returnValue(transaction));
- one(transaction).storeData(typeExtractor, mailClient, data1);
- one(transaction).getStoredDataDirectory();
- final File finalDataSetPath = new File(baseDir, DATA1_NAME);
- will(returnValue(finalDataSetPath));
- one(transaction).commit();
-
- one(shareIdManager).setShareId(DATA_SET_CODE, "1");
-
- allowing(limsService).setStorageConfirmed(with(equal(SESSION_TOKEN)),
- with(equal(Collections.singletonList(DATA_SET_CODE))));
- }
- });
+ one(limsService).registerDataSet(with(equal(SESSION_TOKEN)),
+ with(equal(dataSetInformation.getSampleIdentifier())),
+ with(new ExternalDataMatcher(targetData1)));
+
+ checkSuccessEmailNotification(this, dataSetInformation, DATA_SET_CODE,
+ baseExperiment.getRegistrator().getEmail());
+
+ allowing(storageProcessor).getStorageFormat();
+ will(returnValue(StorageFormat.BDS_DIRECTORY));
+
+ one(storageProcessor).createTransaction(
+ with(any(StorageProcessorTransactionParameters.class)));
+ will(returnValue(transaction));
+ one(transaction).storeData(typeExtractor, mailClient, data1);
+ one(transaction).getStoredDataDirectory();
+ final File finalDataSetPath = new File(baseDir, DATA1_NAME);
+ will(returnValue(finalDataSetPath));
+ one(transaction).commit();
+
+ one(shareIdManager).setShareId(DATA_SET_CODE, "1");
+
+ allowing(limsService).setStorageConfirmed(with(equal(SESSION_TOKEN)),
+ with(equal(Collections.singletonList(DATA_SET_CODE))));
+ }
+ });
final LogMonitoringAppender appender =
LogMonitoringAppender.addAppender(LogCategory.OPERATION,
createLogMsgOfSuccess(dataSetInformation));
@@ -649,22 +650,22 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
final Experiment baseExperiment = baseSample.getExperiment();
prepareForStrategy(data1, baseSample);
context.checking(new Expectations()
+ {
{
- {
- one(limsService).tryGetPropertiesOfSample(SESSION_TOKEN,
- dataSetInformation.getSampleIdentifier());
- will(returnValue(null));
-
- final ExperimentIdentifier experimentIdentifier =
- dataSetInformation.getExperimentIdentifier();
- final String subject =
- String.format(DataStrategyStore.SUBJECT_FORMAT, experimentIdentifier);
- final String body =
- DataStrategyStore.createInvalidSampleCodeMessage(dataSetInformation);
- final String email = baseExperiment.getRegistrator().getEmail();
- one(mailClient).sendMessage(subject, body, null, null, email);
- }
- });
+ one(limsService).tryGetPropertiesOfSample(SESSION_TOKEN,
+ dataSetInformation.getSampleIdentifier());
+ will(returnValue(null));
+
+ final ExperimentIdentifier experimentIdentifier =
+ dataSetInformation.getExperimentIdentifier();
+ final String subject =
+ String.format(DataStrategyStore.SUBJECT_FORMAT, experimentIdentifier);
+ final String body =
+ DataStrategyStore.createInvalidSampleCodeMessage(dataSetInformation);
+ final String email = baseExperiment.getRegistrator().getEmail();
+ one(mailClient).sendMessage(subject, body, null, null, email);
+ }
+ });
handler.handle(isFinishedData1);
assertEquals(false, isFinishedData1.exists());
@@ -708,30 +709,30 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
final Sample baseSample = createBaseSample(dataSetInformation);
prepareForStrategyIDENTIFIED(folder, targetData1, baseSample);
context.checking(new Expectations()
+ {
{
- {
- one(typeExtractor).getProcessorType(folder);
- will(returnValue(EXAMPLE_PROCESSOR_ID));
-
- one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE, folder);
-
- one(storageProcessor).createTransaction(
- with(any(StorageProcessorTransactionParameters.class)));
- will(returnValue(transaction));
- one(transaction).storeData(typeExtractor, mailClient, folder);
- UserFailureException exception =
- new UserFailureException("Could store data by storage processor");
- will(throwException(exception));
-
- one(transaction).rollback(exception);
- will(returnValue(UnstoreDataAction.MOVE_TO_ERROR));
-
- allowing(typeExtractor).getLocatorType(folder);
- allowing(typeExtractor).getDataSetType(folder);
- allowing(typeExtractor).getFileFormatType(folder);
- allowing(typeExtractor).isMeasuredData(folder);
- }
- });
+ one(typeExtractor).getProcessorType(folder);
+ will(returnValue(EXAMPLE_PROCESSOR_ID));
+
+ one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE, folder);
+
+ one(storageProcessor).createTransaction(
+ with(any(StorageProcessorTransactionParameters.class)));
+ will(returnValue(transaction));
+ one(transaction).storeData(typeExtractor, mailClient, folder);
+ UserFailureException exception =
+ new UserFailureException("Could store data by storage processor");
+ will(throwException(exception));
+
+ one(transaction).rollback(exception);
+ will(returnValue(UnstoreDataAction.MOVE_TO_ERROR));
+
+ allowing(typeExtractor).getLocatorType(folder);
+ allowing(typeExtractor).getDataSetType(folder);
+ allowing(typeExtractor).getFileFormatType(folder);
+ allowing(typeExtractor).isMeasuredData(folder);
+ }
+ });
final LogMonitoringAppender appender =
LogMonitoringAppender.addAppender(LogCategory.OPERATION,
createLogMsgOfSuccess(dataSetInformation));
@@ -774,26 +775,26 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
prepareForStrategyIDENTIFIED(folder, targetData1, baseSample);
prepareForRegistration(folder);
context.checking(new Expectations()
+ {
{
- {
- one(storageProcessor).createTransaction(
- with(any(StorageProcessorTransactionParameters.class)));
- will(returnValue(transaction));
- one(transaction).storeData(typeExtractor, mailClient, folder);
- one(transaction).getStoredDataDirectory();
- will(returnValue(new File(baseDir, DATA1_NAME)));
-
- one(limsService).registerDataSet(with(equal(SESSION_TOKEN)),
- with(equal(dataSetInformation.getSampleIdentifier())),
- with(new ExternalDataMatcher(targetData1)));
- EnvironmentFailureException exception =
- new EnvironmentFailureException("Could not register data set folder");
- will(throwException(exception));
-
- one(transaction).rollback(exception);
- one(storageProcessor).getStorageFormat();
- }
- });
+ one(storageProcessor).createTransaction(
+ with(any(StorageProcessorTransactionParameters.class)));
+ will(returnValue(transaction));
+ one(transaction).storeData(typeExtractor, mailClient, folder);
+ one(transaction).getStoredDataDirectory();
+ will(returnValue(new File(baseDir, DATA1_NAME)));
+
+ one(limsService).registerDataSet(with(equal(SESSION_TOKEN)),
+ with(equal(dataSetInformation.getSampleIdentifier())),
+ with(new ExternalDataMatcher(targetData1)));
+ EnvironmentFailureException exception =
+ new EnvironmentFailureException("Could not register data set folder");
+ will(throwException(exception));
+
+ one(transaction).rollback(exception);
+ one(storageProcessor).getStorageFormat();
+ }
+ });
final LogMonitoringAppender appender =
LogMonitoringAppender.addAppender(LogCategory.OPERATION,
createLogMsgOfSuccess(dataSetInformation));
@@ -831,11 +832,11 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
new DynamicTransactionQueryFactory(), true, threadParameters,
new DataSetStorageRecoveryManager());
context.checking(new Expectations()
+ {
{
- {
- one(storageProcessor).setStoreRootDirectory(workingDirectory);
- }
- });
+ one(storageProcessor).setStoreRootDirectory(workingDirectory);
+ }
+ });
handler = new TransferredDataSetHandler(globalState, plugin);
@@ -845,33 +846,33 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
prepareForStrategyIDENTIFIED(data1, targetData1, baseSample);
prepareForRegistration(data1);
context.checking(new Expectations()
+ {
{
- {
- one(limsService).registerDataSet(with(equal(SESSION_TOKEN)),
- with(equal(dataSetInformation.getSampleIdentifier())),
- with(new ExternalDataMatcher(targetData1)));
-
- checkSuccessEmailNotification(this, dataSetInformation, DATA_SET_CODE,
- baseExperiment.getRegistrator().getEmail());
-
- allowing(storageProcessor).getStorageFormat();
- will(returnValue(StorageFormat.BDS_DIRECTORY));
-
- one(storageProcessor).createTransaction(
- with(any(StorageProcessorTransactionParameters.class)));
- will(returnValue(transaction));
- one(transaction).storeData(typeExtractor, mailClient, data1);
- one(transaction).getStoredDataDirectory();
- final File finalDataSetPath = new File(baseDir, DATA1_NAME);
- will(returnValue(finalDataSetPath));
- one(transaction).commit();
-
- one(shareIdManager).setShareId(DATA_SET_CODE, "1");
-
- allowing(limsService).setStorageConfirmed(with(equal(SESSION_TOKEN)),
- with(equal(Collections.singletonList(DATA_SET_CODE))));
- }
- });
+ one(limsService).registerDataSet(with(equal(SESSION_TOKEN)),
+ with(equal(dataSetInformation.getSampleIdentifier())),
+ with(new ExternalDataMatcher(targetData1)));
+
+ checkSuccessEmailNotification(this, dataSetInformation, DATA_SET_CODE,
+ baseExperiment.getRegistrator().getEmail());
+
+ allowing(storageProcessor).getStorageFormat();
+ will(returnValue(StorageFormat.BDS_DIRECTORY));
+
+ one(storageProcessor).createTransaction(
+ with(any(StorageProcessorTransactionParameters.class)));
+ will(returnValue(transaction));
+ one(transaction).storeData(typeExtractor, mailClient, data1);
+ one(transaction).getStoredDataDirectory();
+ final File finalDataSetPath = new File(baseDir, DATA1_NAME);
+ will(returnValue(finalDataSetPath));
+ one(transaction).commit();
+
+ one(shareIdManager).setShareId(DATA_SET_CODE, "1");
+
+ allowing(limsService).setStorageConfirmed(with(equal(SESSION_TOKEN)),
+ with(equal(Collections.singletonList(DATA_SET_CODE))));
+ }
+ });
final LogMonitoringAppender appender =
LogMonitoringAppender.addAppender(LogCategory.OPERATION,
createLogMsgOfSuccess(dataSetInformation));
@@ -879,8 +880,10 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
LogMonitoringAppender
.addAppender(
LogCategory.OPERATION,
- Pattern.compile("P[0-9]+-\\{test-script.sh\\} had command line: \\[sourceTest/java/ch/systemsx/cisd/etlserver/utils/test-script.sh, 4711-42, .*/datastore_server/targets/unit-test-wd/ch.systemsx.cisd.etlserver.TransferredDataSetHandlerTest/data1\\]"),
- Pattern.compile("P[0-9]+-\\{test-script.sh\\} process returned with exit value 1."));
+ Pattern.compile(
+ "P[0-9]+-\\{test-script.sh\\} had command line: \\[sourceTest/java/ch/systemsx/cisd/etlserver/utils/test-script.sh, 4711-42, .*/server-original-data-store/targets/unit-test-wd/ch.systemsx.cisd.etlserver.TransferredDataSetHandlerTest/data1\\]"),
+ Pattern.compile(
+ "P[0-9]+-\\{test-script.sh\\} process returned with exit value 1."));
handler.handle(isFinishedData1);
final File dataSetPath = createDatasetDir(baseDir);
--
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