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 e9c1979332388e275aff58148dd33a83cb9c1de3..655ff02b9fad0973786f5d2e1b659cfa5fbfc8e8 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
@@ -89,11 +89,27 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
static class LiveTransactionState<T extends DataSetInformation> extends
AbstractTransactionState<T> implements RollbackStack.IRollbackStackDelegate
{
- // Wait for up to 5 minutes for the file system to become available
- private static final int MAX_DIRECTORY_AVAILABLE_WAIT_COUNT = 6 * 5;
+ // Default to polling every 10 seconds and waiting for up to 5 minutes
+ private static int fileSystemAvailablityWaitCount = 6 * 5;
- // Poll every 10 seconds
- private static final int STAGING_DIR_AVAILABILITY_POLLING_WAIT_TIME = 10 * 1000;
+ private static int fileSystemAvailablityPollingWaitTimeMs = 10 * 1000;
+
+ /**
+ * These two variables determine together how long the rollback mechanism waits for a file
+ * system that has become unavailable and how often it checks for the file system to become
+ * available.
+ * <p>
+ * The duration the rollback mechanism will wait before giving up equals waitTimeMS *
+ * waitCount;
+ * <p>
+ * Made public for testing.
+ */
+ public static void setFileSystemAvailabilityPollingWaitTimeAndWaitCount(int waitTimeMS,
+ int waitCount)
+ {
+ fileSystemAvailablityWaitCount = waitTimeMS;
+ fileSystemAvailablityPollingWaitTimeMs = waitCount;
+ }
// Keeps track of steps that have been executed and may need to be reverted. Elements are
// kept in the order they need to be reverted.
@@ -680,12 +696,11 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
if (null != FileUtilities.checkDirectoryFullyAccessible(stagingDirectory, "staging"))
{
boolean keepPolling = true;
- for (int waitCount = 0; waitCount < MAX_DIRECTORY_AVAILABLE_WAIT_COUNT
- && keepPolling; ++waitCount)
+ for (int waitCount = 0; waitCount < fileSystemAvailablityWaitCount && keepPolling; ++waitCount)
{
try
{
- Thread.sleep(STAGING_DIR_AVAILABILITY_POLLING_WAIT_TIME);
+ Thread.sleep(fileSystemAvailablityPollingWaitTimeMs);
// If the directory is not accessible (i.e., return not null), wait again
keepPolling =
(null != FileUtilities.checkDirectoryFullyAccessible(
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 3876217f826d148d5205b6a0ecde351eeba787fc..87c3994012ae63313235cca99008239ccd869f30 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
@@ -97,7 +97,6 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
{
File[] rollbackQueue1Files = rollBackStackParentFolder.listFiles(new FilenameFilter()
{
-
public boolean accept(File dir, String name)
{
return name.endsWith(ROLLBACK_QUEUE1_FILE_NAME_SUFFIX);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/RollbackConfigurator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/RollbackConfigurator.java
new file mode 100644
index 0000000000000000000000000000000000000000..510fd5995bfc312f9737815c30f39133f5c53d28
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/RollbackConfigurator.java
@@ -0,0 +1,42 @@
+/*
+ * 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.registrator.api.v1.impl;
+
+/**
+ * A public class for setting rollback configuration variables (which are stored in package-visible
+ * classes).
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class RollbackConfigurator
+{
+ /**
+ * These two variables determine together how long the rollback mechanism waits for a file
+ * system that has become unavailable and how often it checks for the file system to become
+ * available.
+ * <p>
+ * The duration the rollback mechanism will wait before giving up equals waitTimeMS * waitCount;
+ * <p>
+ * Made public for testing.
+ */
+ public static void setFileSystemAvailabilityPollingWaitTimeAndWaitCount(int waitTimeMS,
+ int waitCount)
+ {
+ ch.systemsx.cisd.etlserver.registrator.api.v1.impl.AbstractTransactionState.LiveTransactionState
+ .setFileSystemAvailabilityPollingWaitTimeAndWaitCount(waitTimeMS, waitCount);
+ }
+}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
index 5facd9fa7b5dca8befe90347385b6205c469f81e..bed4ca8a2ee29ab27bab82a50f19c093103bf592 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
@@ -110,6 +110,8 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
public void init()
{
QueueingPathRemoverService.start();
+ ch.systemsx.cisd.etlserver.registrator.api.v1.impl.RollbackConfigurator
+ .setFileSystemAvailabilityPollingWaitTimeAndWaitCount(10, 1);
}
@AfterTest
@@ -238,7 +240,7 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
return threadProperties;
}
- public static final class MockStorageProcessor implements IStorageProcessorTransactional,
+ public static class MockStorageProcessor implements IStorageProcessorTransactional,
Serializable
{
private static final long serialVersionUID = 1L;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorRollbackTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorRollbackTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..90ddfa01a4554ce345f982661ededd4699bde364
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorRollbackTest.java
@@ -0,0 +1,293 @@
+/*
+ * 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.registrator;
+
+import static ch.systemsx.cisd.common.Constants.IS_FINISHED_PREFIX;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.commons.io.FileUtils;
+import org.hamcrest.core.IsAnything;
+import org.jmock.Expectations;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.utilities.ExtendedProperties;
+import ch.systemsx.cisd.etlserver.IStorageProcessorTransactional;
+import ch.systemsx.cisd.etlserver.ITypeExtractor;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class JythonTopLevelDataSetRegistratorRollbackTest extends AbstractJythonDataSetHandlerTest
+{
+ private static final String SCRIPTS_FOLDER =
+ "sourceTest/java/ch/systemsx/cisd/etlserver/registrator/";
+
+ private static final String DATA_SET_CODE = "data-set-code";
+
+ private static final DataSetType DATA_SET_TYPE = new DataSetType("O1");
+
+ private static final String EXPERIMENT_IDENTIFIER = "/SPACE/PROJECT/EXP";
+
+ @BeforeMethod
+ @Override
+ public void setUp() throws IOException
+ {
+ super.setUp();
+
+ didDataSetRollbackHappen = false;
+ didServiceRollbackHappen = false;
+ }
+
+ @Test
+ public void testSimpleTransactionRollback()
+ {
+ setUpHomeDataBaseExpectations();
+ Properties properties =
+ createThreadPropertiesRelativeToScriptsFolder("simple-transaction.py");
+ properties.setProperty(IStorageProcessorTransactional.STORAGE_PROCESSOR_KEY,
+ MockStorageProcessor.class.getName());
+
+ createHandler(properties, false, false);
+ createData();
+ ExperimentBuilder builder = new ExperimentBuilder().identifier(EXPERIMENT_IDENTIFIER);
+ final Experiment experiment = builder.getExperiment();
+ context.checking(new Expectations()
+ {
+ {
+ one(openBisService).createDataSetCode();
+ will(returnValue(DATA_SET_CODE));
+ atLeast(1).of(openBisService).tryToGetExperiment(
+ new ExperimentIdentifierFactory(experiment.getIdentifier())
+ .createIdentifier());
+ will(returnValue(experiment));
+
+ one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
+ new File(new File(stagingDirectory, DATA_SET_CODE), "sub_data_set_1"));
+ one(openBisService)
+ .performEntityOperations(
+ with(new IsAnything<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails>()));
+ will(throwException(new AssertionError("Fail")));
+ }
+ });
+
+ try
+ {
+ handler.handle(markerFile);
+ fail("No IOException thrown");
+ } catch (IOExceptionUnchecked e)
+ {
+ // Make the file system available again and rollback
+ makeFileSystemAvailable(workingDirectory);
+ DataSetRegistrationTransaction.rollbackDeadTransactions(workingDirectory);
+ }
+ assertEquals(1, MockStorageProcessor.instance.incomingDirs.size());
+ assertEquals(0, MockStorageProcessor.instance.calledCommitCount);
+ assertEquals("[]", Arrays.asList(stagingDirectory.list()).toString());
+ assertEquals(
+ "hello world1",
+ FileUtilities.loadToString(
+ new File(workingDirectory, "data_set/sub_data_set_1/read1.me")).trim());
+ assertEquals(
+ "hello world2",
+ FileUtilities.loadToString(
+ new File(workingDirectory, "data_set/sub_data_set_2/read2.me")).trim());
+
+ TestingDataSetHandler theHandler = (TestingDataSetHandler) handler;
+ assertFalse(theHandler.didRollbackDataSetRegistrationFunctionRun);
+ assertFalse(theHandler.didRollbackServiceFunctionRun);
+ assertTrue(theHandler.didTransactionRollbackHappen);
+ assertTrue(theHandler.didRollbackTransactionFunctionRunHappen);
+
+ context.assertIsSatisfied();
+ }
+
+ private void createData()
+ {
+ incomingDataSetFile = createDirectory(workingDirectory, "data_set");
+
+ subDataSet1 = createDirectory(incomingDataSetFile, "sub_data_set_1");
+ subDataSet2 = createDirectory(incomingDataSetFile, "sub_data_set_2");
+
+ FileUtilities.writeToFile(new File(subDataSet1, "read1.me"), "hello world1");
+ FileUtilities.writeToFile(new File(subDataSet2, "read2.me"), "hello world2");
+
+ markerFile = new File(workingDirectory, IS_FINISHED_PREFIX + "data_set");
+ FileUtilities.writeToFile(markerFile, "");
+ }
+
+ @Override
+ protected String getRegistrationScriptsFolderPath()
+ {
+ return SCRIPTS_FOLDER;
+ }
+
+ protected SearchCriteria createTestSearchCriteria(String typeString)
+ {
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE, typeString));
+ sc.addMatchClause(MatchClause.createPropertyMatch("PROP", "VALUE"));
+ return sc;
+ }
+
+ public static final class MockStorageProcessor extends
+ AbstractJythonDataSetHandlerTest.MockStorageProcessor
+ {
+ private static final long serialVersionUID = 1L;
+
+ static MockStorageProcessor instance;
+
+ int calledGetStoreRootDirectoryCount = 0;
+
+ int calledCommitCount = 0;
+
+ File storeRootDirectory;
+
+ String dataSetInfoString;
+
+ protected List<File> incomingDirs = new ArrayList<File>();
+
+ protected List<File> rootDirs = new ArrayList<File>();
+
+ public MockStorageProcessor(ExtendedProperties props)
+ {
+ super(props);
+ instance = this;
+ }
+
+ public File getStoreRootDirectory()
+ {
+ calledGetStoreRootDirectoryCount++;
+ return storeRootDirectory;
+ }
+
+ public void setStoreRootDirectory(File storeRootDirectory)
+ {
+ this.storeRootDirectory = storeRootDirectory;
+ }
+
+ public StorageFormat getStorageFormat()
+ {
+ return StorageFormat.PROPRIETARY;
+ }
+
+ public UnstoreDataAction getDefaultUnstoreDataAction(Throwable exception)
+ {
+ return UnstoreDataAction.LEAVE_UNTOUCHED;
+ }
+
+ public IStorageProcessorTransaction createTransaction(
+ StorageProcessorTransactionParameters parameters)
+ {
+ final File rootDir = parameters.getRootDir();
+ dataSetInfoString = parameters.getDataSetInformation().toString();
+ return new IStorageProcessorTransaction()
+ {
+
+ private static final long serialVersionUID = 1L;
+
+ private File storedFolder;
+
+ public void storeData(ITypeExtractor typeExtractor, IMailClient mailClient,
+ File incomingDataSetFile)
+ {
+
+ incomingDirs.add(incomingDataSetFile);
+ rootDirs.add(rootDir);
+
+ try
+ {
+ if (incomingDataSetFile.isDirectory())
+ {
+ FileUtils.moveDirectoryToDirectory(incomingDataSetFile, new File(
+ rootDir, "original"), true);
+ } else
+ {
+ FileUtils.moveFileToDirectory(incomingDataSetFile, new File(
+ rootDir, "original"), false);
+ }
+ makeFileSystemUnavailable(getStoreRootDirectory());
+ } catch (IOException ex)
+ {
+ throw new IOExceptionUnchecked(ex);
+ }
+ storedFolder = rootDir;
+ }
+
+ public UnstoreDataAction rollback(Throwable exception)
+ {
+ return null;
+ }
+
+ public File getStoredDataDirectory()
+ {
+ return storedFolder;
+ }
+
+ public void commit()
+ {
+ calledCommitCount++;
+ }
+
+ public File tryGetProprietaryData()
+ {
+ return null;
+ }
+ };
+ }
+ }
+
+ /**
+ * Simulate the file system becoming unavailable
+ */
+ private static void makeFileSystemUnavailable(File storeRootDirectory)
+ {
+ new File(storeRootDirectory, "1").renameTo(new File(storeRootDirectory, "1.unavailable"));
+
+ new File(storeRootDirectory, "staging").renameTo(new File(storeRootDirectory,
+ "staging.unavailable"));
+ }
+
+ /**
+ * Simulate the file system becoming available again
+ */
+ private static void makeFileSystemAvailable(File storeRootDirectory)
+ {
+ new File(storeRootDirectory, "1.unavailable").renameTo(new File(storeRootDirectory, "1"));
+
+ new File(storeRootDirectory, "staging.unavailable").renameTo(new File(storeRootDirectory,
+ "staging"));
+ }
+}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
index 7b4d0c1544e86442e301e881031df76b939b9e60..562ffd31ffda45bd18590bc53370978d8e936f4e 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
@@ -99,8 +99,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
setUpHomeDataBaseExpectations();
Properties properties =
createThreadPropertiesRelativeToScriptsFolder("simple-transaction.py");
- final File stagingDir = new File(workingDirectory, "staging");
- properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, false, true);
createData();
@@ -119,7 +117,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
will(returnValue(experiment));
one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
- new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"));
+ new File(new File(stagingDirectory, DATA_SET_CODE), "sub_data_set_1"));
one(openBisService).performEntityOperations(with(atomicatOperationDetails));
will(returnValue(new AtomicEntityOperationResult()));
}
@@ -149,7 +147,8 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
assertEquals(1, MockStorageProcessor.instance.calledCommitCount);
assertEquals(datasetLocation, MockStorageProcessor.instance.rootDirs.get(0));
File incomingDir = MockStorageProcessor.instance.incomingDirs.get(0);
- assertEquals(new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"), incomingDir);
+ assertEquals(new File(new File(stagingDirectory, DATA_SET_CODE), "sub_data_set_1"),
+ incomingDir);
assertEquals("hello world1",
FileUtilities.loadToString(new File(datasetLocation, "read1.me")).trim());
context.assertIsSatisfied();
@@ -161,8 +160,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
setUpHomeDataBaseExpectations();
Properties properties =
createThreadPropertiesRelativeToScriptsFolder("simple-transaction-rollback.py");
- final File stagingDir = new File(workingDirectory, "staging");
- properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, true, false);
createData();
ExperimentBuilder builder = new ExperimentBuilder().identifier(EXPERIMENT_IDENTIFIER);
@@ -182,7 +179,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
handler.handle(markerFile);
assertEquals(0, MockStorageProcessor.instance.incomingDirs.size());
assertEquals(0, MockStorageProcessor.instance.calledCommitCount);
- assertEquals("[]", Arrays.asList(stagingDir.list()).toString());
+ assertEquals("[]", Arrays.asList(stagingDirectory.list()).toString());
assertEquals(
"hello world1",
FileUtilities.loadToString(
@@ -209,8 +206,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
setUpHomeDataBaseExpectations();
Properties properties =
createThreadPropertiesRelativeToScriptsFolder("simple-transaction.py");
- final File stagingDir = new File(workingDirectory, "staging");
- properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, false, false);
createData();
ExperimentBuilder builder = new ExperimentBuilder().identifier(EXPERIMENT_IDENTIFIER);
@@ -226,7 +221,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
will(returnValue(experiment));
one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
- new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"));
+ new File(new File(stagingDirectory, DATA_SET_CODE), "sub_data_set_1"));
one(openBisService)
.performEntityOperations(
with(new IsAnything<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails>()));
@@ -237,7 +232,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
handler.handle(markerFile);
assertEquals(1, MockStorageProcessor.instance.incomingDirs.size());
assertEquals(0, MockStorageProcessor.instance.calledCommitCount);
- assertEquals("[]", Arrays.asList(stagingDir.list()).toString());
+ assertEquals("[]", Arrays.asList(stagingDirectory.list()).toString());
assertEquals(
"hello world1",
FileUtilities.loadToString(
@@ -262,8 +257,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
setUpHomeDataBaseExpectations();
Properties properties =
createThreadPropertiesRelativeToScriptsFolder("two-simple-datasets.py");
- final File stagingDir = new File(workingDirectory, "staging");
- properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, false, true);
createData();
ExperimentBuilder builder1 = new ExperimentBuilder().identifier("/SPACE/PROJECT/EXP1");
@@ -283,8 +276,10 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
.createIdentifier());
will(returnValue(experiment1));
- one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
- new File(new File(stagingDir, DATA_SET_CODE + 1), "sub_data_set_1"));
+ one(dataSetValidator).assertValidDataSet(
+ DATA_SET_TYPE,
+ new File(new File(stagingDirectory, DATA_SET_CODE + 1),
+ "sub_data_set_1"));
one(openBisService).createDataSetCode();
will(returnValue(DATA_SET_CODE + 2));
@@ -294,8 +289,10 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
.createIdentifier());
will(returnValue(experiment2));
- one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
- new File(new File(stagingDir, DATA_SET_CODE + 2), "sub_data_set_2"));
+ one(dataSetValidator).assertValidDataSet(
+ DATA_SET_TYPE,
+ new File(new File(stagingDirectory, DATA_SET_CODE + 2),
+ "sub_data_set_2"));
one(openBisService).performEntityOperations(with(operations));
will(returnValue(new AtomicEntityOperationResult()));
@@ -324,7 +321,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
datasetLocation1), dataSet1.getLocation());
assertEquals(datasetLocation1, MockStorageProcessor.instance.rootDirs.get(0));
File incomingDir1 = MockStorageProcessor.instance.incomingDirs.get(0);
- assertEquals(new File(new File(stagingDir, DATA_SET_CODE + 1), "sub_data_set_1"),
+ assertEquals(new File(new File(stagingDirectory, DATA_SET_CODE + 1), "sub_data_set_1"),
incomingDir1);
assertEquals("hello world1",
FileUtilities.loadToString(new File(datasetLocation1, "read1.me")).trim());
@@ -341,7 +338,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
datasetLocation2), dataSet2.getLocation());
assertEquals(datasetLocation2, MockStorageProcessor.instance.rootDirs.get(1));
File incomingDir2 = MockStorageProcessor.instance.incomingDirs.get(1);
- assertEquals(new File(new File(stagingDir, DATA_SET_CODE + 2), "sub_data_set_2"),
+ assertEquals(new File(new File(stagingDirectory, DATA_SET_CODE + 2), "sub_data_set_2"),
incomingDir2);
assertEquals("hello world2",
FileUtilities.loadToString(new File(datasetLocation2, "read2.me")).trim());
@@ -354,8 +351,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
setUpHomeDataBaseExpectations();
Properties properties =
createThreadPropertiesRelativeToScriptsFolder("transaction-with-new-experiment.py");
- final File stagingDir = new File(workingDirectory, "staging");
- properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, false, true);
createData();
final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicatOperationDetails =
@@ -370,7 +365,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
will(returnValue(EXPERIMENT_PERM_ID));
one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
- new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"));
+ new File(new File(stagingDirectory, DATA_SET_CODE), "sub_data_set_1"));
one(openBisService).performEntityOperations(with(atomicatOperationDetails));
will(returnValue(new AtomicEntityOperationResult()));
}
@@ -402,7 +397,8 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
assertEquals(1, MockStorageProcessor.instance.calledCommitCount);
assertEquals(datasetLocation, MockStorageProcessor.instance.rootDirs.get(0));
File incomingDir = MockStorageProcessor.instance.incomingDirs.get(0);
- assertEquals(new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"), incomingDir);
+ assertEquals(new File(new File(stagingDirectory, DATA_SET_CODE), "sub_data_set_1"),
+ incomingDir);
context.assertIsSatisfied();
}
@@ -412,8 +408,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
setUpHomeDataBaseExpectations();
Properties properties =
createThreadPropertiesRelativeToScriptsFolder("transaction-with-new-sample.py");
- final File stagingDir = new File(workingDirectory, "staging");
- properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, false, true);
createData();
final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicatOperationDetails =
@@ -431,7 +425,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
will(returnValue(SAMPLE_PERM_ID));
one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
- new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"));
+ new File(new File(stagingDirectory, DATA_SET_CODE), "sub_data_set_1"));
one(openBisService).performEntityOperations(with(atomicatOperationDetails));
will(returnValue(new AtomicEntityOperationResult()));
}
@@ -475,7 +469,8 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
assertEquals(1, MockStorageProcessor.instance.calledCommitCount);
assertEquals(datasetLocation, MockStorageProcessor.instance.rootDirs.get(0));
File incomingDir = MockStorageProcessor.instance.incomingDirs.get(0);
- assertEquals(new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"), incomingDir);
+ assertEquals(new File(new File(stagingDirectory, DATA_SET_CODE), "sub_data_set_1"),
+ incomingDir);
context.assertIsSatisfied();
}
@@ -485,8 +480,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
setUpHomeDataBaseExpectations();
Properties properties =
createThreadPropertiesRelativeToScriptsFolder("transaction-with-new-material.py");
- final File stagingDir = new File(workingDirectory, "staging");
- properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, false, true);
createData();
@@ -506,7 +499,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
will(returnValue(experiment));
one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
- new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"));
+ new File(new File(stagingDirectory, DATA_SET_CODE), "sub_data_set_1"));
one(openBisService).performEntityOperations(with(atomicatOperationDetails));
will(returnValue(new AtomicEntityOperationResult()));
}
@@ -544,8 +537,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
setUpHomeDataBaseExpectations();
Properties properties =
createThreadPropertiesRelativeToScriptsFolder("transaction-with-dataset-update.py");
- final File stagingDir = new File(workingDirectory, "staging");
- properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, false, true);
createData();
@@ -572,7 +563,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
will(returnValue(containerDataSet));
one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
- new File(new File(stagingDir, DATA_SET_CODE), "data_set"));
+ new File(new File(stagingDirectory, DATA_SET_CODE), "data_set"));
one(openBisService).performEntityOperations(with(atomicOperationDetails));
will(returnValue(new AtomicEntityOperationResult()));