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Commit 9bb94762 authored by felmer's avatar felmer
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LMS-1612 delete already registered data sets in case of an exception 

SVN: 16980
parent 03ff7663
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eu_basysbio/etc/service.properties
+ 3
− 1
View file @ 9bb94762
......@@ -12,6 +12,8 @@ commandqueue-dir =
# Port
port = 8890
use-ssl = false
# Session timeout in minutes
session-timeout = 720
......@@ -98,7 +100,7 @@ quiet-period = 10
maintenance-plugins = data-set-clean-up
data-set-clean-up.class = ch.systemsx.cisd.etlserver.plugins.DataSetDeletionMaintenanceTask
data-set-clean-up.interval = 30
data-set-clean-up.interval = 300
data-set-clean-up.data-source = data-source
post-registration-upload.class = eu.basysbio.cisd.dss.PostRegistrationDatabaseUploadTask
......
eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandler.java
+ 44
− 19
View file @ 9bb94762
......@@ -27,6 +27,7 @@ import org.apache.log4j.Logger;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.Constants;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.mail.IMailClient;
......@@ -116,12 +117,13 @@ public class TimeSeriesAndTimePointDataSetHandler implements IDataSetHandler
count++;
}
void logAndSendOptinallyAnEMail(Logger logger, IMailClient mailClient, boolean sendEMail)
void logSendEMailAndHandlerError(Logger logger, IMailClient mailClient, boolean sendEMail)
{
if (count < numberOfDerivedDataSets)
{
operationLog.error("Only " + count + " " + type.name + " data sets instead of "
+ numberOfDerivedDataSets + " have been registered.");
int numberOfFailures = numberOfDerivedDataSets - count;
operationLog.error(numberOfFailures + " " + type.name
+ " data sets couldn't be registered.");
if (sendEMail)
{
String subject =
......@@ -130,14 +132,16 @@ public class TimeSeriesAndTimePointDataSetHandler implements IDataSetHandler
Constants.DATE_FORMAT.get().format(
new Date(timeProvider.getTimeInMilliseconds()));
String message =
"Uploading of data set '" + dataSetFileName + "' failed because only "
+ count + " of " + numberOfDerivedDataSets + " " + type.name
+ " data sets could be registered in openBIS.\n\n"
"Uploading of data set '" + dataSetFileName + "' failed because "
+ numberOfFailures + " of " + numberOfDerivedDataSets + " "
+ type.name + " data sets couldn't be registered.\n\n"
+ "Please, contact the help desk for support: "
+ HELPDESK_EMAIL + "\n(Time stamp of failure: " + timeStamp
+ ")";
mailClient.sendMessage(subject, message, null, null, userEMail, HELPDESK_EMAIL);
}
throw new UserFailureException("Not all data sets could be registered. "
+ "For more details see error messages in the log.");
} else
{
if (count > 0 && operationLog.isInfoEnabled())
......@@ -181,10 +185,13 @@ public class TimeSeriesAndTimePointDataSetHandler implements IDataSetHandler
private final ITimeProvider timeProvider;
private final IEncapsulatedOpenBISService service;
public TimeSeriesAndTimePointDataSetHandler(Properties parentProperties,
IDataSetHandler delegator, IEncapsulatedOpenBISService openbisService)
{
this.delegator = delegator;
this.service = openbisService;
this.mailClient = new MailClient(parentProperties);
Properties specificProperties =
ExtendedProperties.getSubset(parentProperties,
......@@ -198,11 +205,13 @@ public class TimeSeriesAndTimePointDataSetHandler implements IDataSetHandler
}
@Private
TimeSeriesAndTimePointDataSetHandler(IDataSetHandler delegator, IMailClient mailClient,
TimeSeriesAndTimePointDataSetHandler(IDataSetHandler delegator,
IEncapsulatedOpenBISService openbisService, IMailClient mailClient,
IDataSetHandler timePointDataSetHandler, File timePointDataSetFolder,
ITimeProvider timeProvider)
{
this.delegator = delegator;
service = openbisService;
this.mailClient = mailClient;
this.timePointDataSetHandler = timePointDataSetHandler;
this.timePointDataSetFolder = timePointDataSetFolder;
......@@ -217,20 +226,36 @@ public class TimeSeriesAndTimePointDataSetHandler implements IDataSetHandler
boolean successful = result.isEmpty() == false;
if (successful)
{
DataSetInformation dataSetInformation = result.get(0);
MessageBuilder builder =
try
{
DataSetInformation dataSetInformation = result.get(0);
MessageBuilder builder =
new MessageBuilder(dataSetInformation.tryGetUploadingUserEmail(), timeProvider);
builder.setDataSetFileName(dataSet);
File[] files = timePointDataSetFolder.listFiles();
handleDerivedDataSets(files, TypeOfDerivedDataSet.TIME_POINT, timePointDataSetHandler,
dataSetInfos, builder);
files = dataSet.getParentFile().listFiles(LCA_MIC_TIME_SERIES_FILE_FILTER);
handleDerivedDataSets(files, TypeOfDerivedDataSet.LCA_MIC_TIME_SERIES, delegator,
dataSetInfos, builder);
DataSetType dataSetType = dataSetInformation.getDataSetType();
boolean lcaMicTimeSeries =
builder.setDataSetFileName(dataSet);
File[] files = timePointDataSetFolder.listFiles();
handleDerivedDataSets(files, TypeOfDerivedDataSet.TIME_POINT, timePointDataSetHandler,
dataSetInfos, builder);
files = dataSet.getParentFile().listFiles(LCA_MIC_TIME_SERIES_FILE_FILTER);
handleDerivedDataSets(files, TypeOfDerivedDataSet.LCA_MIC_TIME_SERIES, delegator,
dataSetInfos, builder);
DataSetType dataSetType = dataSetInformation.getDataSetType();
boolean lcaMicTimeSeries =
dataSetType.getCode().equals(DataSetHandler.LCA_MIC_TIME_SERIES);
builder.logAndSendOptinallyAnEMail(operationLog, mailClient, lcaMicTimeSeries == false);
builder.logSendEMailAndHandlerError(operationLog, mailClient, lcaMicTimeSeries == false);
} catch (RuntimeException ex)
{
// Data sets are deleted in reverse order because of possible parent-child relationships.
for (int i = dataSetInfos.size() - 1; i >= 0; i--)
{
String dataSetCode = dataSetInfos.get(i).getDataSetCode();
if (operationLog.isInfoEnabled())
{
operationLog.info("Delete data set " + dataSetCode);
}
service.deleteDataSet(dataSetCode, "Rollback registration");
}
throw ex;
}
}
return dataSetInfos;
}
......
eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandlerTest.java
+ 42
− 12
View file @ 9bb94762
......@@ -29,17 +29,20 @@ import org.hamcrest.collection.IsArray;
import org.hamcrest.core.IsNull;
import org.jmock.Expectations;
import org.jmock.Mockery;
import org.jmock.Sequence;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogInitializer;
import ch.systemsx.cisd.common.mail.From;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.utilities.ITimeProvider;
import ch.systemsx.cisd.etlserver.IDataSetHandler;
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;
......@@ -85,6 +88,8 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
private File dropBox;
private File timePointFolder;
private ITimeProvider timeProvider;
private IEncapsulatedOpenBISService service;
private Sequence sequence;
@BeforeMethod
public void beforeMethod() throws Exception
......@@ -92,7 +97,9 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
super.setUp();
LogInitializer.init();
context = new Mockery();
sequence = context.sequence("sequence");
delegator = context.mock(IDataSetHandler.class, "delegator");
service = context.mock(IEncapsulatedOpenBISService.class);
timePointDataSetHandler = context.mock(IDataSetHandler.class, "timePointDataSetHandler");
mailClient = context.mock(IMailClient.class);
timeProvider = context.mock(ITimeProvider.class);
......@@ -100,7 +107,7 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
timePointFolder = new File(workingDirectory, "time-point-folder");
timePointFolder.mkdirs();
handler =
new TimeSeriesAndTimePointDataSetHandler(delegator, mailClient,
new TimeSeriesAndTimePointDataSetHandler(delegator, service, mailClient,
timePointDataSetHandler, timePointFolder, timeProvider);
}
......@@ -177,13 +184,15 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
final File tp2 = new File(timePointFolder, "tp2");
tp2.createNewFile();
final DataSetInformation ds2 = new DataSetInformation();
ds2.setDataSetCode("ds2");
final DataSetInformation dataSetInformation = new DataSetInformation();
dataSetInformation.setDataSetCode("ds1");
dataSetInformation.setUploadingUserEmail("john.doe@abc.de");
dataSetInformation.setDataSetType(new DataSetType(DataSetHandler.TIME_SERIES));
String expectedSubject = "BaSysBio: Failed uploading of data set 'drop-box'";
String expectedMessage =
"Uploading of data set 'drop-box' failed "
+ "because only 1 of 2 time point data sets could be registered in openBIS.\n\n"
+ "because 1 of 2 time point data sets couldn't be registered.\n\n"
+ "Please, contact the help desk for support: " + HELPDESK_EMAIL + "\n"
+ "(Time stamp of failure: 1970-01-01 01:01:14 +0100)";
prepareSendingEMail(expectedSubject, expectedMessage, dataSetInformation, true);
......@@ -201,14 +210,24 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
one(timeProvider).getTimeInMilliseconds();
will(returnValue(42 * 42 * 42L));
one(service).deleteDataSet("ds2", "Rollback registration");
inSequence(sequence);
one(service).deleteDataSet("ds1", "Rollback registration");
inSequence(sequence);
}
});
List<DataSetInformation> dataSets = handler.handleDataSet(dropBox);
try
{
handler.handleDataSet(dropBox);
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
assertEquals("Not all data sets could be registered. "
+ "For more details see error messages in the log.", ex.getMessage());
}
assertEquals(2, dataSets.size());
assertSame(dataSetInformation, dataSets.get(0));
assertSame(ds2, dataSets.get(1));
context.assertIsSatisfied();
}
......@@ -220,13 +239,15 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
final File tp2 = new File(workingDirectory, DataSetHandler.LCA_MIC_TIME_SERIES + "2");
tp2.createNewFile();
final DataSetInformation ds2 = new DataSetInformation();
ds2.setDataSetCode("ds2");
final DataSetInformation dataSetInformation = new DataSetInformation();
dataSetInformation.setDataSetCode("ds1");
dataSetInformation.setUploadingUserEmail("john.doe@abc.de");
dataSetInformation.setDataSetType(new DataSetType(DataSetHandler.LCA_MIC));
String expectedSubject = "BaSysBio: Failed uploading of data set 'drop-box'";
String expectedMessage =
"Uploading of data set 'drop-box' failed "
+ "because only 1 of 2 LCA MIC time series data sets could be registered in openBIS.\n\n"
+ "because 1 of 2 LCA MIC time series data sets couldn't be registered.\n\n"
+ "Please, contact the help desk for support: " + HELPDESK_EMAIL + "\n"
+ "(Time stamp of failure: 1970-01-01 01:01:14 +0100)";
prepareSendingEMail(expectedSubject, expectedMessage, dataSetInformation, true);
......@@ -244,14 +265,23 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
one(timeProvider).getTimeInMilliseconds();
will(returnValue(42 * 42 * 42L));
one(service).deleteDataSet("ds2", "Rollback registration");
inSequence(sequence);
one(service).deleteDataSet("ds1", "Rollback registration");
inSequence(sequence);
}
});
List<DataSetInformation> dataSets = handler.handleDataSet(dropBox);
assertEquals(2, dataSets.size());
assertSame(dataSetInformation, dataSets.get(0));
assertSame(ds2, dataSets.get(1));
try
{
handler.handleDataSet(dropBox);
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
assertEquals("Not all data sets could be registered. "
+ "For more details see error messages in the log.", ex.getMessage());
}
context.assertIsSatisfied();
}
......
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