diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/RegistrationStatus.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/RegistrationStatus.java
new file mode 100644
index 0000000000000000000000000000000000000000..0deef8150bd7d108ea3d3fdd9aed21071cc796f8
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/RegistrationStatus.java
@@ -0,0 +1,76 @@
+package ch.systemsx.cisd.etlserver.entityregistration;
+
+/**
+ * An interface to describe success and errors encountered during registration.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+interface IRegistrationStatus
+{
+ boolean isError();
+
+ Throwable getError();
+
+ String getMessage();
+}
+
+/**
+ * Abstract superclass for success and errors.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+abstract class AbstractRegistrationStatus implements IRegistrationStatus
+{
+ protected AbstractRegistrationStatus()
+ {
+ }
+}
+
+class RegistrationError extends AbstractRegistrationStatus
+{
+ private final Throwable error;
+
+ RegistrationError(Throwable error)
+ {
+ this.error = error;
+ }
+
+ public boolean isError()
+ {
+ return true;
+ }
+
+ public Throwable getError()
+ {
+ return error;
+ }
+
+ public String getMessage()
+ {
+ return error.getMessage();
+ }
+}
+
+class RegistrationSuccess extends AbstractRegistrationStatus
+{
+ RegistrationSuccess(String[] registeredMetadata)
+ {
+ }
+
+ public boolean isError()
+ {
+ return false;
+ }
+
+ public Throwable getError()
+ {
+ assert false : "getError() should not be called on a success object";
+
+ return null;
+ }
+
+ public String getMessage()
+ {
+ return "Success";
+ }
+}
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 849cee06646aec971fa63f1d41922ed8f6ca7f9e..5f43a13b6698501657a64c716800d52c362390bd 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
@@ -21,7 +21,9 @@ import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.Reader;
+import java.util.ArrayList;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import javax.activation.DataHandler;
@@ -34,7 +36,6 @@ 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;
@@ -47,10 +48,26 @@ import ch.systemsx.cisd.openbis.generic.shared.parser.GlobalPropertiesLoader;
*/
class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProcessor
{
+ private static final String SUCCESS_FILENAME = "registered.txt";
+
private final File controlFile;
- private final HashMap<SampleDataSetPair, RegistrationErrorWrapper> errorMap =
- new HashMap<SampleDataSetPair, RegistrationErrorWrapper>();
+ private final HashMap<SampleDataSetPair, IRegistrationStatus> errorMap =
+ new HashMap<SampleDataSetPair, IRegistrationStatus>();
+
+ private final HashMap<SampleDataSetPair, IRegistrationStatus> successMap =
+ new HashMap<SampleDataSetPair, IRegistrationStatus>();
+
+ private final HashSet<File> processedDataSetFiles = new HashSet<File>();
+
+ // State that is filled out as a result of processing
+ private ControlFileRegistrationProperties properties;
+
+ private String failureLinesResultSectionOrNull;
+
+ private String unmentionedSubfoldersResultSectionOrNull;
+
+ private String successLinesResultSectionOrNull;
/**
* Utility class for accessing the properties defined in a control file.
@@ -226,8 +243,7 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
logControlFileOverridePropertiesExtracted(overrideProperties);
- ControlFileRegistrationProperties properties =
- new ControlFileRegistrationProperties(overrideProperties, globalState);
+ properties = new ControlFileRegistrationProperties(overrideProperties, globalState);
BisTabFileLoader<SampleDataSetPair> controlFileLoader =
new BisTabFileLoader<SampleDataSetPair>(
@@ -252,7 +268,7 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
throw e;
}
- sendEmailWithErrorMessage(properties, e.getMessage());
+ sendEmailWithErrorMessage(e.getMessage());
return;
} finally
{
@@ -272,26 +288,69 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
sampleDataSet.getDataSetInformation().setUploadingUserId(userId);
SampleAndDataSetRegistrator registrator =
new SampleAndDataSetRegistrator(folder, properties, sampleDataSet);
- RegistrationErrorWrapper resultOrNull = registrator.register();
- if (null != resultOrNull)
+ IRegistrationStatus result = registrator.register();
+ processedDataSetFiles.add(registrator.getDataSetFile());
+ if (result.isError())
{
- errorMap.put(sampleDataSet, resultOrNull);
+ errorMap.put(sampleDataSet, result);
+ } else
+ {
+ successMap.put(sampleDataSet, result);
}
}
- if (false == errorMap.isEmpty())
+
+ sendResultsEmail();
+ }
+
+ private void sendResultsEmail()
+ {
+
+ createFailureLinesSection();
+ createUnmentionedFoldersSection();
+ createSuccessfulLinesSection();
+
+ boolean wasSuccessful = true;
+
+ StringBuilder resultEmail = new StringBuilder();
+ if (null != failureLinesResultSectionOrNull)
+ {
+ resultEmail.append(failureLinesResultSectionOrNull);
+ resultEmail.append("\n");
+ wasSuccessful = false;
+ }
+ if (null != unmentionedSubfoldersResultSectionOrNull)
+ {
+ resultEmail.append(unmentionedSubfoldersResultSectionOrNull);
+ resultEmail.append("\n");
+ wasSuccessful = false;
+ }
+ if (null != successLinesResultSectionOrNull)
{
- sendEmailWithErrorMessage(properties, createErrorMessageFromErrorMap());
+ resultEmail.append(successLinesResultSectionOrNull);
}
+ if (wasSuccessful)
+ {
+ sendEmailWithSuccessMessage(resultEmail.toString());
+ } else
+ {
+ sendEmailWithErrorMessage(resultEmail.toString());
+ }
}
- private String createErrorMessageFromErrorMap()
+ private void createFailureLinesSection()
{
+ if (errorMap.isEmpty())
+ {
+ failureLinesResultSectionOrNull = null;
+ return;
+ }
+
StringBuilder sb = new StringBuilder();
sb.append("Encountered errors in the following lines:\n");
for (SampleDataSetPair pair : errorMap.keySet())
{
- RegistrationErrorWrapper error = errorMap.get(pair);
+ IRegistrationStatus error = errorMap.get(pair);
sb.append("# ");
sb.append(error.getMessage());
sb.append("\n");
@@ -308,26 +367,107 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
}
sb.append("\n");
}
- return sb.toString();
+ failureLinesResultSectionOrNull = sb.toString();
+ }
+
+ private void createUnmentionedFoldersSection()
+ {
+ if (false == globalState.areUnmentionedFoldersAnError())
+ {
+ unmentionedSubfoldersResultSectionOrNull = null;
+ return;
+ }
+ // Make sure all folders were processed
+ ArrayList<File> unprocessedFiles = getUnprocessedDataSetList();
+
+ if (unprocessedFiles.isEmpty())
+ {
+ unmentionedSubfoldersResultSectionOrNull = null;
+ return;
+ }
+
+ StringBuilder sb = new StringBuilder();
+ sb.append("The following subfolders were in the uploaded folder, but were not mentioned in the control file:\n");
+ for (File file : unprocessedFiles)
+ {
+ sb.append(file.getName());
+ sb.append(",");
+ }
+
+ // remove the final comma
+ sb.deleteCharAt(sb.length() - 1);
+
+ unmentionedSubfoldersResultSectionOrNull = sb.toString();
+ }
+
+ private void createSuccessfulLinesSection()
+ {
+ if (errorMap.isEmpty())
+ {
+ successLinesResultSectionOrNull = null;
+ return;
+ }
+
+ StringBuilder sb = new StringBuilder();
+ sb.append("The following lines were successfully registered:\n");
+ for (SampleDataSetPair pair : successMap.keySet())
+ {
+ sb.append("# ");
+ String[] tokens = pair.getTokens();
+ int i = 0;
+ for (String token : tokens)
+ {
+ sb.append(token);
+ if (++i < tokens.length)
+ {
+ sb.append("\t");
+ }
+ }
+ sb.append("\n");
+ }
+ successLinesResultSectionOrNull = sb.toString();
}
- private void logControlFileOverridePropertiesExtracted(ControlFileOverrideProperties properties)
+ private void logControlFileOverridePropertiesExtracted(
+ ControlFileOverrideProperties overrideProperties)
{
String message =
String.format(
"Global properties extracted from file '%s': SAMPLE_TYPE(%s) DATA_SET_TYPE(%s) USER(%s)",
- controlFile.getName(), properties.trySampleType(),
- properties.tryDataSetType(), properties.tryUserString());
+ controlFile.getName(), overrideProperties.trySampleType(),
+ overrideProperties.tryDataSetType(), overrideProperties.tryUserString());
logInfo(message);
}
+ /**
+ * Send an email message to the person who uploaded the file, telling them that everything went
+ * ok.
+ */
+ private void sendEmailWithSuccessMessage(String message)
+ {
+ // Create an email and send it.
+ try
+ {
+ String subject = createSuccessEmailSubject();
+ String content = createSuccessEmailContent();
+ String filename = SUCCESS_FILENAME;
+ EMailAddress recipient = new EMailAddress(properties.getUser().getEmail());
+ DataSource dataSource = new ByteArrayDataSource(message, "text/plain");
+
+ globalState.getMailClient().sendEmailMessageWithAttachment(subject, content, filename,
+ new DataHandler(dataSource), null, null, recipient);
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
/**
* Send an email message to the person who uploaded the file. This method is only called if we
* have a valid email address to contact. Otherwise, errors are forwarded to a higher level for
* handling.
*/
- private void sendEmailWithErrorMessage(ControlFileRegistrationProperties properties,
- String message)
+ private void sendEmailWithErrorMessage(String message)
{
// Log it
logError(message);
@@ -360,4 +500,37 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
.format("Not all samples and data sets specified in the control file, %s, could be registered / updated. The errors are detailed in the attachment. Each faulty line is reproduced, preceded by a comment explaining the cause of the error.",
controlFile);
}
+
+ private String createSuccessEmailSubject()
+ {
+ return String.format("Sample / Data Set Registration Succeeded -- %s", controlFile);
+ }
+
+ private String createSuccessEmailContent()
+ {
+ return String
+ .format("The registration/update of samples and the registration of data sets was successful specified in the control file, %s, was successful.",
+ controlFile);
+ }
+
+ private ArrayList<File> getUnprocessedDataSetList()
+ {
+ File[] files = folder.listFiles();
+ ArrayList<File> unprcessedDataSets = new ArrayList<File>();
+ for (File file : files)
+ {
+ if (controlFile.equals(file))
+ {
+ continue;
+ }
+ // See if it was handled already
+ if (processedDataSetFiles.contains(file))
+ {
+ continue;
+ }
+ unprcessedDataSets.add(file);
+ }
+
+ return unprcessedDataSets;
+ }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationGlobalState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationGlobalState.java
index a33aa4d4c06b1de7533f49ddd2749c78c133bcd2..e384ae0df02c4fb590fcaf913b5f337d3721dd1a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationGlobalState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationGlobalState.java
@@ -58,6 +58,10 @@ class SampleAndDataSetRegistrationGlobalState
private final String controlFilePattern;
+ private final boolean alwaysCleanupAfterProcessing;
+
+ private final boolean unmentionedSubfolderIsFailure;
+
private final Logger operationLog;
private IMailClient mailClient;
@@ -66,7 +70,8 @@ class SampleAndDataSetRegistrationGlobalState
IEncapsulatedOpenBISService openbisService, SpaceIdentifier spaceIdentifierOrNull,
SampleType sampleTypeOrNull, DataSetType dataSetTypeOrNull,
SampleRegistrationMode sampleRegistrationMode, List<String> errorEmailRecipientsOrNull,
- String controlFilePattern, Logger operationLog)
+ String controlFilePattern, boolean alwaysCleanupAfterProcessing,
+ boolean unmentionedSubfolderIsFailure, Logger operationLog)
{
this.delegator = delegator;
this.openbisService = openbisService;
@@ -76,6 +81,8 @@ class SampleAndDataSetRegistrationGlobalState
this.sampleRegistrationMode = sampleRegistrationMode;
this.errorEmailRecipientsOrNull = errorEmailRecipientsOrNull;
this.controlFilePattern = controlFilePattern;
+ this.alwaysCleanupAfterProcessing = alwaysCleanupAfterProcessing;
+ this.unmentionedSubfolderIsFailure = unmentionedSubfolderIsFailure;
this.operationLog = operationLog;
}
@@ -174,4 +181,14 @@ class SampleAndDataSetRegistrationGlobalState
{
return controlFilePattern;
}
+
+ public boolean alwaysCleanUpAfterProcessing()
+ {
+ return alwaysCleanupAfterProcessing;
+ }
+
+ public boolean areUnmentionedFoldersAnError()
+ {
+ return unmentionedSubfolderIsFailure;
+ }
}
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 4919eb8580f53026bdcbe8484152e8181bd8c088..453e1fc896a71219f8f8d6cf5ed635dc5311c873 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
@@ -67,7 +67,13 @@ public class SampleAndDataSetRegistrationHandler implements IDataSetHandlerWithM
static final String CONTROL_FILE_REGEX_PATTERN = "control-file-regex-pattern";
- private static final String DEFAULT_CONTROL_FILE_REGEX_PATTERN = ".*.[Tt][Ss][Vv]";
+ private static final String DEFAULT_CONTROL_FILE_REGEX_PATTERN = ".*\\.[Tt][Ss][Vv]";
+
+ static final String CONTROL_FILE_ALWAYS_CLEANUP_AFTER_PROCESSING =
+ "always-cleanup-after-processing";
+
+ static final String CONTROL_FILE_UNMENTIONED_SUBFOLDER_IS_FAILURE =
+ "unmentioned-subfolder-is-failure";
private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
SampleAndDataSetRegistrationHandler.class);
@@ -134,9 +140,18 @@ public class SampleAndDataSetRegistrationHandler implements IDataSetHandlerWithM
PropertyUtils.getProperty(specificProperties, CONTROL_FILE_REGEX_PATTERN,
DEFAULT_CONTROL_FILE_REGEX_PATTERN);
+ boolean deleteFilesOnFailure =
+ PropertyUtils.getBoolean(specificProperties,
+ CONTROL_FILE_ALWAYS_CLEANUP_AFTER_PROCESSING, true);
+
+ boolean unmentionedSubfolderIsFailure =
+ PropertyUtils.getBoolean(specificProperties,
+ CONTROL_FILE_UNMENTIONED_SUBFOLDER_IS_FAILURE, true);
+
return new SampleAndDataSetRegistrationGlobalState(delegator, service, spaceIdentifier,
sampleTypeOrNull, dataSetTypeOrNull, registrationMode, errorEmailRecipients,
- controlFilePattern, operationLog);
+ controlFilePattern, deleteFilesOnFailure, unmentionedSubfolderIsFailure,
+ operationLog);
}
public void initializeMailClient(IMailClient mailClient)
@@ -158,8 +173,11 @@ public class SampleAndDataSetRegistrationHandler implements IDataSetHandlerWithM
throw new CheckedExceptionTunnel(ex);
} finally
{
- FileOperations.getMonitoredInstanceForCurrentThread().deleteRecursively(file);
- logFileDeletion(file);
+ if (globalState.alwaysCleanUpAfterProcessing())
+ {
+ FileOperations.getMonitoredInstanceForCurrentThread().deleteRecursively(file);
+ logFileDeletion(file);
+ }
}
return createReturnValue();
}
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 66eecad09ae115c9918b4a0199faaea2c010f321..7c6c9215d3f7bf09813da98c38e082fca92662f4 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
@@ -40,57 +40,21 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
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;
// State that is updated during the registration
+
+ // The file/folder to register
+ private File dataSetFile;
+
// The sample, if the sample exists, null otherwise.
private Sample sampleOrNull;
private boolean didSucceed = false;
- private RegistrationErrorWrapper failureException = null;
+ private IRegistrationStatus failureException = null;
SampleAndDataSetRegistrator(File folder, ControlFileRegistrationProperties properties,
SampleDataSetPair sampleDataSetPair)
@@ -105,18 +69,18 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
*
* @return An exception if one was encountered, otherwise null.
*/
- public RegistrationErrorWrapper register()
+ public IRegistrationStatus register()
{
- File dataSetFile = new File(folder, sampleDataSetPair.getFolderName());
+ dataSetFile = new File(folder, sampleDataSetPair.getFolderName());
try
{
- checkDataSetFileNotEmpty(dataSetFile);
+ checkDataSetFileNotEmpty();
checkExperimentExists();
retrieveSampleOrNull();
checkConformanceToMode();
} catch (UserFailureException ex)
{
- return new RegistrationErrorWrapper(ex);
+ return new RegistrationError(ex);
}
if (globalState.getDelegator() instanceof IExtensibleDataSetHandler)
@@ -129,7 +93,22 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
logDataRegistered();
}
}
- return failureException;
+ if (null == failureException)
+ {
+ return new RegistrationSuccess(sampleDataSetPair.getTokens());
+ } else
+ {
+ return failureException;
+ }
+ }
+
+ /**
+ * Return the file that we treat as a data set. This is only valid *after* register has been
+ * called.
+ */
+ public File getDataSetFile()
+ {
+ return dataSetFile;
}
/**
@@ -159,7 +138,7 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
}
}
- private void checkDataSetFileNotEmpty(File dataSetFile)
+ private void checkDataSetFileNotEmpty()
{
if (0 == dataSetFile.list().length)
{
@@ -239,13 +218,13 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
} catch (UserFailureException e)
{
didSucceed = false;
- failureException = new RegistrationErrorWrapper(e);
+ failureException = new RegistrationError(e);
throw e;
} catch (Throwable e)
{
logError("Could not register " + sampleDataSetPair + " in openBIS", e);
didSucceed = false;
- failureException = new RegistrationErrorWrapper(e);
+ failureException = new RegistrationError(e);
throw e;
}
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
index 3897a1727be7e6eca66beb9e6ca9aeb8fcc1be67..305ce74230fef499b7d6a057e42bf5126b1985d3 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
@@ -111,10 +111,10 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
final RecordingMatcher<DataHandler> attachmentMatcher = new RecordingMatcher<DataHandler>();
final RecordingMatcher<EMailAddress[]> addressesMatcher =
new RecordingMatcher<EMailAddress[]>();
- setupPartialSuccessErrorEmailExpectations(attachmentMatcher, addressesMatcher,
- "missing-sample-identifier");
+ final String folderName = "missing-sample-identifier";
+ setupPartialSuccessErrorEmailExpectations(attachmentMatcher, addressesMatcher, folderName);
- File workingCopy = createWorkingCopyOfTestFolder("missing-sample-identifier");
+ File workingCopy = createWorkingCopyOfTestFolder(folderName);
initializeDefaultDataSetHandler();
handler.handleDataSet(workingCopy);
@@ -125,8 +125,44 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
+ "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ "Encountered errors in the following lines:\n"
+ "# Illegal empty identifier\n"
- + "\t/MYSPACE/MYPROJ/EXP2\tVAL11\tVAL21\tVAL31\tFILE_TYPE\tVAL41\tVAL51\tds2/\n";
- checkAppenderContent(logText, "missing-sample-identifier");
+ + "\t/MYSPACE/MYPROJ/EXP2\tVAL11\tVAL21\tVAL31\tFILE_TYPE\tVAL41\tVAL51\tds2/\n\n"
+ + "The following lines were successfully registered:\n"
+ + "# /MYSPACE/S3\t/MYSPACE/MYPROJ/EXP3\tVAL12\tVAL22\tVAL32\tFILE_TYPE\tVAL42\tVAL52\tds3/\n"
+ + "# /MYSPACE/S1\t/MYSPACE/MYPROJ/EXP1\tVAL10\tVAL20\tVAL30\tFILE_TYPE\tVAL40\tVAL50\tds1/\n";
+ checkAppenderContent(logText, folderName);
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testNotAllFoldersMentioned()
+ {
+ final RecordingMatcher<DataSetInformation> dataSetInfoMatcher =
+ new RecordingMatcher<DataSetInformation>();
+ final RecordingMatcher<NewSample> newSampleMatcher = new RecordingMatcher<NewSample>();
+
+ setupOpenBisExpectations();
+ NewExternalData externalData = setupDataSetHandlerExpectations(dataSetInfoMatcher, 1);
+ setupUpdateSampleExistsExpectations("S1", false);
+ setupRegisterSampleAndDataSetExpectations(externalData, newSampleMatcher, 1);
+
+ final String folderName = "not-all-subfolders-mentioned";
+ final RecordingMatcher<DataHandler> attachmentMatcher = new RecordingMatcher<DataHandler>();
+ final RecordingMatcher<EMailAddress[]> addressesMatcher =
+ new RecordingMatcher<EMailAddress[]>();
+ setupPartialSuccessErrorEmailExpectations(attachmentMatcher, addressesMatcher, folderName);
+
+ File workingCopy = createWorkingCopyOfTestFolder(folderName);
+
+ initializeDefaultDataSetHandler();
+ handler.handleDataSet(workingCopy);
+
+ String logText =
+ "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) USER(test@test.test)\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "The following subfolders were in the uploaded folder, but were not mentioned in the control file:\n"
+ + "ds2,ds3\n";
+ checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
}
@@ -145,7 +181,13 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
setupUpdateSampleExistsExpectations("S3", false);
setupRegisterSampleAndDataSetExpectations(externalData, newSampleMatcher, 3);
- File workingCopy = createWorkingCopyOfTestFolder("basic-example");
+ final String folderName = "basic-example";
+ final RecordingMatcher<DataHandler> attachmentMatcher = new RecordingMatcher<DataHandler>();
+ final RecordingMatcher<EMailAddress[]> addressesMatcher =
+ new RecordingMatcher<EMailAddress[]>();
+ setupSuccessEmailExpectations(attachmentMatcher, addressesMatcher, folderName);
+
+ File workingCopy = createWorkingCopyOfTestFolder(folderName);
initializeDefaultDataSetHandler();
handler.handleDataSet(workingCopy);
@@ -155,7 +197,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
+ "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
- checkAppenderContent(logText, "basic-example");
+ checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
}
@@ -174,7 +216,13 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
setupUpdateSampleExistsExpectations("S3", false);
setupRegisterSampleAndDataSetExpectations(externalData, newSampleMatcher, 3);
- File workingCopy = createWorkingCopyOfTestFolder("empty-lines");
+ final String folderName = "empty-lines";
+ final RecordingMatcher<DataHandler> attachmentMatcher = new RecordingMatcher<DataHandler>();
+ final RecordingMatcher<EMailAddress[]> addressesMatcher =
+ new RecordingMatcher<EMailAddress[]>();
+ setupSuccessEmailExpectations(attachmentMatcher, addressesMatcher, folderName);
+
+ File workingCopy = createWorkingCopyOfTestFolder(folderName);
initializeDefaultDataSetHandler();
handler.handleDataSet(workingCopy);
@@ -184,7 +232,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
+ "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
- checkAppenderContent(logText, "empty-lines");
+ checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
}
@@ -204,7 +252,13 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
setupUpdateSampleExistsExpectations("S3", true);
setupUpdateSampleAndRegisterDataSetExpectations(externalData, sampleUpdatesMatcher, 3);
- File workingCopy = createWorkingCopyOfTestFolder("basic-example");
+ final String folderName = "basic-example";
+ final RecordingMatcher<DataHandler> attachmentMatcher = new RecordingMatcher<DataHandler>();
+ final RecordingMatcher<EMailAddress[]> addressesMatcher =
+ new RecordingMatcher<EMailAddress[]>();
+ setupSuccessEmailExpectations(attachmentMatcher, addressesMatcher, folderName);
+
+ File workingCopy = createWorkingCopyOfTestFolder(folderName);
initializeDefaultDataSetHandler();
handler.handleDataSet(workingCopy);
@@ -214,7 +268,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
+ "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
- checkAppenderContent(logText, "basic-example");
+ checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
}
@@ -236,7 +290,14 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
setupRegisterSampleAndDataSetExpectations(externalData, newSampleMatcher, 2);
setupUpdateSampleAndRegisterDataSetExpectations(externalData, sampleUpdatesMatcher, 1);
- File workingCopy = createWorkingCopyOfTestFolder("basic-example");
+ final String folderName = "basic-example";
+
+ final RecordingMatcher<DataHandler> attachmentMatcher = new RecordingMatcher<DataHandler>();
+ final RecordingMatcher<EMailAddress[]> addressesMatcher =
+ new RecordingMatcher<EMailAddress[]>();
+ setupSuccessEmailExpectations(attachmentMatcher, addressesMatcher, folderName);
+
+ File workingCopy = createWorkingCopyOfTestFolder(folderName);
initializeDefaultDataSetHandler();
handler.handleDataSet(workingCopy);
@@ -246,7 +307,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
+ "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
- checkAppenderContent(logText, "basic-example");
+ checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
}
@@ -266,8 +327,8 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
handler.handleDataSet(workingCopy);
String errorText =
- "Folder (no-control) for sample/dataset registration contains no control files matching the configured pattern: .*.[Tt][Ss][Vv].\n"
- + "Folder contents:\n" + "\t.svn\n" + "\tnot-a-tsv.txt\n";
+ "Folder (no-control) for sample/dataset registration contains no control files matching the configured pattern: .*\\.[Tt][Ss][Vv].\n"
+ + "Folder contents:\n" + "\tnot-a-tsv.txt\n";
// Check the log
checkAppenderContent(errorText, "no-control");
@@ -292,8 +353,8 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
handler.handleDataSet(workingCopy);
String errorText =
- "Folder (empty-folder) for sample/dataset registration contains no control files matching the configured pattern: .*.[Tt][Ss][Vv].\n"
- + "Folder contents:\n" + "\t.svn\n";
+ "Folder (empty-folder) for sample/dataset registration contains no control files matching the configured pattern: .*\\.[Tt][Ss][Vv].\n"
+ + "Folder contents:\n";
// Check the log
checkAppenderContent(errorText, "empty-folder");
@@ -339,6 +400,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
File workingCopy = new File(workingDirectory, folderName);
FileOperations.getInstance().copy(dataSetFile, workingCopy);
+ FileOperations.getInstance().deleteRecursively(new File(workingCopy, ".svn"));
return workingCopy;
}
@@ -356,7 +418,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
will(returnValue(Collections.singletonList(admin)));
}
});
- setupErrorEmailExpectations(
+ setupEmailExpectations(
attachmentMatcher,
addressesMatcher,
"Sample / Data Set Registration Error -- targets/unit-test-wd/ch.systemsx.cisd.etlserver.entityregistration.SampleAndDatasetRegistrationHandlerTest/"
@@ -364,14 +426,14 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
"When trying to process the files in the folder, targets/unit-test-wd/ch.systemsx.cisd.etlserver.entityregistration.SampleAndDatasetRegistrationHandlerTest/"
+ folderName
+ ", errors were encountered. These errors are detailed in the attachment.",
- folderName);
+ "errors.txt", folderName);
}
private void setupPartialSuccessErrorEmailExpectations(
final RecordingMatcher<DataHandler> attachmentMatcher,
final RecordingMatcher<EMailAddress[]> addressesMatcher, final String folderName)
{
- setupErrorEmailExpectations(
+ setupEmailExpectations(
attachmentMatcher,
addressesMatcher,
"Sample / Data Set Registration Error -- targets/unit-test-wd/ch.systemsx.cisd.etlserver.entityregistration.SampleAndDatasetRegistrationHandlerTest/"
@@ -379,18 +441,32 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
"Not all samples and data sets specified in the control file, targets/unit-test-wd/ch.systemsx.cisd.etlserver.entityregistration.SampleAndDatasetRegistrationHandlerTest/"
+ folderName
+ "/control.tsv, could be registered / updated. The errors are detailed in the attachment. Each faulty line is reproduced, preceded by a comment explaining the cause of the error.",
+ "errors.txt", folderName);
+ }
+
+ private void setupSuccessEmailExpectations(
+ final RecordingMatcher<DataHandler> attachmentMatcher,
+ final RecordingMatcher<EMailAddress[]> addressesMatcher, final String folderName)
+ {
+ setupEmailExpectations(
+ attachmentMatcher,
+ addressesMatcher,
+ "Sample / Data Set Registration Succeeded -- targets/unit-test-wd/ch.systemsx.cisd.etlserver.entityregistration.SampleAndDatasetRegistrationHandlerTest/"
+ + folderName + "/control.tsv",
+ "The registration/update of samples and the registration of data sets was successful specified in the control file, targets/unit-test-wd/ch.systemsx.cisd.etlserver.entityregistration.SampleAndDatasetRegistrationHandlerTest/"
+ + folderName + "/control.tsv, was successful.", "registered.txt",
folderName);
}
- private void setupErrorEmailExpectations(final RecordingMatcher<DataHandler> attachmentMatcher,
+ private void setupEmailExpectations(final RecordingMatcher<DataHandler> attachmentMatcher,
final RecordingMatcher<EMailAddress[]> addressesMatcher, final String emailSubject,
- final String emailBody, final String folderName)
+ final String emailBody, final String attachmentName, final String folderName)
{
context.checking(new Expectations()
{
{
one(mailClient).sendEmailMessageWithAttachment(with(emailSubject),
- with(emailBody), with("errors.txt"), with(attachmentMatcher),
+ with(emailBody), with(attachmentName), with(attachmentMatcher),
with(new IsNull<EMailAddress>()), with(new IsNull<EMailAddress>()),
with(addressesMatcher));
}
@@ -427,7 +503,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
ExperimentIdentifier experimentId =
new ExperimentIdentifier(DatabaseInstanceIdentifier.HOME,
SPACE_CODE, "MYPROJ", "EXP" + i);
- oneOf(openbisService).tryToGetExperiment(experimentId);
+ allowing(openbisService).tryToGetExperiment(experimentId);
Experiment exp = new Experiment();
exp.setIdentifier(experimentId.toString());
will(returnValue(exp));
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/not-all-subfolders-mentioned/control.tsv b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/not-all-subfolders-mentioned/control.tsv
index a8d70ccf5927b1d1155673eb9c0f4d2722d2d386..7c75791bb13500e9f02aa6bf3df4d88ba5e74cc3 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/not-all-subfolders-mentioned/control.tsv
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/not-all-subfolders-mentioned/control.tsv
@@ -7,5 +7,4 @@
# Data
S_identifier S_experiment S_PROP1 S_PROP2 S_PROP3 D_file_type D_PROP1 D_PROP2 FOLDER
/MYSPACE/S1 /MYSPACE/MYPROJ/EXP1 VAL10 VAL20 VAL30 FILE_TYPE VAL40 VAL50 ds1/
-/MYSPACE/S2 /MYSPACE/MYPROJ/EXP2 VAL11 VAL21 VAL31 FILE_TYPE VAL41 VAL51 ds2/
-/MYSPACE/S3 /MYSPACE/MYPROJ/EXP3 VAL12 VAL22 VAL32 FILE_TYPE VAL42 VAL52 ds3/
+