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Commit d0e6e839 authored by cramakri's avatar cramakri
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LMS-1940 Refactorings + skip empty lines in the control file. 

SVN: 19211
parent 8867d292
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datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/AbstractSampleAndDataSetProcessor.java
+ 5
− 0
View file @ d0e6e839
......@@ -47,4 +47,9 @@ public class AbstractSampleAndDataSetProcessor
globalState.getOperationLog().error(message);
}
protected void logError(String message, Throwable e)
{
globalState.getOperationLog().error(message, e);
}
}
\ No newline at end of file
datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
+ 2
− 3
View file @ d0e6e839
......@@ -210,7 +210,7 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
(isSampleKnown()) ? "Updated sample, registered data set %s"
: "Registered sample/data set pair %s";
String message = String.format(messageFormat, sampleDataSetPair);
globalState.getOperationLog().info(message);
logInfo(message);
}
public void registerDataSetInApplicationServer(NewExternalData data) throws Throwable
......@@ -243,8 +243,7 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
throw e;
} catch (Throwable e)
{
globalState.getOperationLog().error(
"Could not register " + sampleDataSetPair + " in openBIS", e);
logError("Could not register " + sampleDataSetPair + " in openBIS", e);
didSucceed = false;
failureException = new RegistrationErrorWrapper(e);
throw e;
......
datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPair.java
+ 1
− 1
View file @ d0e6e839
......@@ -92,7 +92,7 @@ public class SampleDataSetPair
return dataSetInformation;
}
@BeanProperty(label = SAMPLE_IDENTIFIER, optional = false)
@BeanProperty(label = SAMPLE_IDENTIFIER, optional = true)
public void setSampleIdentifier(String sampleIdentifier)
{
this.newSample.setIdentifier(sampleIdentifier);
......
datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactory.java
+ 16
− 0
View file @ d0e6e839
......@@ -157,6 +157,22 @@ class SampleDataSetPairParserObjectFactory extends AbstractParserObjectFactory<S
@Override
public SampleDataSetPair createObject(final String[] lineTokens) throws ParserException
{
boolean allTokensAreEmpty = true;
for (String token : lineTokens)
{
if (token.trim().length() > 0)
{
allTokensAreEmpty = false;
break;
}
}
// Skip empty lines
if (allTokensAreEmpty)
{
return null;
}
final SampleDataSetPair newSampleDataSet = super.createObject(lineTokens);
newSampleDataSet.setTokens(lineTokens);
setProperties(newSampleDataSet, lineTokens);
......
datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
+ 114
− 18
View file @ d0e6e839
......@@ -94,6 +94,43 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
context.assertIsSatisfied();
}
@Test
public void testRegisteringMissingSampleIdentifier()
{
final RecordingMatcher<DataSetInformation> dataSetInfoMatcher =
new RecordingMatcher<DataSetInformation>();
final RecordingMatcher<NewSample> newSampleMatcher = new RecordingMatcher<NewSample>();
setupOpenBisExpectations();
NewExternalData externalData = setupDataSetHandlerExpectations(dataSetInfoMatcher, 2);
setupUpdateSampleExistsExpectations("S1", false);
setupUpdateSampleExistsExpectations("S3", false);
setupRegisterSampleAndDataSetExpectations(externalData, newSampleMatcher, 2);
// Error email on the line with the missing sample identifier
final RecordingMatcher<DataHandler> attachmentMatcher = new RecordingMatcher<DataHandler>();
final RecordingMatcher<EMailAddress[]> addressesMatcher =
new RecordingMatcher<EMailAddress[]>();
setupPartialSuccessErrorEmailExpectations(attachmentMatcher, addressesMatcher,
"missing-sample-identifier");
File workingCopy = createWorkingCopyOfTestFolder("missing-sample-identifier");
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"
+ "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");
context.assertIsSatisfied();
}
@Test
public void testRegisteringBasicControlFile()
{
......@@ -102,7 +139,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
final RecordingMatcher<NewSample> newSampleMatcher = new RecordingMatcher<NewSample>();
setupOpenBisExpectations();
NewExternalData externalData = setupDataSetHandlerExpectations(dataSetInfoMatcher);
NewExternalData externalData = setupDataSetHandlerExpectations(dataSetInfoMatcher, 3);
setupUpdateSampleExistsExpectations("S1", false);
setupUpdateSampleExistsExpectations("S2", false);
setupUpdateSampleExistsExpectations("S3", false);
......@@ -123,6 +160,35 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
context.assertIsSatisfied();
}
@Test
public void testRegisteringWithEmptyLinesInControlFile()
{
final RecordingMatcher<DataSetInformation> dataSetInfoMatcher =
new RecordingMatcher<DataSetInformation>();
final RecordingMatcher<NewSample> newSampleMatcher = new RecordingMatcher<NewSample>();
setupOpenBisExpectations();
NewExternalData externalData = setupDataSetHandlerExpectations(dataSetInfoMatcher, 3);
setupUpdateSampleExistsExpectations("S1", false);
setupUpdateSampleExistsExpectations("S2", false);
setupUpdateSampleExistsExpectations("S3", false);
setupRegisterSampleAndDataSetExpectations(externalData, newSampleMatcher, 3);
File workingCopy = createWorkingCopyOfTestFolder("empty-lines");
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"
+ "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");
context.assertIsSatisfied();
}
@Test
public void testOnlyUpdates()
{
......@@ -132,7 +198,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
new RecordingMatcher<SampleUpdatesDTO>();
setupOpenBisExpectations();
NewExternalData externalData = setupDataSetHandlerExpectations(dataSetInfoMatcher);
NewExternalData externalData = setupDataSetHandlerExpectations(dataSetInfoMatcher, 3);
setupUpdateSampleExistsExpectations("S1", true);
setupUpdateSampleExistsExpectations("S2", true);
setupUpdateSampleExistsExpectations("S3", true);
......@@ -163,7 +229,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
new RecordingMatcher<SampleUpdatesDTO>();
setupOpenBisExpectations();
NewExternalData externalData = setupDataSetHandlerExpectations(dataSetInfoMatcher);
NewExternalData externalData = setupDataSetHandlerExpectations(dataSetInfoMatcher, 3);
setupUpdateSampleExistsExpectations("S1", false);
setupUpdateSampleExistsExpectations("S2", true);
setupUpdateSampleExistsExpectations("S3", false);
......@@ -192,7 +258,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
final RecordingMatcher<EMailAddress[]> addressesMatcher =
new RecordingMatcher<EMailAddress[]>();
setupErrorEmailExpectations(attachmentMatcher, addressesMatcher, "no-control");
setupFailureErrorEmailExpectations(attachmentMatcher, addressesMatcher, "no-control");
File workingCopy = createWorkingCopyOfTestFolder("no-control");
......@@ -218,7 +284,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
final RecordingMatcher<EMailAddress[]> addressesMatcher =
new RecordingMatcher<EMailAddress[]>();
setupErrorEmailExpectations(attachmentMatcher, addressesMatcher, "empty-folder");
setupFailureErrorEmailExpectations(attachmentMatcher, addressesMatcher, "empty-folder");
File workingCopy = createWorkingCopyOfTestFolder("empty-folder");
......@@ -276,7 +342,8 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
return workingCopy;
}
private void setupErrorEmailExpectations(final RecordingMatcher<DataHandler> attachmentMatcher,
private void setupFailureErrorEmailExpectations(
final RecordingMatcher<DataHandler> attachmentMatcher,
final RecordingMatcher<EMailAddress[]> addressesMatcher, final String folderName)
{
context.checking(new Expectations()
......@@ -287,16 +354,45 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
admin.setUserId("test");
one(openbisService).listAdministrators();
will(returnValue(Collections.singletonList(admin)));
one(mailClient)
.sendEmailMessageWithAttachment(
with("Sample / Data Set Registration Error -- targets/unit-test-wd/ch.systemsx.cisd.etlserver.entityregistration.SampleAndDatasetRegistrationHandlerTest/"
+ folderName),
with("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."),
with("errors.txt"), with(attachmentMatcher),
with(new IsNull<EMailAddress>()),
with(new IsNull<EMailAddress>()), with(addressesMatcher));
}
});
setupErrorEmailExpectations(
attachmentMatcher,
addressesMatcher,
"Sample / Data Set Registration Error -- targets/unit-test-wd/ch.systemsx.cisd.etlserver.entityregistration.SampleAndDatasetRegistrationHandlerTest/"
+ folderName,
"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);
}
private void setupPartialSuccessErrorEmailExpectations(
final RecordingMatcher<DataHandler> attachmentMatcher,
final RecordingMatcher<EMailAddress[]> addressesMatcher, final String folderName)
{
setupErrorEmailExpectations(
attachmentMatcher,
addressesMatcher,
"Sample / Data Set Registration Error -- targets/unit-test-wd/ch.systemsx.cisd.etlserver.entityregistration.SampleAndDatasetRegistrationHandlerTest/"
+ folderName + "/control.tsv",
"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.",
folderName);
}
private void setupErrorEmailExpectations(final RecordingMatcher<DataHandler> attachmentMatcher,
final RecordingMatcher<EMailAddress[]> addressesMatcher, final String emailSubject,
final String emailBody, final String folderName)
{
context.checking(new Expectations()
{
{
one(mailClient).sendEmailMessageWithAttachment(with(emailSubject),
with(emailBody), with("errors.txt"), with(attachmentMatcher),
with(new IsNull<EMailAddress>()), with(new IsNull<EMailAddress>()),
with(addressesMatcher));
}
});
}
......@@ -316,7 +412,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
}
private NewExternalData setupDataSetHandlerExpectations(
final RecordingMatcher<DataSetInformation> dataSetInfoMatcher)
final RecordingMatcher<DataSetInformation> dataSetInfoMatcher, final int count)
{
final NewExternalData externalData = new NewExternalData();
context.checking(new Expectations()
......@@ -337,7 +433,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
will(returnValue(exp));
}
exactly(3).of(delegator).handleDataSet(with(fileMatcher),
exactly(count).of(delegator).handleDataSet(with(fileMatcher),
with(dataSetInfoMatcher), with(registratorMatcher));
will(new CustomAction("Call registrator")
{
......
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