From d6f4d48e47b83680d1849f4973f2d5ddf7abbb2f Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Tue, 5 Jul 2011 14:48:45 +0000
Subject: [PATCH] [LMS-2350] minor: working unit test
SVN: 21996
---
.../dss/test/SanofiDropboxJythonTest.java | 170 ++++++++++++++++--
sanofi/sourceTest/python/unit-tests.py | 11 --
2 files changed, 156 insertions(+), 25 deletions(-)
delete mode 100644 sanofi/sourceTest/python/unit-tests.py
diff --git a/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java b/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java
index 36d0b06d103..4aa95aad3e9 100644
--- a/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java
+++ b/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonTest.java
@@ -33,12 +33,20 @@ import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.eodsql.MockDataSet;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.mail.From;
import ch.systemsx.cisd.common.test.AssertionUtil;
import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.AbstractJythonDataSetHandlerTest;
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationService;
+import ch.systemsx.cisd.etlserver.registrator.DataSetStorageAlgorithmRunner;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
+import ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
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;
@@ -52,6 +60,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuil
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@@ -92,11 +101,27 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
private static final String COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND";
- private static final String DATASET_DIR_NAME = "batchNr_plateCode.variant_2011.06.28";
+ private static final String IMAGE_DATA_SET_DIR_NAME = "batchNr_plateCode.variant_2011.07.05";
- private static final String DATA_SET_CODE = "data-set-code";
+ private static final String OVERLAYS_DATA_SET_DIR_NAME = "overlays";
- private static final DataSetType DATA_SET_TYPE = new DataSetType("HCS_IMAGE_RAW");
+ private static final String ANALYSIS_DATA_SET_FILE_NAME = "LC80463-RS101117.xml";
+
+ private static final String IMAGE_DATA_SET_CODE = "data-set-code";
+
+ private static final DataSetType IMAGE_DATA_SET_TYPE = new DataSetType("HCS_IMAGE_RAW");
+
+ private static final String IMAGE_DATA_SET_BATCH_PROP = "ACQUISITION_BATCH";
+
+ private static final String OVERLAY_DATA_SET_CODE = "overlay-data-set-code";
+
+ private static final DataSetType OVERLAY_DATA_SET_TYPE = new DataSetType(
+ "HCS_IMAGE_SEGMENTATION");
+
+ private static final String ANALYSIS_DATA_SET_CODE = "analysis-data-set-code";
+
+ private static final DataSetType ANALYSIS_DATA_SET_TYPE = new DataSetType(
+ "HCS_ANALYSIS_WELL_FEATURES");
private static final String EXPERIMENT_IDENTIFIER = "/SANOFI/PROJECT/EXP";
private static final String PLATE_IDENTIFIER = "/SANOFI/TEST-PLATE";
@@ -112,7 +137,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
public void testHappyCaseWithLibraryCreation() throws IOException
{
setUpHomeDataBaseExpectations();
- Properties properties = createThreadPropertiesRelativeToScriptsFolder("sanofi-dropbox.py");
+ Properties properties =
+ createThreadPropertiesRelativeToScriptsFolder("dropbox-all-in-one-with-library.py");
createHandler(properties, false, true);
createData();
@@ -146,17 +172,36 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
will(returnValue("well-permId"));
one(openBisService).createDataSetCode();
- will(returnValue(DATA_SET_CODE));
+ will(returnValue(IMAGE_DATA_SET_CODE));
- one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
- new File(new File(stagingDirectory, DATA_SET_CODE), DATASET_DIR_NAME));
+ one(openBisService).createDataSetCode();
+ will(returnValue(OVERLAY_DATA_SET_CODE));
+
+ one(openBisService).createDataSetCode();
+ will(returnValue(ANALYSIS_DATA_SET_CODE));
+
+ one(dataSetValidator).assertValidDataSet(
+ IMAGE_DATA_SET_TYPE,
+ new File(new File(stagingDirectory, IMAGE_DATA_SET_CODE),
+ IMAGE_DATA_SET_DIR_NAME));
+
+ one(dataSetValidator).assertValidDataSet(
+ OVERLAY_DATA_SET_TYPE,
+ new File(new File(stagingDirectory, OVERLAY_DATA_SET_CODE),
+ OVERLAYS_DATA_SET_DIR_NAME));
+
+ one(dataSetValidator).assertValidDataSet(
+ ANALYSIS_DATA_SET_TYPE,
+ new File(new File(stagingDirectory, ANALYSIS_DATA_SET_CODE),
+ ANALYSIS_DATA_SET_FILE_NAME));
SampleIdentifier sampleIdentifier =
SampleIdentifierFactory.parse(plate.getIdentifier());
- one(openBisService).tryGetSampleWithExperiment(sampleIdentifier);
+ exactly(4).of(openBisService).tryGetSampleWithExperiment(sampleIdentifier);
will(returnValue(plate));
- one(openBisService).getPropertiesOfTopSampleRegisteredFor(sampleIdentifier);
+ exactly(3).of(openBisService).getPropertiesOfTopSampleRegisteredFor(
+ sampleIdentifier);
will(returnValue(new IEntityProperty[0]));
one(openBisService).performEntityOperations(with(atomicatOperationDetails));
@@ -187,11 +232,20 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
List<? extends NewExternalData> dataSetsRegistered =
atomicatOperationDetails.recordedObject().getDataSetRegistrations();
- assertEquals(1, dataSetsRegistered.size());
+ assertEquals(3, dataSetsRegistered.size());
+
+ NewExternalData imageDataSet = dataSetsRegistered.get(0);
+ assertEquals(IMAGE_DATA_SET_CODE, imageDataSet.getCode());
+ assertEquals(IMAGE_DATA_SET_TYPE, imageDataSet.getDataSetType());
+ assertHasProperty(imageDataSet, IMAGE_DATA_SET_BATCH_PROP, "batchNr");
+
+ NewExternalData overlayDataSet = dataSetsRegistered.get(1);
+ assertEquals(OVERLAY_DATA_SET_CODE, overlayDataSet.getCode());
+ assertEquals(OVERLAY_DATA_SET_TYPE, overlayDataSet.getDataSetType());
- NewExternalData dataSet = dataSetsRegistered.get(0);
- assertEquals(DATA_SET_CODE, dataSet.getCode());
- assertEquals(DATA_SET_TYPE, dataSet.getDataSetType());
+ NewExternalData analysisDataSet = dataSetsRegistered.get(2);
+ assertEquals(ANALYSIS_DATA_SET_CODE, analysisDataSet.getCode());
+ assertEquals(ANALYSIS_DATA_SET_TYPE, analysisDataSet.getDataSetType());
AssertionUtil
.assertContains(
@@ -201,6 +255,22 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
context.assertIsSatisfied();
}
+ private void assertHasProperty(NewExternalData dataSet, String propCode, String propValue)
+ {
+ for (NewProperty prop : dataSet.getDataSetProperties())
+ {
+ if (prop.getPropertyCode().equals(propCode))
+ {
+ assertEquals("Invalid value in property " + propCode, propValue, prop.getValue());
+ return;
+ }
+ }
+
+ fail(String.format("No property with code %s was found in data set %s", propCode,
+ dataSet.getCode()));
+
+ }
+
private void assertAllSamplesHaveContainer(List<NewSample> newSamples,
String containerIdentifier)
{
@@ -294,7 +364,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
private void createData() throws IOException
{
- File dataDirectory = new File("./sourceTest/examples/" + DATASET_DIR_NAME);
+ File dataDirectory = new File("./sourceTest/resources/" + IMAGE_DATA_SET_DIR_NAME);
FileUtils.copyDirectoryToDirectory(dataDirectory, workingDirectory);
incomingDataSetFile = new File(workingDirectory, dataDirectory.getName());
@@ -339,4 +409,76 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
{
return "dist/etc/sanofi-dropbox/";
}
+
+ @Override
+ protected void createHandler(Properties threadProperties, final boolean registrationShouldFail,
+ boolean shouldReThrowException)
+ {
+ TopLevelDataSetRegistratorGlobalState globalState = createGlobalState(threadProperties);
+
+ handler = new TestingPlateDataSetHandler(globalState, registrationShouldFail,
+ shouldReThrowException);
+ }
+
+
+ private class TestingPlateDataSetHandler extends JythonPlateDataSetHandler
+ {
+ private final boolean shouldRegistrationFail;
+
+ private final boolean shouldReThrowRollbackException;
+
+ public TestingPlateDataSetHandler(TopLevelDataSetRegistratorGlobalState globalState,
+ boolean shouldRegistrationFail, boolean shouldReThrowRollbackException)
+ {
+ super(globalState);
+ this.shouldRegistrationFail = shouldRegistrationFail;
+ this.shouldReThrowRollbackException = shouldReThrowRollbackException;
+ }
+
+ @Override
+ public void registerDataSetInApplicationServer(DataSetInformation dataSetInformation,
+ NewExternalData data) throws Throwable
+ {
+ if (shouldRegistrationFail)
+ {
+ throw new UserFailureException("Didn't work.");
+ } else
+ {
+ super.registerDataSetInApplicationServer(dataSetInformation, data);
+ }
+ }
+
+ @Override
+ public void rollback(DataSetRegistrationService<DataSetInformation> service,
+ Throwable throwable)
+ {
+ super.rollback(service, throwable);
+ if (shouldReThrowRollbackException)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(throwable);
+ } else
+ {
+ throwable.printStackTrace();
+ }
+ }
+
+ @Override
+ public void didRollbackTransaction(DataSetRegistrationService<DataSetInformation> service,
+ DataSetRegistrationTransaction<DataSetInformation> transaction,
+ DataSetStorageAlgorithmRunner<DataSetInformation> algorithmRunner,
+ Throwable throwable)
+ {
+ super.didRollbackTransaction(service, transaction, algorithmRunner, throwable);
+
+ if (shouldReThrowRollbackException)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(throwable);
+ } else
+ {
+ throwable.printStackTrace();
+ }
+ }
+
+ }
+
}
\ No newline at end of file
diff --git a/sanofi/sourceTest/python/unit-tests.py b/sanofi/sourceTest/python/unit-tests.py
deleted file mode 100644
index ac84070940f..00000000000
--- a/sanofi/sourceTest/python/unit-tests.py
+++ /dev/null
@@ -1,11 +0,0 @@
-import unittest
-
-class DropboxUnitTests(unittest.TestCase):
-
- def test_parse_incoming_dir_name(self):
- self.assertEqual(("batchName", "barCode"), parse_incoming_dirname("batchName barCode 2011-06-28"))
- self.assertEqual(("batchName", "barCode"), parse_incoming_dirname("batchName barCode 2011-06-28"))
-
- def test_parse_incoming_dir_name(self):
- self.assertEqual(("batchName", "barCode"), parse_incoming_dirname("batchName barCode 2011-06-28"))
- self.assertEqual(("batchName", "barCode"), parse_incoming_dirname("batchName barCode 2011-06-28"))
\ No newline at end of file
--
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