From d4f5f00e065ee879f1d63d6cd6a8fe1163925e2d Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Wed, 13 Jul 2011 09:30:27 +0000
Subject: [PATCH] [LMS-2332] added unit test to verify creation of wells with
non-unique materials
SVN: 22111
---
.../dss/test/SanofiDropboxJythonTest.java | 103 +++++++++++++++++-
1 file changed, 101 insertions(+), 2 deletions(-)
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 90990f83ae0..874f27540ea 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
@@ -57,6 +57,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
@@ -393,6 +394,93 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
context.assertIsSatisfied();
}
+ @Test
+ public void testHappyCaseWithLibraryCreationAndNonUniqueMaterials() throws IOException
+ {
+ createDataSetHandler(false, true);
+ final Sample plate = plateWithLibTemplateAndGeometry("0.75\tH\n54.12\tL", "8_WELLS_2X4");
+
+ final MockDataSet<Map<String, Object>> queryResult = new MockDataSet<Map<String, Object>>();
+ queryResult.add(createQueryResult("A1", "material-1"));
+ queryResult.add(createQueryResult("B1", "material-1"));
+
+ setDataSetExpectations();
+ context.checking(new Expectations()
+ {
+ {
+ one(dataSourceQueryService).select(with(any(String.class)),
+ with(any(String.class)), with(anything()));
+ will(returnValue(queryResult));
+
+ one(openBisService).listMaterials(with(materialCriteria), with(equal(true)));
+ will(returnValue(Collections.emptyList()));
+
+ exactly(4).of(openBisService).createPermId();
+ will(returnValue("well-permId"));
+
+ SampleIdentifier sampleIdentifier =
+ SampleIdentifierFactory.parse(plate.getIdentifier());
+ exactly(4).of(openBisService).tryGetSampleWithExperiment(sampleIdentifier);
+ will(returnValue(plate));
+
+ exactly(3).of(openBisService).getPropertiesOfTopSampleRegisteredFor(
+ sampleIdentifier);
+ will(returnValue(new IEntityProperty[0]));
+
+ one(openBisService).performEntityOperations(with(atomicatOperationDetails));
+ will(returnValue(new AtomicEntityOperationResult()));
+
+ one(mailClient).sendMessage(with(any(String.class)), with(email),
+ with(aNull(String.class)), with(any(From.class)),
+ with(equal(EXPERIMENT_RECIPIENTS)));
+ }
+ });
+
+ handler.handle(markerFile);
+
+ assertEquals(MATERIAL_TYPE, materialCriteria.recordedObject().tryGetMaterialType()
+ .getCode());
+ assertEquals(true, queryResult.hasCloseBeenInvoked());
+
+ List<NewSample> registeredSamples =
+ atomicatOperationDetails.recordedObject().getSampleRegistrations();
+
+ assertEquals(4, registeredSamples.size());
+ assertAllSamplesHaveContainer(registeredSamples, plate.getIdentifier());
+ assertCompoundWell(registeredSamples, "A1", "0.75", "material-1");
+ assertPositiveControl(registeredSamples, "A2");
+ assertCompoundWell(registeredSamples, "B1", "54.12", "material-1");
+
+ List<? extends NewExternalData> dataSetsRegistered =
+ atomicatOperationDetails.recordedObject().getDataSetRegistrations();
+ 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 analysisDataSet = dataSetsRegistered.get(2);
+ assertEquals(ANALYSIS_DATA_SET_CODE, analysisDataSet.getCode());
+ assertEquals(ANALYSIS_DATA_SET_TYPE, analysisDataSet.getDataSetType());
+
+ Map<String, List<NewMaterial>> materialsRegistered =
+ atomicatOperationDetails.recordedObject().getMaterialRegistrations();
+ assertEquals(1, materialsRegistered.size());
+ assertEquals("material-1", materialsRegistered.get(MATERIAL_TYPE).get(0).getCode());
+
+ AssertionUtil
+ .assertContains(
+ "New data from folder 'batchNr_plateCode.variant_2011.07.05' has been successfully registered in plate "
+ + "<a href='https://bwl27.sanofi-aventis.com:8443/openbis#entity=SAMPLE&sample_type=PLATE&action=SEARCH&code=plateCode'>plateCode</a>",
+ email.recordedObject());
+ context.assertIsSatisfied();
+ }
+
private void assertHasProperty(NewExternalData dataSet, String propCode, String propValue)
{
for (NewProperty prop : dataSet.getDataSetProperties())
@@ -446,6 +534,13 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
private void assertCompoundWell(List<NewSample> newSamples, String wellCode,
String concentration)
+ {
+ String materialCode = getMaterialCodeByWellCode(wellCode);
+ assertCompoundWell(newSamples, wellCode, concentration, materialCode);
+ }
+
+ private void assertCompoundWell(List<NewSample> newSamples, String wellCode,
+ String concentration, String materialCode)
{
NewSample newSample = findByWellCode(newSamples, wellCode);
assertEquals(COMPOUND_WELL_TYPE, newSample.getSampleType().getCode());
@@ -457,7 +552,6 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
assertEquals("Invalid concentration value for well '" + wellCode + "': ", concentration,
concentrationProp.tryGetAsString());
- String materialCode = getMaterialCodeByWellCode(wellCode);
MaterialIdentifier materialIdentifier = new MaterialIdentifier(materialCode, MATERIAL_TYPE);
IEntityProperty wellMaterialProp =
@@ -579,10 +673,15 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
}
private Map<String, Object> createQueryResult(String wellCode)
+ {
+ return createQueryResult(wellCode, getMaterialCodeByWellCode(wellCode));
+ }
+
+ private Map<String, Object> createQueryResult(String wellCode, String materialCode)
{
Map<String, Object> result = new HashMap<String, Object>();
result.put("WELL_CODE", wellCode);
- result.put("MATERIAL_CODE", getMaterialCodeByWellCode(wellCode));
+ result.put("MATERIAL_CODE", materialCode);
result.put("ABASE_COMPOUND_ID", wellCode + "_compound_id");
result.put("ABASE_COMPOUND_BATCH_ID", wellCode + "_compound_batch_id");
return result;
--
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