From 934c8a018fdee719092aa8c35187c4b2b1944a10 Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Wed, 29 Jun 2011 14:49:24 +0000
Subject: [PATCH] [LMS-2332] improved unit testing
SVN: 21904
---
.../dist/etc/sanofi-dropbox/sanofi-dropbox.py | 42 ++++++----
.../dss/test/SanofiDropboxJythonTest.java | 83 ++++++++++++++++---
2 files changed, 99 insertions(+), 26 deletions(-)
diff --git a/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py b/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
index 6399023c814..a264b81b6ae 100644
--- a/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
+++ b/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
@@ -57,9 +57,12 @@ class PlateInitializer:
LIBRARY_TEMPLATE_PROPNAME = "LIBRARY_TEMPLATE"
- WELL_TYPE = "COMPOUND_WELL"
- WELL_CONCENTRATION_PROPNAME = "CONCENTRATION"
- WELL_MATERIAL_PROPNAME = "COMPOUND_BATCH"
+ POSITIVE_CONTROL_TYPE = "POSITIVE_CONTROL"
+ NEGATIVE_CONTROL_TYPE = "NEGATIVE_CONTROL"
+
+ COMPOUND_WELL_TYPE = "COMPOUND_WELL"
+ COMPOUND_WELL_CONCENTRATION_PROPNAME = "CONCENTRATION"
+ COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND_BATCH"
MATERIAL_TYPE = "COMPOUND_BATCH"
MATERIAL_ID_PROPNAME = "COMPOUND_ID"
@@ -116,8 +119,8 @@ class PlateInitializer:
sanofiMaterials = []
for materialMap in list(queryResult):
- wellCode = str(materialMap['WELLCODE'])
- materialCode = str(materialMap['MATERIALCODE'])
+ wellCode = str(materialMap['WELL_CODE'])
+ materialCode = str(materialMap['MATERIAL_CODE'])
sanofiId = str(materialMap['ABASE_COMPOUND_ID'])
sanofiBatchId = str(materialMap['ABASE_COMPOUND_BATCH_ID'])
material = SanofiMaterial(wellCode, materialCode, sanofiId, sanofiBatchId)
@@ -170,22 +173,33 @@ class PlateInitializer:
raise RuntimeError("No material found for wellCode " + wellCode)
def createWells(self, library, sanofiMaterials, openbisMaterials):
- controlWellTypes = { "H" : "posti", "L" : "negative"};
+ controlWellTypes = { "H" : self.POSITIVE_CONTROL_TYPE, \
+ "L" : self.NEGATIVE_CONTROL_TYPE};
+
for wellCode in library:
- libraryValue = library[wellCode].uppercase()
+ libraryValue = library[wellCode].upper()
+ prefixedWellCode = plate.code + ":" + wellCode
+
if libraryValue in controlWellTypes:
+ # CONTROL_WELL
+ wellType = controlWellTypes[libraryValue]
+ well = transaction.createNewSample(prefixedWellCode, wellType)
+ well.setContainer(plate)
pass
- else:
- try
+ else:
+ # COMPOUND_WELL
+ concentration = libraryValue
+ try:
+ float(concentration)
except ValueError:
- raise RuntimeError("TODO...")
- well = transaction.createNewSample(plate.code +":" + wellCode, self.WELL_TYPE)
+ raise RuntimeError("A non-numeric value '%s' detected in well '%s'" % (libraryValue, wellCode))
+ well = transaction.createNewSample(prefixedWellCode, self.COMPOUND_WELL_TYPE)
well.setContainer(plate)
- concentration = library[wellCode]
- well.setPropertyValue(self.WELL_CONCENTRATION_PROPNAME, concentration)
+ well.setPropertyValue(self.COMPOUND_WELL_CONCENTRATION_PROPNAME, concentration)
materialCode = self.getByWellCode(wellCode, sanofiMaterials).materialCode
material = openbisMaterials[materialCode]
- well.setMaterialPropertyValue(self.WELL_MATERIAL_PROPNAME, material)
+ # TODO KE: make material property creation possible
+ #well.setPropertyValue(self.COMPOUND_WELL_MATERIAL_PROPNAME, material)
def createWellsAndMaterials(self):
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 f69e8b5b9de..6c9d26b7a87 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
@@ -23,6 +23,7 @@ import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import java.util.Properties;
@@ -42,6 +43,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchCl
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.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
@@ -51,6 +53,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
/**
* <pre>
@@ -69,12 +72,23 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
private static final String LIBRARY_TEMPLATE_PROPNAME = "LIBRARY_TEMPLATE";
private static final String MATERIAL_TYPE = "COMPOUND_BATCH";
+
+ private static final String POSITIVE_CONTROL_TYPE = "POSITIVE_CONTROL";
+
+ private static final String NEGATIVE_CONTROL_TYPE = "NEGATIVE_CONTROL";
+
+ private static final String COMPOUND_WELL_TYPE = "COMPOUND_WELL";
+
+ private static final String COMPOUND_WELL_CONCENTRATION_PROPNAME = "CONCENTRATION";
+
+ // TODO KE: implement me
+ // private static final String COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND_BATCH";
private static final String DATASET_DIR_NAME = "batchNr_plateCode.variant_2011.06.28";
private static final String DATA_SET_CODE = "data-set-code";
- private static final DataSetType DATA_SET_TYPE = new DataSetType("DATA_SET_TYPE");
+ private static final DataSetType DATA_SET_TYPE = new DataSetType("HCS_IMAGE_RAW");
private static final String EXPERIMENT_IDENTIFIER = "/SANOFI/PROJECT/EXP";
private static final String PLATE_IDENTIFIER = "/SANOFI/TEST-PLATE";
@@ -89,8 +103,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
queryService = context.mock(IDataSourceQueryService.class);
}
- @Test(enabled = false)
- public void testSimpleTransaction() throws IOException
+ @Test
+ public void testHappyCaseWithLibraryCreation() throws IOException
{
setUpHomeDataBaseExpectations();
Properties properties = createThreadPropertiesRelativeToScriptsFolder("sanofi-dropbox.py");
@@ -120,11 +134,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
one(openBisService).listMaterials(with(materialCriteria), with(equal(true)));
will(returnValue(Collections.emptyList()));
- one(openBisService).createPermId();
- will(returnValue("A0-permId"));
-
- one(openBisService).createPermId();
- will(returnValue("B0-permId"));
+ exactly(4).of(openBisService).createPermId();
+ will(returnValue("well-permId"));
one(openBisService).createDataSetCode();
will(returnValue(DATA_SET_CODE));
@@ -147,20 +158,68 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
handler.handle(markerFile);
- assertEquals(MATERIAL_TYPE, materialCriteria.recordedObject().tryGetMaterialType());
+ assertEquals(MATERIAL_TYPE, materialCriteria.recordedObject().tryGetMaterialType()
+ .getCode());
assertEquals(true, queryResult.hasCloseBeenInvoked());
- assertEquals(1, atomicatOperationDetails.recordedObject().getDataSetRegistrations().size());
+ List<NewSample> registeredSamples =
+ atomicatOperationDetails.recordedObject().getSampleRegistrations();
+
+ assertCompoundWell(registeredSamples, "A0", "1.45");
+ assertPositiveControl(registeredSamples, "A1");
+ assertCompoundWell(registeredSamples, "B0", "0.13");
+ assertNegativeControl(registeredSamples, "B1");
- NewExternalData dataSet =
- atomicatOperationDetails.recordedObject().getDataSetRegistrations().get(0);
+ List<? extends NewExternalData> dataSetsRegistered =
+ atomicatOperationDetails.recordedObject().getDataSetRegistrations();
+ assertEquals(1, dataSetsRegistered.size());
+ NewExternalData dataSet = dataSetsRegistered.get(0);
assertEquals(DATA_SET_CODE, dataSet.getCode());
assertEquals(DATA_SET_TYPE, dataSet.getDataSetType());
context.assertIsSatisfied();
}
+ private NewSample findByWellCode(List<NewSample> newSamples, String wellCode)
+ {
+ for (NewSample newSample : newSamples)
+ {
+ if (newSample.getIdentifier().endsWith(":" + wellCode))
+ {
+ return newSample;
+ }
+ }
+ throw new RuntimeException("Failed to find sample registration for well " + wellCode);
+ }
+
+ private void assertNegativeControl(List<NewSample> newSamples, String wellCode)
+ {
+ NewSample newSample = findByWellCode(newSamples, wellCode);
+ assertEquals(NEGATIVE_CONTROL_TYPE, newSample.getSampleType().getCode());
+ assertEquals(0, newSample.getProperties().length);
+ }
+
+ private void assertPositiveControl(List<NewSample> newSamples, String wellCode)
+ {
+ NewSample newSample = findByWellCode(newSamples, wellCode);
+ assertEquals(POSITIVE_CONTROL_TYPE, newSample.getSampleType().getCode());
+ assertEquals(0, newSample.getProperties().length);
+ }
+
+ private void assertCompoundWell(List<NewSample> newSamples, String wellCode,
+ String concentration)
+ {
+ NewSample newSample = findByWellCode(newSamples, wellCode);
+ assertEquals(COMPOUND_WELL_TYPE, newSample.getSampleType().getCode());
+ IEntityProperty concentrationProp =
+ EntityHelper.tryFindProperty(newSample.getProperties(),
+ COMPOUND_WELL_CONCENTRATION_PROPNAME);
+ assertNotNull(concentrationProp);
+ assertEquals("Invalid concentration value for well '" + wellCode + "': ", concentration,
+ concentrationProp.tryGetAsString());
+ }
+
private void setUpPlateSearchExpectations(final Sample plate)
{
context.checking(new Expectations()
--
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