From 32f09db895878805477a896ab6c8b81fd6716a91 Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Wed, 29 Jun 2011 15:34:12 +0000
Subject: [PATCH] [LMS-2332] added support for parsing geometry from plate
property
SVN: 21912
---
.../dist/etc/sanofi-dropbox/sanofi-dropbox.py | 16 +++--
.../dss/test/SanofiDropboxJythonTest.java | 60 +++++++++++++------
2 files changed, 53 insertions(+), 23 deletions(-)
diff --git a/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py b/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
index a264b81b6ae..ee09bf9ca99 100644
--- a/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
+++ b/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
@@ -2,6 +2,7 @@ import ch.systemsx.cisd.etlserver.registrator.api.v1.MaterialIdentifierCollectio
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria as SearchCriteria
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause as MatchClause
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute as MatchClauseAttribute
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants as ScreeningConstants
PLATE_TYPE = "PLATE"
@@ -76,11 +77,17 @@ class PlateInitializer:
return chr(ord('A') + x) + str(y)
def getPlateDimensions(self):
- # TODO KE: implement me
- return (2, 2)
+ """
+ parses the plate geometry property from the form "384_WELLS_16X24"
+ to a tuple of integers (plateHeight, plateWidth)
+ """
+ plateGeometryString = plate.getPropertyValue(ScreeningConstants.PLATE_GEOMETRY)
+ widthByHeight = plateGeometryString.split("_")[-1]
+ dimensions = map(int, widthByHeight.split("X"))
+ return (dimensions[0], dimensions[1])
def validateLibraryDimensions(self, csvLists):
- (plateWidth, plateHeight) = self.getPlateDimensions()
+ (plateHeight, plateWidth) = self.getPlateDimensions()
assert plateHeight == len(csvLists), \
"Plate geometry (height=%i) does not agree with LIBRARY_TEMPLATE (height=%i)." % (plateHeight, len(csvLists))
@@ -198,8 +205,7 @@ class PlateInitializer:
well.setPropertyValue(self.COMPOUND_WELL_CONCENTRATION_PROPNAME, concentration)
materialCode = self.getByWellCode(wellCode, sanofiMaterials).materialCode
material = openbisMaterials[materialCode]
- # TODO KE: make material property creation possible
- #well.setPropertyValue(self.COMPOUND_WELL_MATERIAL_PROPNAME, material)
+ well.setPropertyValue(self.COMPOUND_WELL_MATERIAL_PROPNAME, material.getMaterialIdentifier())
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 bf96eb7e040..983660ce870 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
@@ -43,6 +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.MaterialIdentifier;
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;
@@ -54,6 +55,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
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;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
* <pre>
@@ -81,8 +83,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
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 COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND_BATCH";
private static final String DATASET_DIR_NAME = "batchNr_plateCode.variant_2011.06.28";
@@ -111,14 +112,16 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
createHandler(properties, false, true, queryService);
createData();
- final String libraryTemplate = "1.45, H\n0.12, L";
- final Sample plate = createPlate(libraryTemplate);
+ final String libraryTemplate = "1.45, 20.701, H\n0.12, 0.002, L";
+ final Sample plate = createPlate(libraryTemplate, "6_WELLS_2X3");
setUpPlateSearchExpectations(plate);
setUpLibraryTemplateExpectations(plate);
final MockDataSet<Map<String, Object>> queryResult = new MockDataSet<Map<String, Object>>();
queryResult.add(createQueryResult("A0"));
+ queryResult.add(createQueryResult("A1"));
queryResult.add(createQueryResult("B0"));
+ queryResult.add(createQueryResult("B1"));
final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicatOperationDetails =
new RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails>();
@@ -134,7 +137,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
one(openBisService).listMaterials(with(materialCriteria), with(equal(true)));
will(returnValue(Collections.emptyList()));
- exactly(4).of(openBisService).createPermId();
+ exactly(6).of(openBisService).createPermId();
will(returnValue("well-permId"));
one(openBisService).createDataSetCode();
@@ -164,12 +167,15 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
List<NewSample> registeredSamples =
atomicatOperationDetails.recordedObject().getSampleRegistrations();
-
+
+ assertEquals(6, registeredSamples.size());
assertAllSamplesHaveContainer(registeredSamples, plate.getIdentifier());
assertCompoundWell(registeredSamples, "A0", "1.45");
- assertPositiveControl(registeredSamples, "A1");
+ assertCompoundWell(registeredSamples, "A1", "20.701");
+ assertPositiveControl(registeredSamples, "A2");
assertCompoundWell(registeredSamples, "B0", "0.12");
- assertNegativeControl(registeredSamples, "B1");
+ assertCompoundWell(registeredSamples, "B1", "0.002");
+ assertNegativeControl(registeredSamples, "B2");
List<? extends NewExternalData> dataSetsRegistered =
atomicatOperationDetails.recordedObject().getDataSetRegistrations();
@@ -222,12 +228,24 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
{
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());
+
+ String materialCode = getMaterialCodeByWellCode(wellCode);
+ MaterialIdentifier materialIdentifier = new MaterialIdentifier(materialCode, MATERIAL_TYPE);
+
+ IEntityProperty wellMaterialProp =
+ EntityHelper.tryFindProperty(newSample.getProperties(),
+ COMPOUND_WELL_MATERIAL_PROPNAME);
+ assertNotNull(wellMaterialProp);
+ assertEquals("Invalid material found in well '" + wellCode + "': ",
+ materialIdentifier.print(), wellMaterialProp.tryGetAsString());
+
}
private void setUpPlateSearchExpectations(final Sample plate)
@@ -271,16 +289,17 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
FileUtilities.writeToFile(markerFile, "");
}
- private Sample createPlate(String libraryTemplate)
+ private Sample createPlate(String libraryTemplate, String plateGeometry)
{
- ExperimentBuilder experimentBuilder =
- new ExperimentBuilder().identifier(EXPERIMENT_IDENTIFIER).property(
- LIBRARY_TEMPLATE_PROPNAME,
- libraryTemplate);
-
- SampleBuilder sampleBuilder =
- new SampleBuilder().identifier(PLATE_IDENTIFIER).experiment(
- experimentBuilder.getExperiment());
+ ExperimentBuilder experimentBuilder = new ExperimentBuilder();
+ experimentBuilder.identifier(EXPERIMENT_IDENTIFIER);
+ experimentBuilder.property(LIBRARY_TEMPLATE_PROPNAME, libraryTemplate);
+
+ SampleBuilder sampleBuilder = new SampleBuilder();
+ sampleBuilder.experiment(experimentBuilder.getExperiment());
+ sampleBuilder.identifier(PLATE_IDENTIFIER);
+ sampleBuilder.property(ScreeningConstants.PLATE_GEOMETRY, plateGeometry);
+
final Sample plate = sampleBuilder.getSample();
return plate;
}
@@ -289,12 +308,17 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
{
Map<String, Object> result = new HashMap<String, Object>();
result.put("WELL_CODE", wellCode);
- result.put("MATERIAL_CODE", wellCode + "_material_code");
+ result.put("MATERIAL_CODE", getMaterialCodeByWellCode(wellCode));
result.put("ABASE_COMPOUND_ID", wellCode + "_compound_id");
result.put("ABASE_COMPOUND_BATCH_ID", wellCode + "_compound_batch_id");
return result;
}
+ private String getMaterialCodeByWellCode(String wellCode)
+ {
+ return wellCode + "_material_code";
+ }
+
@Override
protected String getRegistrationScriptsFolderPath()
{
--
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