diff --git a/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py b/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
index 037baf878d676a6266c86dc4cc6fdf46f5ef6047..cd3f29d742974789eff33232a916ebd040bf951f 100644
--- a/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
+++ b/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
@@ -1,3 +1,5 @@
+import re
+
from ch.systemsx.cisd.common.mail import From
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
@@ -98,14 +100,25 @@ class SanofiMaterial:
A data structure class holding compound materials as they exist in the Abase (Sanofi) database.
"""
def __init__(self, wellCode, materialCode, sanofiId, sanofiBatchId):
- self.wellCode = wellCode
+ self.wellCode = self.normalizeWellCode(wellCode)
self.materialCode = materialCode
self.sanofiId = sanofiId
self.sanofiBatchId = sanofiBatchId
+
+ def normalizeWellCode(self, wellCode):
+ """ normalizes Sanofi wellCodes openBIS wellCodes e.g. AB007 to AB7 """
+ return re.sub("(?<=\w)(0+)(?=\d)", "", wellCode)
class PlateInitializer:
ABASE_DATA_SOURCE = "abase-datasource"
- ABASE_QUERY = "TODO: this a query provided by Matt"
+ ABASE_QUERY = """select
+ ptodwellreference WELL_CODE,
+ translate(objdbatchref,'{/:()+','{_____') MATERIAL_CODE,
+ objdbatchref ABASE_COMPOUND_BATCH_ID,
+ objdid ABASE_COMPOUND_ID,
+ olptid ABASE_PLATE_CODE
+ from sysadmin.plteobjd
+ where olptid = ?{1}"""
LIBRARY_TEMPLATE_PROPNAME = "LIBRARY_TEMPLATE"
@@ -113,10 +126,10 @@ class PlateInitializer:
NEGATIVE_CONTROL_TYPE = "NEGATIVE_CONTROL"
COMPOUND_WELL_TYPE = "COMPOUND_WELL"
- COMPOUND_WELL_CONCENTRATION_PROPNAME = "CONCENTRATION"
- COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND_BATCH"
+ COMPOUND_WELL_CONCENTRATION_PROPNAME = "CONCENTRATION_M"
+ COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND"
- MATERIAL_TYPE = "COMPOUND_BATCH"
+ MATERIAL_TYPE = "COMPOUND"
MATERIAL_ID_PROPNAME = "COMPOUND_ID"
MATERIAL_BATCH_ID_PROPNAME = "COMPOUND_BATCH_ID"
@@ -125,9 +138,16 @@ class PlateInitializer:
self.plate = plate
self.plateCode = plate.getCode()
self.experimentId = plate.getExperiment().getExperimentIdentifier()
+
+ def wellColumn(self, x):
+ numLetters = 26
+ if x < numLetters:
+ return chr(ord('A') + x)
+ else:
+ return self.wellColumn((x / numLetters) - 1) + self.wellColumn( x % numLetters)
def getWellCode(self, x, y):
- return chr(ord('A') + x) + str(y)
+ return self.wellColumn(x) + str(y + 1)
def getPlateDimensions(self):
"""
@@ -146,14 +166,15 @@ class PlateInitializer:
if plateHeight != len(tsvLines) :
raise RuntimeError("The geometry property of plate %(plateCode)s (height=%(plateHeight)s)"
" does not agree with the value of the %(LIBRARY_TEMPLATE_PROPNAME)s"
- " property in experiment %(experimentId)s (height=%(numLines)s)." % vars())
+ " property in experiment %(experimentId)s (height=%(numLines)s)." % vars(self))
for i in range(0, len(tsvLines)):
lineWidth = len(tsvLines[i])
if plateWidth != lineWidth:
- raise RuntimeError("The geometry property of plate %(plateCode)s (width=%(plateWidth)s)"
- " does not agree with the value of the %(LIBRARY_TEMPLATE_PROPNAME)s"
- " property in experiment %(experimentId)s (line=%(i)s, width=%(lineWidth)s)." % vars())
+ raise RuntimeError("The geometry property of plate %s (width=%s)"
+ " does not agree with the value of the %s"
+ " property in experiment %s (line=%s, width=%s)." % \
+ (plateCode, plateWidth, self.LIBRARY_TEMPLATE_PROPNAME, self.experimentId, i, lineWidth))
def parseLibraryTemplate(self):
template = experiment.getPropertyValue(self.LIBRARY_TEMPLATE_PROPNAME)
@@ -179,7 +200,7 @@ class PlateInitializer:
In case the plate is not found in Abase return None.
"""
queryService = state.getDataSourceQueryService()
- queryResult = queryService.select(self.ABASE_DATA_SOURCE, self.ABASE_QUERY, [plate.code])
+ queryResult = queryService.select(self.ABASE_DATA_SOURCE, self.ABASE_QUERY, [self.plateCode])
sanofiMaterials = []
for materialMap in list(queryResult):
@@ -240,7 +261,10 @@ class PlateInitializer:
controlWellTypes = { "H" : self.POSITIVE_CONTROL_TYPE, \
"L" : self.NEGATIVE_CONTROL_TYPE};
- for wellCode in library:
+ for wellCode in library:
+ if not library[wellCode]:
+ continue
+
libraryValue = library[wellCode].upper()
prefixedWellCode = self.plateCode + ":" + wellCode
@@ -255,9 +279,10 @@ class PlateInitializer:
try:
float(concentration)
except ValueError:
- raise RuntimeError("The specified value for well %(wellCode)s in the property "
- " %(LIBRARY_TEMPLATE_PROPNAME)s of experiment %(experimentId)s is invalid. "
- "Allowed values are 'H', 'L' or number, but %(libraryValue)s' was found." % vars())
+ raise RuntimeError("The specified value for well %s in the property "
+ " %s of experiment %s is invalid. Allowed values are 'H', 'L'"
+ " or number, but '%s' was found." % \
+ (wellCode, self.LIBRARY_TEMPLATE_PROPNAME, self.experimentId, libraryValue))
well = self.transaction.createNewSample(prefixedWellCode, self.COMPOUND_WELL_TYPE)
well.setContainer(self.plate)
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 bc56399d187b3231d2c23843443a8e1d2040ab20..de1c95805f0df2a6a3766592b3e2acb6df8fa34d 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
@@ -80,7 +80,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
private static final String[] EXPERIMENT_RECIPIENTS = new String[]
{ "admin@sanofi.com", "mickey@mouse.org" };
- private static final String MATERIAL_TYPE = "COMPOUND_BATCH";
+ private static final String MATERIAL_TYPE = "COMPOUND";
private static final String POSITIVE_CONTROL_TYPE = "POSITIVE_CONTROL";
@@ -88,9 +88,9 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
private static final String COMPOUND_WELL_TYPE = "COMPOUND_WELL";
- private static final String COMPOUND_WELL_CONCENTRATION_PROPNAME = "CONCENTRATION";
+ private static final String COMPOUND_WELL_CONCENTRATION_PROPNAME = "CONCENTRATION_M";
- private static final String COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND_BATCH";
+ private static final String COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND";
private static final String DATASET_DIR_NAME = "batchNr_plateCode.variant_2011.06.28";
@@ -116,16 +116,15 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
createHandler(properties, false, true);
createData();
- final String libraryTemplate = "1.45\t20.701\tH\n0.12\t0.002\tL";
+ final String libraryTemplate = "1.45\t\tH\n0.12\t0.002\tL";
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"));
+ queryResult.add(createQueryResult("B2"));
final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicatOperationDetails =
new RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails>();
@@ -143,7 +142,7 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
one(openBisService).listMaterials(with(materialCriteria), with(equal(true)));
will(returnValue(Collections.emptyList()));
- exactly(6).of(openBisService).createPermId();
+ exactly(5).of(openBisService).createPermId();
will(returnValue("well-permId"));
one(openBisService).createDataSetCode();
@@ -178,14 +177,13 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
List<NewSample> registeredSamples =
atomicatOperationDetails.recordedObject().getSampleRegistrations();
- assertEquals(6, registeredSamples.size());
+ assertEquals(5, registeredSamples.size());
assertAllSamplesHaveContainer(registeredSamples, plate.getIdentifier());
- assertCompoundWell(registeredSamples, "A0", "1.45");
- assertCompoundWell(registeredSamples, "A1", "20.701");
- assertPositiveControl(registeredSamples, "A2");
- assertCompoundWell(registeredSamples, "B0", "0.12");
- assertCompoundWell(registeredSamples, "B1", "0.002");
- assertNegativeControl(registeredSamples, "B2");
+ assertCompoundWell(registeredSamples, "A1", "1.45");
+ assertPositiveControl(registeredSamples, "A3");
+ assertCompoundWell(registeredSamples, "B1", "0.12");
+ assertCompoundWell(registeredSamples, "B2", "0.002");
+ assertNegativeControl(registeredSamples, "B3");
List<? extends NewExternalData> dataSetsRegistered =
atomicatOperationDetails.recordedObject().getDataSetRegistrations();