From acb1cd2314b7b8100aab30aba9fe33c04dd5e373 Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Fri, 1 Jul 2011 09:08:02 +0000
Subject: [PATCH] [LMS-2332] further improvements 1) allow empty wells in the
library template (no well sample will be created in openBIS) 2) handle Sanofi
wellCode format (e.g. AC007 is translated to AC7) 3) bugfix: well rows start
counting from 1 (not from 0)
SVN: 21946
---
.../dist/etc/sanofi-dropbox/sanofi-dropbox.py | 55 ++++++++++++++-----
.../dss/test/SanofiDropboxJythonTest.java | 26 ++++-----
2 files changed, 52 insertions(+), 29 deletions(-)
diff --git a/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py b/sanofi/dist/etc/sanofi-dropbox/sanofi-dropbox.py
index 037baf878d6..cd3f29d7429 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 bc56399d187..de1c95805f0 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();
--
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