diff --git a/sanofi/dist/etc/sanofi-dropbox/plateinitializer.py b/sanofi/dist/etc/sanofi-dropbox/plateinitializer.py
index bc54e4dda6556e8e6da48d6503619d23993ae635..613af1d08bf1fdf8ef93d41c96dbf9397cd3ccea 100644
--- a/sanofi/dist/etc/sanofi-dropbox/plateinitializer.py
+++ b/sanofi/dist/etc/sanofi-dropbox/plateinitializer.py
@@ -18,11 +18,10 @@ class SanofiMaterial:
"""
A data structure class holding compound materials as they exist in the Abase (Sanofi) database.
"""
- def __init__(self, wellCode, materialCode, sanofiId, sanofiBatchId):
+ def __init__(self, wellCode, compoundBatchId, compoundId):
self.wellCode = self.normalizeWellCode(wellCode)
- self.materialCode = materialCode
- self.sanofiId = sanofiId
- self.sanofiBatchId = sanofiBatchId
+ self.compoundBatchId = compoundBatchId
+ self.compoundId = compoundId
def normalizeWellCode(self, wellCode):
""" normalizes Sanofi wellCodes to openBIS wellCodes e.g. AB007 to AB7 """
@@ -30,10 +29,17 @@ class SanofiMaterial:
class PlateInitializer:
ABASE_DATA_SOURCE = "abase-datasource"
+# ABASE_PRODUCTION_QUERY = """select
+# ptodwellreference WELL_CODE,
+# translate(objdbatchref,'{/:()+','{_____') MATERIAL_CODE,
+# translate(objdid,'{/:()+','{_____') ABASE_COMPOUND_ID,
+# olptid ABASE_PLATE_CODE
+# from sysadmin.plteobjd
+# where olptid = ?{1}"""
+
ABASE_PRODUCTION_QUERY = """select
ptodwellreference WELL_CODE,
- translate(objdbatchref,'{/:()+','{_____') MATERIAL_CODE,
- objdbatchref ABASE_COMPOUND_BATCH_ID,
+ objdbatchref MATERIAL_CODE,
objdid ABASE_COMPOUND_ID,
olptid ABASE_PLATE_CODE
from sysadmin.plteobjd
@@ -42,7 +48,7 @@ class PlateInitializer:
# used for integration testing from openBIS team members
ABASE_TEST_MODE_QUERY = """select
WELL_CODE, MATERIAL_CODE, ABASE_COMPOUND_ID,
- ABASE_COMPOUND_BATCH_ID, ABASE_PLATE_CODE
+ ABASE_PLATE_CODE
from plates
where ABASE_PLATE_CODE = ?{1}"""
@@ -53,12 +59,12 @@ class PlateInitializer:
COMPOUND_WELL_TYPE = "COMPOUND_WELL"
COMPOUND_WELL_CONCENTRATION_PROPNAME = "CONCENTRATION_M"
- COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND"
+ COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND_BATCH"
- MATERIAL_TYPE = "COMPOUND"
- MATERIAL_ID_PROPNAME = "COMPOUND_ID"
- MATERIAL_BATCH_ID_PROPNAME = "COMPOUND_BATCH_ID"
-
+ MATERIAL_BATCH_TYPE = "COMPOUND_BATCH"
+ MATERIAL_COMPOUND_TYPE = "COMPOUND"
+ MATERIAL_ID_PROPNAME = "COMPOUND"
+
def __init__(self, transaction, state, plate, experiment, testMode):
self.transaction = transaction
self.state = state
@@ -151,7 +157,7 @@ class PlateInitializer:
raise RuntimeException("No column '%s' in the query results from the ABASE Database" % (code))
material = SanofiMaterial(val('WELL_CODE'), val('MATERIAL_CODE'), \
- val('ABASE_COMPOUND_ID'), val('ABASE_COMPOUND_BATCH_ID'))
+ val('ABASE_COMPOUND_ID'))
sanofiMaterials.append(material)
@@ -159,34 +165,53 @@ class PlateInitializer:
return sanofiMaterials
- def createMaterial(self, sanofiMaterial):
- material = self.transaction.createNewMaterial(sanofiMaterial.materialCode, self.MATERIAL_TYPE)
- material.setPropertyValue(self.MATERIAL_ID_PROPNAME, sanofiMaterial.sanofiId)
- material.setPropertyValue(self.MATERIAL_BATCH_ID_PROPNAME, sanofiMaterial.sanofiBatchId)
+ def createCompoundBatchMaterial(self, sanofiMaterial):
+ material = self.transaction.createNewMaterial(sanofiMaterial.compoundBatchId, self.MATERIAL_BATCH_TYPE)
+ material.setPropertyValue(self.MATERIAL_ID_PROPNAME, sanofiMaterial.compoundId)
return material
- def getOrCreateMaterials(self, template, sanofiMaterials):
- materialsByCode = {}
- for sanofiMaterial in sanofiMaterials:
- materialsByCode[ sanofiMaterial.materialCode ] = sanofiMaterial
+ def createCompoundMaterial(self, sanofiMaterial):
+ material = self.transaction.createNewMaterial(sanofiMaterial.compoundId, self.MATERIAL_COMPOUND_TYPE)
+ return material
+ def findExistingMaterials(self, materialType, materialCodes):
materialIdentifiers = MaterialIdentifierCollection()
- for materialCode in materialsByCode:
- materialIdentifiers.addIdentifier(self.MATERIAL_TYPE, materialCode)
+ for materialCode in materialCodes:
+ materialIdentifiers.addIdentifier(materialType, materialCode)
searchService = self.transaction.getSearchService()
- existingMaterials = list(searchService.listMaterials(materialIdentifiers))
-
- existingMaterialsByCode = {}
+ return list(searchService.listMaterials(materialIdentifiers))
+
+ def createNonExistingMaterials(self, sanofiMaterialsByCode, existingMaterials, createFunction):
+ materialsByCode = {}
for material in existingMaterials:
- existingMaterialsByCode[ material.getCode() ] = material
-
- for materialCode in materialsByCode:
- if not materialCode in existingMaterialsByCode:
- sanofiMaterial = materialsByCode[materialCode]
- openbisMaterial = self.createMaterial(sanofiMaterial)
- existingMaterialsByCode[materialCode] = openbisMaterial
+ materialsByCode[ material.getCode() ] = material
+
+ for materialCode in sanofiMaterialsByCode:
+ if not materialCode in materialsByCode:
+ sanofiMaterial = sanofiMaterialsByCode[materialCode]
+ materialsByCode[materialCode] = createFunction(sanofiMaterial)
+
+ return materialsByCode
+
+
+ def getOrCreateMaterials(self, template, sanofiMaterials):
+ materialsByBatchId = {}
+ materialsByCompoundId = {}
+
+ for sanofiMaterial in sanofiMaterials:
+ materialsByBatchId[ sanofiMaterial.compoundBatchId ] = sanofiMaterial
+ materialsByCompoundId[ sanofiMaterial.compoundId ] = sanofiMaterial
+
+ existingCompoundMaterials = self.findExistingMaterials(self.MATERIAL_COMPOUND_TYPE, materialsByCompoundId)
+ allCompoundMaterialsByCode = self.createNonExistingMaterials(materialsByCompoundId, existingCompoundMaterials, self.createCompoundMaterial)
+
+ existingBatchMaterials = self.findExistingMaterials(self.MATERIAL_BATCH_TYPE, materialsByBatchId)
+ allBatchMaterialsByCode = self.createNonExistingMaterials(materialsByBatchId, existingBatchMaterials, self.createCompoundBatchMaterial)
- return existingMaterialsByCode
+ # returns a dict UNION
+ allMaterialsByCode = dict(allCompoundMaterialsByCode)
+ allMaterialsByCode.update(allBatchMaterialsByCode)
+ return allMaterialsByCode
def getByWellCode(self, wellCode, sanofiMaterials):
@@ -233,7 +258,7 @@ class PlateInitializer:
well.setContainer(self.plate)
concentration = self.parseConcentration(templateValue)
well.setPropertyValue(self.COMPOUND_WELL_CONCENTRATION_PROPNAME, concentration)
- materialCode = sanofiMaterial.materialCode
+ materialCode = sanofiMaterial.compoundBatchId
material = openbisMaterials[materialCode]
well.setPropertyValue(self.COMPOUND_WELL_MATERIAL_PROPNAME, material.getMaterialIdentifier())
diff --git a/sanofi/resource/master-data/sanofi-master-data.py b/sanofi/resource/master-data/sanofi-master-data.py
new file mode 100644
index 0000000000000000000000000000000000000000..507b981b4862ca7c95215ff57552920aa23d753d
--- /dev/null
+++ b/sanofi/resource/master-data/sanofi-master-data.py
@@ -0,0 +1,72 @@
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
+
+tr = service.transaction()
+#
+# Materials
+#
+material_type_COMPOUND = tr.getMaterialType('COMPOUND')
+if not material_type_COMPOUND:
+ material_type_COMPOUND = tr.createNewMaterialType('COMPOUND')
+ material_type_COMPOUND.setDescription('Compound material')
+
+material_type_COMPOUND_BATCH = tr.createNewMaterialType('COMPOUND_BATCH')
+material_type_COMPOUND_BATCH.setDescription('Compound batch material')
+
+prop_type_COMPOUND = tr.createNewPropertyType('COMPOUND', DataType.MATERIAL)
+prop_type_COMPOUND.setLabel('Compound material')
+tr.assignPropertyType(material_type_COMPOUND_BATCH, prop_type_COMPOUND)
+
+
+#
+# Experiment + Properties
+#
+
+experiment_type_COMPOUND_HCS = tr.getExperimentType('COMPOUND_HCS')
+
+prop_type_OBSERVER_EMAILS = tr.createNewPropertyType('OBSERVER_EMAILS', DataType.VARCHAR)
+prop_type_OBSERVER_EMAILS.setLabel('Observer e-mails')
+tr.assignPropertyType(experiment_type_COMPOUND_HCS, prop_type_OBSERVER_EMAILS)
+
+prop_type_LIBRARY_TEMPLATE = tr.createNewPropertyType('LIBRARY_TEMPLATE', DataType.MULTILINE_VARCHAR)
+prop_type_LIBRARY_TEMPLATE.setLabel('Library Template')
+tr.assignPropertyType(experiment_type_COMPOUND_HCS, prop_type_LIBRARY_TEMPLATE)
+
+#
+# Samples
+#
+
+samp_type_POSITIVE_CONTROL = tr.createNewSampleType('POSITIVE_CONTROL')
+samp_type_POSITIVE_CONTROL.setListable(False)
+samp_type_POSITIVE_CONTROL.setGeneratedCodePrefix('P')
+
+
+samp_type_NEGATIVE_CONTROL = tr.createNewSampleType('NEGATIVE_CONTROL')
+samp_type_NEGATIVE_CONTROL.setListable(False)
+samp_type_NEGATIVE_CONTROL.setGeneratedCodePrefix('N')
+
+
+samp_type_COMPOUND_WELL = tr.createNewSampleType('COMPOUND_WELL')
+samp_type_COMPOUND_WELL.setListable(False)
+samp_type_COMPOUND_WELL.setGeneratedCodePrefix('C')
+
+
+
+prop_type_COMPOUND_BATCH = tr.createNewPropertyType('COMPOUND_BATCH', DataType.MATERIAL)
+prop_type_COMPOUND_BATCH.setLabel('Compound batch material')
+tr.assignPropertyType(samp_type_COMPOUND_WELL, prop_type_COMPOUND_BATCH)
+
+tr.assignPropertyType(samp_type_COMPOUND_WELL, prop_type_COMPOUND)
+
+prop_type_CONCENTRATION_M = tr.createNewPropertyType('CONCENTRATION_M', DataType.REAL)
+prop_type_CONCENTRATION_M.setLabel('Concentration (M)')
+tr.assignPropertyType(samp_type_COMPOUND_WELL, prop_type_CONCENTRATION_M)
+
+#
+# Data Sets
+#
+data_set_type_HCS_IMAGE_RAW = tr.getDataSetType('HCS_IMAGE_RAW')
+
+prop_type_ACQUISITION_BATCH = tr.createNewPropertyType('ACQUISITION_BATCH', DataType.VARCHAR)
+prop_type_ACQUISITION_BATCH.setLabel('Acquisition Batch')
+tr.assignPropertyType(data_set_type_HCS_IMAGE_RAW, prop_type_ACQUISITION_BATCH)
+
diff --git a/sanofi/resource/mock-abase-db/mock-abase-db.sql b/sanofi/resource/mock-abase-db/mock-abase-db.sql
index ae34c8ae1c23fcc5d7084f18c188f4917d90b950..c3d8e6b9dde1e62141be9532f6d231f7282eae64 100644
--- a/sanofi/resource/mock-abase-db/mock-abase-db.sql
+++ b/sanofi/resource/mock-abase-db/mock-abase-db.sql
@@ -1,50 +1,50 @@
-CREATE TABLE plates (WELL_CODE VARCHAR NOT NULL, MATERIAL_CODE VARCHAR NOT NULL, ABASE_COMPOUND_ID VARCHAR NOT NULL, ABASE_COMPOUND_BATCH_ID VARCHAR NOT NULL, ABASE_PLATE_CODE VARCHAR NOT NULL);
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A001', 'COMPOUND-1', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A002', 'COMPOUND-2', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A003', 'COMPOUND-3', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A004', 'COMPOUND-4', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A005', 'COMPOUND-5', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A006', 'COMPOUND-6', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A007', 'COMPOUND-7', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A008', 'COMPOUND-8', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A009', 'COMPOUND-9', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A010', 'COMPOUND-10', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A011', 'COMPOUND-11', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A012', 'COMPOUND-12', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A013', 'COMPOUND-13', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A014', 'COMPOUND-14', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A015', 'COMPOUND-15', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A016', 'COMPOUND-16', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A017', 'COMPOUND-17', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A018', 'COMPOUND-18', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A019', 'COMPOUND-19', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A020', 'COMPOUND-20', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A021', 'COMPOUND-21', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A022', 'COMPOUND-22', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A023', 'COMPOUND-23', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('A024', 'COMPOUND-24', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
+CREATE TABLE plates (WELL_CODE VARCHAR NOT NULL, MATERIAL_CODE VARCHAR NOT NULL, ABASE_COMPOUND_ID VARCHAR NOT NULL, ABASE_PLATE_CODE VARCHAR NOT NULL);
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A001', 'COMPOUND-BATCH-1', 'COMPOUND-1', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A002', 'COMPOUND-BATCH-2', 'COMPOUND-2', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A003', 'COMPOUND-BATCH-3', 'COMPOUND-3', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A004', 'COMPOUND-BATCH-4', 'COMPOUND-4', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A005', 'COMPOUND-BATCH-5', 'COMPOUND-5', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A006', 'COMPOUND-BATCH-6', 'COMPOUND-6', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A007', 'COMPOUND-BATCH-7', 'COMPOUND-7', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A008', 'COMPOUND-BATCH-8', 'COMPOUND-8', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A009', 'COMPOUND-BATCH-9', 'COMPOUND-9', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A010', 'COMPOUND-BATCH-10', 'COMPOUND-10', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A011', 'COMPOUND-BATCH-11', 'COMPOUND-11', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A012', 'COMPOUND-BATCH-12', 'COMPOUND-12', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A013', 'COMPOUND-BATCH-13', 'COMPOUND-13', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A014', 'COMPOUND-BATCH-14', 'COMPOUND-14', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A015', 'COMPOUND-BATCH-15', 'COMPOUND-15', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A016', 'COMPOUND-BATCH-16', 'COMPOUND-16', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A017', 'COMPOUND-BATCH-17', 'COMPOUND-17', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A018', 'COMPOUND-BATCH-18', 'COMPOUND-18', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A019', 'COMPOUND-BATCH-19', 'COMPOUND-19', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A020', 'COMPOUND-BATCH-20', 'COMPOUND-20', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A021', 'COMPOUND-BATCH-21', 'COMPOUND-21', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A022', 'COMPOUND-BATCH-22', 'COMPOUND-22', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A023', 'COMPOUND-BATCH-23', 'COMPOUND-23', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('A024', 'COMPOUND-BATCH-24', 'COMPOUND-24', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P001', 'COMPOUND-1', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P002', 'COMPOUND-2', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P003', 'COMPOUND-3', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P004', 'COMPOUND-4', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P005', 'COMPOUND-5', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P006', 'COMPOUND-6', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P007', 'COMPOUND-7', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P008', 'COMPOUND-8', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P009', 'COMPOUND-9', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P010', 'COMPOUND-10', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P011', 'COMPOUND-11', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P012', 'COMPOUND-12', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P013', 'COMPOUND-13', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P014', 'COMPOUND-14', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P015', 'COMPOUND-15', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P016', 'COMPOUND-16', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P017', 'COMPOUND-17', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P018', 'COMPOUND-18', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P019', 'COMPOUND-19', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P020', 'COMPOUND-20', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P021', 'COMPOUND-21', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P022', 'COMPOUND-22', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P023', 'COMPOUND-23', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
-INSERT INTO plates (well_code, material_code, abase_compound_id, abase_compound_batch_id, abase_plate_code) values ('P024', 'COMPOUND-24', 'ABASE Compound (1)', 'ABASE Batch Compound (1)', 'PLATE1');
\ No newline at end of file
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P001', 'COMPOUND-BATCH-1', 'COMPOUND-1', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P002', 'COMPOUND-BATCH-2', 'COMPOUND-2', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P003', 'COMPOUND-BATCH-3', 'COMPOUND-3', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P004', 'COMPOUND-BATCH-4', 'COMPOUND-4', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P005', 'COMPOUND-BATCH-5', 'COMPOUND-5', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P006', 'COMPOUND-BATCH-6', 'COMPOUND-6', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P007', 'COMPOUND-BATCH-7', 'COMPOUND-7', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P008', 'COMPOUND-BATCH-8', 'COMPOUND-8', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P009', 'COMPOUND-BATCH-9', 'COMPOUND-9', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P010', 'COMPOUND-BATCH-10', 'COMPOUND-10', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P011', 'COMPOUND-BATCH-11', 'COMPOUND-11', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P012', 'COMPOUND-BATCH-12', 'COMPOUND-12', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P013', 'COMPOUND-BATCH-13', 'COMPOUND-13', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P014', 'COMPOUND-BATCH-14', 'COMPOUND-14', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P015', 'COMPOUND-BATCH-15', 'COMPOUND-15', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P016', 'COMPOUND-BATCH-16', 'COMPOUND-16', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P017', 'COMPOUND-BATCH-17', 'COMPOUND-17', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P018', 'COMPOUND-BATCH-18', 'COMPOUND-18', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P019', 'COMPOUND-BATCH-19', 'COMPOUND-19', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P020', 'COMPOUND-BATCH-20', 'COMPOUND-20', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P021', 'COMPOUND-BATCH-21', 'COMPOUND-21', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P022', 'COMPOUND-BATCH-22', 'COMPOUND-22', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P023', 'COMPOUND-BATCH-23', 'COMPOUND-23', 'PLATE1');
+INSERT INTO plates (well_code, material_code, abase_compound_id, abase_plate_code) values ('P024', 'COMPOUND-BATCH-24', 'COMPOUND-24', 'PLATE1');
\ No newline at end of file
diff --git a/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonRollbackTest.java b/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonRollbackTest.java
index 18f477c24f03751de3692a223bcc1b4fc2490a5d..f80f05b15a3fc891096989fc8ff76ad80f6f06fe 100644
--- a/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonRollbackTest.java
+++ b/sanofi/sourceTest/java/ch/systemsx/cisd/sanofi/dss/test/SanofiDropboxJythonRollbackTest.java
@@ -158,7 +158,8 @@ public class SanofiDropboxJythonRollbackTest extends AbstractJythonDataSetHandle
with(any(String.class)), with(anything()));
will(returnValue(queryResult));
- one(openBisService).listMaterials(with(materialCriteria), with(equal(true)));
+ exactly(2).of(openBisService).listMaterials(with(materialCriteria),
+ with(equal(true)));
will(returnValue(Collections.emptyList()));
exactly(4).of(openBisService).createPermId();
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 3c5cf2edf3a6fb6baab3957780ff52a01bb21f57..cb19f009f36dd9af9d2882a3e139f1e302a32c72 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
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.sanofi.dss.test;
+
import static ch.systemsx.cisd.common.Constants.IS_FINISHED_PREFIX;
import static ch.systemsx.cisd.common.test.AssertionUtil.assertContains;
@@ -76,12 +77,6 @@ import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
- * <pre>
- * Things not tested
- * - skip well creation when plate library already exists
- * - skip material creation for preexisting materials
- * </pre>
- *
* @author Kaloyan Enimanev
*/
public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
@@ -101,7 +96,9 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
final String[] ALL_EMAILS = new String[]
{ "admin@sanofi.com", "admin@openbis.org", "donald@duck.com", "mickey@mouse.org" };
- private static final String MATERIAL_TYPE = "COMPOUND";
+ private static final String COMPOUND_MATERIAL_TYPE = "COMPOUND";
+
+ private static final String BATCH_MATERIAL_TYPE = "COMPOUND_BATCH";
private static final String POSITIVE_CONTROL_TYPE = "POSITIVE_CONTROL";
@@ -111,7 +108,10 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
private static final String COMPOUND_WELL_CONCENTRATION_PROPNAME = "CONCENTRATION_M";
- private static final String COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND";
+ // TODO KE: Use this constant after the feedback from Matt
+ //private static final String COMPOUND_WELL_MATERIAL_PROPNAME = "COMPOUND";
+
+ private static final String COMPOUND_WELL_BATCH_PROPNAME = "COMPOUND_BATCH";
private static final String IMAGE_DATA_SET_DIR_NAME = "batchNr_plateCode.variant_2011.07.05";
@@ -348,7 +348,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
with(any(String.class)), with(anything()));
will(returnValue(queryResult));
- one(openBisService).listMaterials(with(materialCriteria), with(equal(true)));
+ exactly(2).of(openBisService).listMaterials(with(materialCriteria),
+ with(equal(true)));
will(returnValue(Collections.emptyList()));
exactly(5).of(openBisService).createPermId();
@@ -374,8 +375,10 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
handler.handle(markerFile);
- assertEquals(MATERIAL_TYPE, materialCriteria.recordedObject().tryGetMaterialType()
- .getCode());
+ assertEquals(COMPOUND_MATERIAL_TYPE, materialCriteria.getRecordedObjects().get(0)
+ .tryGetMaterialType().getCode());
+ assertEquals(BATCH_MATERIAL_TYPE, materialCriteria.getRecordedObjects().get(1)
+ .tryGetMaterialType().getCode());
assertEquals(true, queryResult.hasCloseBeenInvoked());
List<NewSample> registeredSamples =
@@ -494,7 +497,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
with(any(String.class)), with(anything()));
will(returnValue(queryResult));
- one(openBisService).listMaterials(with(materialCriteria), with(equal(true)));
+ exactly(2).of(openBisService).listMaterials(with(materialCriteria),
+ with(equal(true)));
will(returnValue(Collections.emptyList()));
exactly(3).of(openBisService).createPermId();
@@ -520,8 +524,10 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
handler.handle(markerFile);
- assertEquals(MATERIAL_TYPE, materialCriteria.recordedObject().tryGetMaterialType()
- .getCode());
+ assertEquals(COMPOUND_MATERIAL_TYPE, materialCriteria.getRecordedObjects().get(0)
+ .tryGetMaterialType().getCode());
+ assertEquals(BATCH_MATERIAL_TYPE, materialCriteria.getRecordedObjects().get(1)
+ .tryGetMaterialType().getCode());
assertEquals(true, queryResult.hasCloseBeenInvoked());
List<NewSample> registeredSamples =
@@ -566,8 +572,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
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"));
+ queryResult.add(createQueryResult("A1", "batch_material", "compound_material"));
+ queryResult.add(createQueryResult("B1", "batch_material", "compound_material"));
setDataSetExpectations();
setUpListAdministratorExpectations();
@@ -579,7 +585,8 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
with(any(String.class)), with(anything()));
will(returnValue(queryResult));
- one(openBisService).listMaterials(with(materialCriteria), with(equal(true)));
+ exactly(2).of(openBisService).listMaterials(with(materialCriteria),
+ with(equal(true)));
will(returnValue(Collections.emptyList()));
exactly(4).of(openBisService).createPermId();
@@ -605,8 +612,10 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
handler.handle(markerFile);
- assertEquals(MATERIAL_TYPE, materialCriteria.recordedObject().tryGetMaterialType()
- .getCode());
+ assertEquals(COMPOUND_MATERIAL_TYPE, materialCriteria.getRecordedObjects().get(0)
+ .tryGetMaterialType().getCode());
+ assertEquals(BATCH_MATERIAL_TYPE, materialCriteria.getRecordedObjects().get(1)
+ .tryGetMaterialType().getCode());
assertEquals(true, queryResult.hasCloseBeenInvoked());
List<NewSample> registeredSamples =
@@ -614,9 +623,9 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
assertEquals(4, registeredSamples.size());
assertAllSamplesHaveContainer(registeredSamples, plate.getIdentifier());
- assertCompoundWell(registeredSamples, "A1", "0.75", "material-1");
+ assertCompoundWell(registeredSamples, "A1", "0.75", "batch_material", "compound_material");
assertPositiveControl(registeredSamples, "A2");
- assertCompoundWell(registeredSamples, "B1", "54.12", "material-1");
+ assertCompoundWell(registeredSamples, "B1", "54.12", "batch_material", "compound_material");
List<? extends NewExternalData> dataSetsRegistered =
atomicatOperationDetails.recordedObject().getDataSetRegistrations();
@@ -637,8 +646,17 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
Map<String, List<NewMaterial>> materialsRegistered =
atomicatOperationDetails.recordedObject().getMaterialRegistrations();
- assertEquals(1, materialsRegistered.size());
- assertEquals("material-1", materialsRegistered.get(MATERIAL_TYPE).get(0).getCode());
+ assertEquals(2, materialsRegistered.size());
+
+ final List<NewMaterial> compoundMaterialsRegistered =
+ materialsRegistered.get(COMPOUND_MATERIAL_TYPE);
+ assertEquals(1, compoundMaterialsRegistered.size());
+ assertEquals("compound_material", compoundMaterialsRegistered.get(0).getCode());
+
+ final List<NewMaterial> batchMaterialsRegistered =
+ materialsRegistered.get(BATCH_MATERIAL_TYPE);
+ assertEquals(1, batchMaterialsRegistered.size());
+ assertEquals("batch_material", batchMaterialsRegistered.get(0).getCode());
AssertionUtil
.assertContains(
@@ -702,12 +720,14 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
private void assertCompoundWell(List<NewSample> newSamples, String wellCode,
String concentration)
{
- String materialCode = getMaterialCodeByWellCode(wellCode);
- assertCompoundWell(newSamples, wellCode, concentration, materialCode);
+ String batchMaterialCode = getBatchMaterialCodeByWellCode(wellCode);
+ String compoundMaterialCode = getCompoundMaterialCodeByWellCode(wellCode);
+ assertCompoundWell(newSamples, wellCode, concentration, batchMaterialCode,
+ compoundMaterialCode);
}
private void assertCompoundWell(List<NewSample> newSamples, String wellCode,
- String concentration, String materialCode)
+ String concentration, String batchMaterialCode, String compoundMaterialCode)
{
NewSample newSample = findByWellCode(newSamples, wellCode);
assertEquals(COMPOUND_WELL_TYPE, newSample.getSampleType().getCode());
@@ -719,15 +739,24 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
assertEquals("Invalid concentration value for well '" + wellCode + "': ", concentration,
concentrationProp.tryGetAsString());
- MaterialIdentifier materialIdentifier = new MaterialIdentifier(materialCode, MATERIAL_TYPE);
-
- IEntityProperty wellMaterialProp =
+ MaterialIdentifier batchMaterialIdentifier =
+ new MaterialIdentifier(batchMaterialCode, BATCH_MATERIAL_TYPE);
+ IEntityProperty batchMaterialProp =
EntityHelper.tryFindProperty(newSample.getProperties(),
- COMPOUND_WELL_MATERIAL_PROPNAME);
- assertNotNull(wellMaterialProp);
- assertEquals("Invalid material found in well '" + wellCode + "': ",
- materialIdentifier.print(), wellMaterialProp.tryGetAsString());
-
+ COMPOUND_WELL_BATCH_PROPNAME);
+ assertNotNull(batchMaterialProp);
+ assertEquals("Invalid batch material found in well '" + wellCode + "': ",
+ batchMaterialIdentifier.print(), batchMaterialProp.tryGetAsString());
+ // TODO KE: check created BATCH MATERIAL properties (we need to have a "COMPOUND" property !)
+ //
+ // MaterialIdentifier compoundMaterialIdentifier =
+ // new MaterialIdentifier(compoundMaterialCode, COMPOUND_MATERIAL_TYPE);
+ // IEntityProperty compoundMaterialProp =
+ // EntityHelper.tryFindProperty(newSample.getProperties(),
+ // COMPOUND_WELL_MATERIAL_PROPNAME);
+ // assertNotNull(compoundMaterialProp);
+ // assertEquals("Invalid compound material found in well '" + wellCode + "': ",
+ // compoundMaterialIdentifier.print(), compoundMaterialProp.tryGetAsString());
}
public Sample plateWithLibTemplateAndGeometry(String libraryTemplate, String plateGeometry)
@@ -865,22 +894,28 @@ public class SanofiDropboxJythonTest extends AbstractJythonDataSetHandlerTest
private Map<String, Object> createQueryResult(String wellCode)
{
- return createQueryResult(wellCode, getMaterialCodeByWellCode(wellCode));
+ return createQueryResult(wellCode, getBatchMaterialCodeByWellCode(wellCode),
+ getCompoundMaterialCodeByWellCode(wellCode));
}
- private Map<String, Object> createQueryResult(String wellCode, String materialCode)
+ private Map<String, Object> createQueryResult(String wellCode, String batchMaterialCode,
+ String compoundMaterialCode)
{
Map<String, Object> result = new HashMap<String, Object>();
result.put("WELL_CODE", wellCode);
- result.put("MATERIAL_CODE", materialCode);
- result.put("ABASE_COMPOUND_ID", wellCode + "_compound_id");
- result.put("ABASE_COMPOUND_BATCH_ID", wellCode + "_compound_batch_id");
+ result.put("MATERIAL_CODE", batchMaterialCode);
+ result.put("ABASE_COMPOUND_ID", compoundMaterialCode);
return result;
}
- private String getMaterialCodeByWellCode(String wellCode)
+ private String getBatchMaterialCodeByWellCode(String wellCode)
+ {
+ return wellCode + "_batch_material";
+ }
+
+ private String getCompoundMaterialCodeByWellCode(String wellCode)
{
- return wellCode + "_material_code";
+ return wellCode + "_compound_material";
}
@Override