diff --git a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes/weismigration/migration.py b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes/weismigration/migration.py
index f3936d9ecab9e1ed62f7418a2865a5dc641c99d5..ce03c48b8f9026aab5d13ba983e676fd46c8c88d 100644
--- a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes/weismigration/migration.py
+++ b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes/weismigration/migration.py
@@ -195,37 +195,37 @@ def setPlasmidParents(tr, definition, entity, properties):
if propertyValue is not None and propertyDefinition[0] == "PCR_3_OLIGO" or propertyDefinition[0] == "PCR_5_OLIGO":
propertyValue = unicode(propertyValue)
if re.match ("UC# ", propertyValue) and not re.search("/", propertyValue):
- parentCode = "/MATERIALS/"+ propertyValue.replace("UC# ", "US").strip(" ")
+ parentCode = "/MATERIALS/"+ propertyValue.replace("UC# ", "UC").strip(" ")
currentParentsList = entity.getParentSampleIdentifiers()
currentParentsList.add(parentCode)
entity.setParentSampleIdentifiers(currentParentsList)
elif re.match ("UC#", propertyValue) and not re.search("/", propertyValue):
- parentCode= "/MATERIALS/"+ propertyValue.replace("UC#", "US").strip(" ")
+ parentCode= "/MATERIALS/"+ propertyValue.replace("UC#", "UC").strip(" ")
currentParentsList = entity.getParentSampleIdentifiers()
currentParentsList.add(parentCode)
entity.setParentSampleIdentifiers(currentParentsList)
elif re.match ("UC #", propertyValue) and not re.search("/", propertyValue):
- parentCode= "/MATERIALS/"+ propertyValue.replace("UC #", "US").strip(" ")
+ parentCode= "/MATERIALS/"+ propertyValue.replace("UC #", "UC").strip(" ")
currentParentsList = entity.getParentSampleIdentifiers()
currentParentsList.add(parentCode)
entity.setParentSampleIdentifiers(currentParentsList)
elif re.match ("UC ", propertyValue) and not re.search("/", propertyValue):
- parentCode="/MATERIALS/"+ propertyValue.replace("UC ", "US").strip(" ")
+ parentCode="/MATERIALS/"+ propertyValue.replace("UC ", "UC").strip(" ")
currentParentsList = entity.getParentSampleIdentifiers()
currentParentsList.add(parentCode)
entity.setParentSampleIdentifiers(currentParentsList)
elif re.match ("UC1388cc", propertyValue):
- parentCode="/MATERIALS/"+ propertyValue.replace("UC1388cc", "US1388").strip(" ")
+ parentCode="/MATERIALS/"+ propertyValue.replace("UC1388cc", "UC1388").strip(" ")
currentParentsList = entity.getParentSampleIdentifiers()
currentParentsList.add(parentCode)
entity.setParentSampleIdentifiers(currentParentsList)
elif re.match ("UC2396c", propertyValue):
- parentCode="/MATERIALS/"+ propertyValue.replace("UC2396c", "US2396").strip(" ")
+ parentCode="/MATERIALS/"+ propertyValue.replace("UC2396c", "UC2396").strip(" ")
currentParentsList = entity.getParentSampleIdentifiers()
currentParentsList.add(parentCode)
entity.setParentSampleIdentifiers(currentParentsList)
elif re.match ("UC", propertyValue) and not re.search("/", propertyValue):
- parentCode= "/MATERIALS/"+ propertyValue.replace("UC", "US").strip(" ")
+ parentCode= "/MATERIALS/"+ propertyValue.strip(" ")
currentParentsList = entity.getParentSampleIdentifiers()
currentParentsList.add(parentCode)
entity.setParentSampleIdentifiers(currentParentsList)
@@ -234,6 +234,13 @@ def setPlasmidParents(tr, definition, entity, properties):
currentParentsList = entity.getParentSampleIdentifiers()
currentParentsList.add(parentCode)
entity.setParentSampleIdentifiers(currentParentsList)
+ elif re.match ("Ch", propertyValue):
+ parentCode="/MATERIALS/"+ propertyValue.replace("Ch", "CH").strip(" ")
+ currentParentsList = entity.getParentSampleIdentifiers()
+ currentParentsList.add(parentCode)
+ entity.setParentSampleIdentifiers(currentParentsList)
+ else:
+ print "PARENT NOT SET: ", propertyDefinition[0] , propertyValue
@@ -368,7 +375,7 @@ class FileMakerEntityAdaptor(EntityAdaptor):
##
## Customer specific logic: different sample types
##
-class FMPeterOpenBISDTO(OpenBISDTO):
+class FMOpenBISDTO(OpenBISDTO):
def isSampleCacheable(self):
return True
@@ -379,6 +386,7 @@ class FMPeterOpenBISDTO(OpenBISDTO):
sampleID2Sample[self.values["NAME"]] = self.values
sample = getSampleForUpdate("/MATERIALS/"+code, None, tr)
if sample is not None:
+ #needs_update = db_val != prop_val
lastModificationData = self.values["MODIFICATION_DATE"].strip()
lastModificationData = str(datetime.strptime(lastModificationData, "%Y-%m-%d"))[:10]
lastModificationOpenBIS = sample.getPropertyValue("MODIFICATION_DATE")[:10]
@@ -389,13 +397,13 @@ class FMPeterOpenBISDTO(OpenBISDTO):
print "* ERROR [" + str(code) + "] - Invalid Code found for '" + self.__class__.__name__ + "'"
raise Exception('Invalid Code found ' + str(code))
-class FMPeterMultipleValuesAdaptor(FileMakerEntityAdaptor):
+class FMMultipleValuesAdaptor(FileMakerEntityAdaptor):
selectMultipleValuesQuery = None
entityIdFieldName = None
entityCodeFieldName = None
def addEntity(self, values):
- self.entities.append(FMPeterEntityMultipleValuesOpenBISDTO(values, self.definition))
+ self.entities.append(FMEntityMultipleValuesOpenBISDTO(values, self.definition))
def init(self):
print "Reading MultipleValueses for: " + self.__class__.__name__
@@ -409,12 +417,12 @@ class FMPeterMultipleValuesAdaptor(FileMakerEntityAdaptor):
if entityId is not None:
if entityId in sampleID2Sample:
entityNumber = sampleID2Sample[entityId][self.entityCodeFieldName]
+ print "entityNumber: ", entityNumber, entityId
if entityNumber is not None:
values = {}
values["DISRUPTIONS"] = result.getString("disruptions")
values["MARKERS"] = result.getString("markers")
values["UNMARKED_MUTATIONS"] = result.getString("unmarked mutations")
-
allMultipleValueses = []
if entityNumber in MultipleValueses:
@@ -440,7 +448,7 @@ class FMPeterMultipleValuesAdaptor(FileMakerEntityAdaptor):
result.close()
preparedStatement.close()
-class FMPeterEntityMultipleValuesOpenBISDTO(OpenBISDTO):
+class FMEntityMultipleValuesOpenBISDTO(OpenBISDTO):
def getIdentifier(self, tr):
return self.values["*CODE"]
@@ -460,8 +468,7 @@ class FMPeterEntityMultipleValuesOpenBISDTO(OpenBISDTO):
for propertyCode, propertyValue in MultipleValues.iteritems():
if propertyValue is not None:
- propertyValue = unicode(propertyValue)
- print "PROPCODE", propertyCode, str(MultipleValuesNum), propertyValue
+ propertyValue = unicode(propertyValue)
sample.setPropertyValue(propertyCode + "_" + str(MultipleValuesNum), propertyValue)
def isMultipleValuesPressent(self, MultipleValuesSignature, tr):
@@ -471,10 +478,10 @@ class FMPeterEntityMultipleValuesOpenBISDTO(OpenBISDTO):
storedSignature = "";
for propertyCode in definitions.getRepetitionPropertyCodes():
propertyValue = sample.getPropertyValue(propertyCode + "_" + str(MultipleValuesNum))
- print propertyCode+ "_" + str(MultipleValuesNum), propertyValue
+
if propertyValue is not None:
propertyValue = unicode(propertyValue)
- storedSignature += propertyValue
+ storedSignature += propertyValue
if storedSignature == MultipleValuesSignature:
#print "Found MultipleValues " + storedSignature.encode('ascii', 'ignore')
return True
@@ -485,13 +492,16 @@ class FMPeterEntityMultipleValuesOpenBISDTO(OpenBISDTO):
MultipleValuesSignature = "";
for propertyCode in definitions.getRepetitionPropertyCodes():
propertyValue = MultipleValues[propertyCode]
-
+ #print "propertyValue = MultipleValues[propertyCode]: " , propertyValue
if propertyValue is not None:
propertyValue = unicode(propertyValue)
MultipleValuesSignature += propertyValue
if not self.isMultipleValuesPressent(MultipleValuesSignature, tr):
return False
return True
+
+
+
##
## Antibodies
##
@@ -507,7 +517,7 @@ class AntibodyAdaptor(FileMakerEntityAdaptor):
self.entities.append(AntibodyOpenBISDTO(values, self.definition))
-class AntibodyOpenBISDTO(FMPeterOpenBISDTO):
+class AntibodyOpenBISDTO(FMOpenBISDTO):
def isSampleCacheable(self):
return False
@@ -534,27 +544,26 @@ class AntibodyOpenBISDTO(FMPeterOpenBISDTO):
class StrainAdaptor(FileMakerEntityAdaptor):
def init(self):
- self.selectQuery = "SELECT * FROM \"Weis Lab Yeast Strains\""
+ self.selectQuery = "SELECT * FROM \"Weis Lab Yeast Strains\" "
self.definition = definitions.strainDefinition
FileMakerEntityAdaptor.init(self)
def addEntity(self, values):
self.entities.append(StrainOpenBISDTO(values, self.definition))
-class StrainOpenBISDTO(FMPeterOpenBISDTO):
+class StrainOpenBISDTO(FMOpenBISDTO):
def write(self, tr):
code = self.values["NAME"]
if code is not None:
sample = getSampleForUpdate("/MATERIALS/"+code,"STRAIN", tr)
setEntityProperties(tr, self.definition, sample, self.values)
- print setEntityProperties(tr, self.definition, sample, self.values)
-
+
def getIdentifier(self, tr):
code = self.values["NAME"]
return code
-class StrainMultipleValuesAdaptor(FMPeterMultipleValuesAdaptor):
+class StrainMultipleValuesAdaptor(FMMultipleValuesAdaptor):
selectMultipleValuesQuery = "SELECT * FROM \"Weis Lab Yeast Strains\""
entityIdFieldName = "KWY number"
entityCodeFieldName = "NAME"
@@ -571,7 +580,7 @@ class PlasmidAdaptor(FileMakerEntityAdaptor):
def addEntity(self, values):
self.entities.append(PlasmidOpenBISDTO(values, self.definition))
-class PlasmidOpenBISDTO(FMPeterOpenBISDTO):
+class PlasmidOpenBISDTO(FMOpenBISDTO):
def write(self, tr):
code = "PKW" + self.values["NAME"]
if code is not None:
@@ -599,11 +608,18 @@ class OligoAdaptor(FileMakerEntityAdaptor):
def addEntity(self, values):
self.entities.append(OligoOpenBISDTO(values, self.definition))
-class OligoOpenBISDTO(FMPeterOpenBISDTO):
+class OligoOpenBISDTO(FMOpenBISDTO):
def write(self, tr):
code = self.values["NAME"]
if code is not None:
- sample = getSampleForUpdate("/MATERIALS/"+code,"OLIGO", tr)
+ if re.search("CHCH", code):
+ code = code.replace("CHCH", "CH")
+ sample = getSampleForUpdate("/MATERIALS/"+code,"OLIGO", tr)
+ elif re.search("CH", code):
+ sample = getSampleForUpdate("/MATERIALS/"+code,"OLIGO", tr)
+ elif re.search("US", code):
+ code = code.replace("US", "UC")
+ sample = getSampleForUpdate("/MATERIALS/"+code,"OLIGO", tr)
setEntityProperties(tr, self.definition, sample, self.values);
def getIdentifier(self, tr):
@@ -626,7 +642,7 @@ class ChemicalAdaptor(FileMakerEntityAdaptor):
self.entities.append(ChemicalOpenBISDTO(values, self.definition))
-class ChemicalOpenBISDTO(FMPeterOpenBISDTO):
+class ChemicalOpenBISDTO(FMOpenBISDTO):
def isSampleCacheable(self):
return False
@@ -652,7 +668,7 @@ class EnzymeAdaptor(FileMakerEntityAdaptor):
def addEntity(self, values):
self.entities.append(EnzymeOpenBISDTO(values, self.definition))
-class EnzymeOpenBISDTO(FMPeterOpenBISDTO):
+class EnzymeOpenBISDTO(FMOpenBISDTO):
def isSampleCacheable(self):
return False
@@ -671,35 +687,21 @@ class EnzymeOpenBISDTO(FMPeterOpenBISDTO):
-#fmConnString = "jdbc:filemaker://127.0.0.1/"
-fmConnString = "jdbc:filemaker://fmsrv.ethz.ch/"
+fmConnString = "jdbc:filemaker://127.0.0.1/"
+#fmConnString = "jdbc:filemaker://fmsrv.ethz.ch/"
fmUser= "admin"
fmPass = "nucleus"
-# adaptors = [ AntibodyAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_antibodies_Peter"),
-# AntibodyMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_antibody_MultipleValueses_Peter"),
-# PlasmidAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_plasmids_Peter"),
-# PlasmidMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_plasmid_MultipleValueses_Peter"),
-# StrainAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_strains_Peter"),
-# StrainMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_strain_MultipleValueses_Peter"),
-# OligoAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_oligos_Peter"),
-# OligoMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_oligo_MultipleValueses_Peter"),
-# CellAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_cells_Peter"),
-# CellMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_cell_MultipleValueses_Peter"),
-# SirnaAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_Main_Menu_Peter"),
-# ChemicalAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_Main_Menu_Peter"),
-# DocumentsAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_documents_Peter")]
-
adaptors = [
#EnzymeAdaptor(fmConnString, fmUser, fmPass, "Weis_Restriction_enzymes"),
- #hemicalAdaptor(fmConnString, fmUser, fmPass, "Weis_Chemicals"),
+ #ChemicalAdaptor(fmConnString, fmUser, fmPass, "Weis_Chemicals"),
#AntibodyAdaptor(fmConnString, fmUser, fmPass, "Weis _Antibodies"),
#OligoAdaptor(fmConnString, fmUser, fmPass, "Weis_Oligos"),
- #PlasmidAdaptor(fmConnString, fmUser, fmPass, "Weis_Plasmids"),
- StrainAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains"),
- StrainMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains")
+ PlasmidAdaptor(fmConnString, fmUser, fmPass, "Weis_Plasmids"),
+ #StrainAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains_070715_Clone_for_testing2"),
+ #StrainMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains_070715_Clone_for_testing2")
]