Skip to content
Snippets Groups Projects
Commit fa77d0ec authored by barillac's avatar barillac
Browse files

adapted to Weis lab def 

SVN: 34301
parent 40e579ad
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
plasmid/source/core-plugins/weismigration/1/dss/drop-boxes/weismigration/migration.py
+ 90
− 101
View file @ fa77d0ec
...@@ -68,7 +68,7 @@ def setEntityProperties(tr, definition, entity, properties): ...@@ -68,7 +68,7 @@ def setEntityProperties(tr, definition, entity, properties):
for propertyCode, propertyValue in properties.iteritems(): for propertyCode, propertyValue in properties.iteritems():
propertyDefinition = definitions.getPropertyDefinitionByCode(definition, propertyCode) propertyDefinition = definitions.getPropertyDefinitionByCode(definition, propertyCode)
if propertyValue is not None: if propertyValue is not None:
propertyValue = unicode(propertyValue) propertyValue = unicode(propertyValue)
if propertyDefinition is not None and propertyDefinition[3] == DataType.TIMESTAMP and propertyValue is not None: if propertyDefinition is not None and propertyDefinition[3] == DataType.TIMESTAMP and propertyValue is not None:
date_val = datetime.strptime(propertyValue, "%Y") date_val = datetime.strptime(propertyValue, "%Y")
...@@ -129,9 +129,12 @@ def setEntityProperties(tr, definition, entity, properties): ...@@ -129,9 +129,12 @@ def setEntityProperties(tr, definition, entity, properties):
entity.setPropertyValue("COMPANY", propertyValue) entity.setPropertyValue("COMPANY", propertyValue)
else: else:
entity.setPropertyValue(propertyCode, propertyValue) entity.setPropertyValue(propertyCode, propertyValue)
def setEntityParents(tr, definition, entity, properties):
def setPlasmidParents(tr, definition, entity, properties):
for propertyCode, propertyValue in properties.iteritems(): for propertyCode, propertyValue in properties.iteritems():
propertyDefinition = definitions.getPropertyDefinitionByCode(definition, propertyCode) propertyDefinition = definitions.getPropertyDefinitionByCode(definition, propertyCode)
...@@ -171,11 +174,8 @@ def setEntityParents(tr, definition, entity, properties): ...@@ -171,11 +174,8 @@ def setEntityParents(tr, definition, entity, properties):
else: else:
print "NO PARENT WAS SET FOR THIS FOUND VALUE:", propertyValue print "NO PARENT WAS SET FOR THIS FOUND VALUE:", propertyValue
# elif propertyDefinition[0] == "INSERT":
# if re.match()
#entity.setParentSampleIdentifiers()
## ##
...@@ -256,8 +256,8 @@ def getSampleForUpdate(sampleIdentifier, sampleType, tr): ...@@ -256,8 +256,8 @@ def getSampleForUpdate(sampleIdentifier, sampleType, tr):
#print "Cache Create " + sampleIdentifier + ":" + str(sampleType) #print "Cache Create " + sampleIdentifier + ":" + str(sampleType)
if sampleType == "ANTIBODY": if sampleType == "ANTIBODY":
experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/ANTIBODIES", sampleType, tr) experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/ANTIBODIES", sampleType, tr)
# elif sampleType == "STRAIN": elif sampleType == "STRAIN":
# experiment = getExperimentForUpdate("/MATERIALS/YEASTS/YEAST_COLLECTION_1", sampleType, tr) experiment = getExperimentForUpdate("/MATERIALS/YEASTS/YEAST_COLLECTION_1", sampleType, tr)
elif sampleType == "PLASMID": elif sampleType == "PLASMID":
experiment = getExperimentForUpdate("/MATERIALS/PLASMIDS/PLASMID_COLLECTION_1", sampleType, tr) experiment = getExperimentForUpdate("/MATERIALS/PLASMIDS/PLASMID_COLLECTION_1", sampleType, tr)
elif sampleType == "CHEMICAL": elif sampleType == "CHEMICAL":
...@@ -329,124 +329,107 @@ class FMPeterOpenBISDTO(OpenBISDTO): ...@@ -329,124 +329,107 @@ class FMPeterOpenBISDTO(OpenBISDTO):
print "* ERROR [" + str(code) + "] - Invalid Code found for '" + self.__class__.__name__ + "'" print "* ERROR [" + str(code) + "] - Invalid Code found for '" + self.__class__.__name__ + "'"
raise Exception('Invalid Code found ' + str(code)) raise Exception('Invalid Code found ' + str(code))
class FMPeterBoxAdaptor(FileMakerEntityAdaptor): class FMPeterMultipleValuesAdaptor(FileMakerEntityAdaptor):
selectBoxQuery = None selectMultipleValuesQuery = None
entityIdFieldName = None entityIdFieldName = None
entityCodeFieldName = None entityCodeFieldName = None
def addEntity(self, values): def addEntity(self, values):
self.entities.append(FMPeterEntityBoxOpenBISDTO(values, self.definition)) self.entities.append(FMPeterEntityMultipleValuesOpenBISDTO(values, self.definition))
def init(self): def init(self):
#print "Reading boxes for: " + self.__class__.__name__ print "Reading MultipleValueses for: " + self.__class__.__name__
emptyBox = 0 emptyMultipleValues = 0
boxes = {} MultipleValueses = {}
EntityAdaptor.init(self) EntityAdaptor.init(self)
preparedStatement = self.connection.prepareStatement(self.selectBoxQuery) preparedStatement = self.connection.prepareStatement(self.selectMultipleValuesQuery)
result = preparedStatement.executeQuery() result = preparedStatement.executeQuery()
while result.next(): while result.next():
entityId = unicode(result.getString(self.entityIdFieldName)) entityId = unicode(result.getString(self.entityIdFieldName))
if entityId is not None: if entityId is not None:
if entityId in sampleID2Sample: if entityId in sampleID2Sample:
antibodyNumber = sampleID2Sample[entityId][self.entityCodeFieldName] entityNumber = sampleID2Sample[entityId][self.entityCodeFieldName]
if antibodyNumber is not None: if entityNumber is not None:
values = {} values = {}
values["STORAGE_NAME"] = result.getString("location") values["DISRUPTIONS"] = result.getString("disruptions")
values["STORAGE_ROW"] = None values["MARKERS"] = result.getString("markers")
values["STORAGE_COLUMN"] = None values["UNMARKED_MUTATIONS"] = result.getString("unmarked mutations")
values["STORAGE_BOX_NAME"] = result.getString("box label")
values["STORAGE_USER"] = result.getString("frozen by")
values["STORAGE_BOX_POSITION"] = result.getString("position")
allBoxes = [] allMultipleValueses = []
if antibodyNumber in boxes: if entityNumber in MultipleValueses:
allBoxes = boxes[antibodyNumber] allMultipleValueses = MultipleValueses[entityNumber]
else: else:
boxes[antibodyNumber] = allBoxes MultipleValueses[entityNumber] = allMultipleValueses
allBoxes.append(values) allMultipleValueses.append(values)
else: else:
#The antibody is not there. What the *#%$& #The entity is not there. What the *#%$&
emptyBox += 1 emptyMultipleValues += 1
else: else:
#The antibody is not there. What the *#%$& #The entity is not there. What the *#%$&
emptyBox += 1 emptyMultipleValues += 1
print "- ERROR ADAPTOR Boxes positions with empty entityId for " + self.__class__.__name__ + ":" + str(emptyBox) print "- ERROR ADAPTOR MultipleValueses positions with empty entityId for " + self.__class__.__name__ + ":" + str(emptyMultipleValues)
for entiyCode, allBoxes in boxes.iteritems(): for entiyCode, allMultipleValueses in MultipleValueses.iteritems():
self.addEntity({ self.addEntity({
"*CODE" : entiyCode, "*CODE" : entiyCode,
"*BOXESLIST" : allBoxes "*MultipleValuesESLIST" : allMultipleValueses
}) })
result.close() result.close()
preparedStatement.close() preparedStatement.close()
class FMPeterEntityBoxOpenBISDTO(OpenBISDTO): class FMPeterEntityMultipleValuesOpenBISDTO(OpenBISDTO):
def getIdentifier(self, tr): def getIdentifier(self, tr):
return self.values["*CODE"] return self.values["*CODE"]
def write(self, tr): def write(self, tr):
sample = getSampleForUpdate("/MATERIALS/"+self.values["*CODE"], None, tr) sample = getSampleForUpdate("/MATERIALS/"+self.values["*CODE"], None, tr)
print "* INFO Boxes size: " + str(len(self.values["*BOXESLIST"])) print "* INFO MultipleValueses size: " + str(len(self.values["*MultipleValuesESLIST"]))
#Delete old boxes #Delete old MultipleValueses
for boxNum in range(1, definitions.numberOfStorageGroups+1): for MultipleValuesNum in range(1, definitions.numberOfRepetitions+1):
for propertyCode in definitions.getStorageGroupPropertyCodes(): for propertyCode in definitions.getRepetitionPropertyCodes():
sample.setPropertyValue(propertyCode + "_" + str(boxNum), None) sample.setPropertyValue(propertyCode + "_" + str(MultipleValuesNum), None)
#Add new boxes #Add new MultipleValueses
boxNum = 1 MultipleValuesNum = 0
for box in self.values["*BOXESLIST"]: for MultipleValues in self.values["*MultipleValuesESLIST"]:
boxNum += 1 MultipleValuesNum += 1
for propertyCode, propertyValue in box.iteritems(): for propertyCode, propertyValue in MultipleValues.iteritems():
if propertyCode == "STORAGE_NAME":
freezerName = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("FREEZER", propertyValue)
if freezerName is None:
#print repr("NOT FOUND FEEZER: " + self.values["ANTIBODY_ID_NR"] + " : '" + unicode(propertyValue) + "'")
propertyValue = None
else:
propertyValue = freezerName
if propertyCode == "STORAGE_USER":
storageUser = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("LAB_MEMBERS", propertyValue)
if storageUser is None:
#print repr("NOT FOUND USER: " + self.values["ANTIBODY_ID_NR"] + " : '" + unicode(propertyValue) + "'")
propertyValue = None
else:
propertyValue = storageUser
if propertyValue is not None: if propertyValue is not None:
propertyValue = unicode(propertyValue) propertyValue = unicode(propertyValue)
sample.setPropertyValue(propertyCode + "_" + str(boxNum), propertyValue) print "PROPCODE", propertyCode, str(MultipleValuesNum), propertyValue
sample.setPropertyValue(propertyCode + "_" + str(MultipleValuesNum), propertyValue)
def isBoxPressent(self, boxSignature, tr): def isMultipleValuesPressent(self, MultipleValuesSignature, tr):
sample = getSampleForUpdate("/MATERIALS/"+self.values["*CODE"], None, tr) sample = getSampleForUpdate("/MATERIALS/"+self.values["*CODE"], None, tr)
if sample is not None: if sample is not None:
for boxNum in range(1, definitions.numberOfStorageGroups+1): for MultipleValuesNum in range(1, definitions.numberOfRepetitions+1):
storedSignature = ""; storedSignature = "";
for propertyCode in definitions.getStorageGroupPropertyCodes(): for propertyCode in definitions.getRepetitionPropertyCodes():
propertyValue = sample.getPropertyValue(propertyCode + "_" + str(boxNum)) propertyValue = sample.getPropertyValue(propertyCode + "_" + str(MultipleValuesNum))
print propertyCode+ "_" + str(MultipleValuesNum), propertyValue
if propertyValue is not None: if propertyValue is not None:
propertyValue = unicode(propertyValue) propertyValue = unicode(propertyValue)
storedSignature += propertyValue storedSignature += propertyValue
if storedSignature == boxSignature: if storedSignature == MultipleValuesSignature:
#print "Found Box " + storedSignature.encode('ascii', 'ignore') #print "Found MultipleValues " + storedSignature.encode('ascii', 'ignore')
return True return True
return False return False
def isInOpenBIS(self, tr): def isInOpenBIS(self, tr):
for box in self.values["*BOXESLIST"]: for MultipleValues in self.values["*MultipleValuesESLIST"]:
boxSignature = ""; MultipleValuesSignature = "";
for propertyCode in definitions.getStorageGroupPropertyCodes(): for propertyCode in definitions.getRepetitionPropertyCodes():
propertyValue = box[propertyCode] propertyValue = MultipleValues[propertyCode]
if propertyCode == "STORAGE_NAME":
propertyValue = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("FREEZER", propertyValue)
if propertyCode == "STORAGE_USER":
propertyValue = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("LAB_MEMBERS_INITIALS", propertyValue)
if propertyValue is not None: if propertyValue is not None:
propertyValue = unicode(propertyValue) propertyValue = unicode(propertyValue)
boxSignature += propertyValue MultipleValuesSignature += propertyValue
if not self.isBoxPressent(boxSignature, tr): if not self.isMultipleValuesPressent(MultipleValuesSignature, tr):
return False return False
return True return True
## ##
...@@ -486,7 +469,7 @@ class AntibodyOpenBISDTO(FMPeterOpenBISDTO): ...@@ -486,7 +469,7 @@ class AntibodyOpenBISDTO(FMPeterOpenBISDTO):
class StrainAdaptor(FileMakerEntityAdaptor): class StrainAdaptor(FileMakerEntityAdaptor):
def init(self): def init(self):
self.selectQuery = "SELECT * FROM \"boxit strains\"" self.selectQuery = "SELECT * FROM \"Weis Lab Yeast Strains\""
self.definition = definitions.strainDefinition self.definition = definitions.strainDefinition
FileMakerEntityAdaptor.init(self) FileMakerEntityAdaptor.init(self)
...@@ -495,16 +478,20 @@ class StrainAdaptor(FileMakerEntityAdaptor): ...@@ -495,16 +478,20 @@ class StrainAdaptor(FileMakerEntityAdaptor):
class StrainOpenBISDTO(FMPeterOpenBISDTO): class StrainOpenBISDTO(FMPeterOpenBISDTO):
def write(self, tr): def write(self, tr):
code = self.values["STRAIN_ID_NR"] code = self.values["NAME"]
if code is not None: if code is not None:
sample = getSampleForUpdate("/MATERIALS/"+code,"STRAIN", tr) sample = getSampleForUpdate("/MATERIALS/"+code,"STRAIN", tr)
setEntityProperties(tr, self.definition, sample, self.values); setEntityProperties(tr, self.definition, sample, self.values)
print setEntityProperties(tr, self.definition, sample, self.values)
def getIdentifier(self, tr): def getIdentifier(self, tr):
code = self.values["STRAIN_ID_NR"] code = self.values["NAME"]
return code return code
class StrainMultipleValuesAdaptor(FMPeterMultipleValuesAdaptor):
selectMultipleValuesQuery = "SELECT * FROM \"Weis Lab Yeast Strains\""
entityIdFieldName = "KWY number"
entityCodeFieldName = "NAME"
## ##
## Plasmids ## Plasmids
## ##
...@@ -524,8 +511,8 @@ class PlasmidOpenBISDTO(FMPeterOpenBISDTO): ...@@ -524,8 +511,8 @@ class PlasmidOpenBISDTO(FMPeterOpenBISDTO):
if code is not None: if code is not None:
sample = getSampleForUpdate("/MATERIALS/"+code,"PLASMID", tr) sample = getSampleForUpdate("/MATERIALS/"+code,"PLASMID", tr)
setEntityProperties(tr, self.definition, sample, self.values) setEntityProperties(tr, self.definition, sample, self.values)
setEntityParents(tr, self.definition, sample, self.values) setPlasmidParents(tr, self.definition, sample, self.values)
print "SETPARENTS", setEntityParents(tr, self.definition, sample, self.values) print "SETPARENTS", setPlasmidParents(tr, self.definition, sample, self.values)
def getIdentifier(self, tr): def getIdentifier(self, tr):
code = "PKW" +self.values["NAME"] code = "PKW" +self.values["NAME"]
...@@ -621,19 +608,19 @@ fmConnString = "jdbc:filemaker://127.0.0.1/" ...@@ -621,19 +608,19 @@ fmConnString = "jdbc:filemaker://127.0.0.1/"
fmUser= "admin" fmUser= "admin"
fmPass = "nucleus" fmPass = "nucleus"
# adaptors = [ AntibodyAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibodies_Peter"), # adaptors = [ AntibodyAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_antibodies_Peter"),
# AntibodyBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibody_boxes_Peter"), # AntibodyMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_antibody_MultipleValueses_Peter"),
# PlasmidAdaptor(fmConnString, fmUser, fmPass, "BOXIT_plasmids_Peter"), # PlasmidAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_plasmids_Peter"),
# PlasmidBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_plasmid_boxes_Peter"), # PlasmidMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_plasmid_MultipleValueses_Peter"),
# StrainAdaptor(fmConnString, fmUser, fmPass, "BOXIT_strains_Peter"), # StrainAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_strains_Peter"),
# StrainBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_strain_boxes_Peter"), # StrainMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_strain_MultipleValueses_Peter"),
# OligoAdaptor(fmConnString, fmUser, fmPass, "BOXIT_oligos_Peter"), # OligoAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_oligos_Peter"),
# OligoBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_oligo_boxes_Peter"), # OligoMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_oligo_MultipleValueses_Peter"),
# CellAdaptor(fmConnString, fmUser, fmPass, "BOXIT_cells_Peter"), # CellAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_cells_Peter"),
# CellBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_cell_boxes_Peter"), # CellMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_cell_MultipleValueses_Peter"),
# SirnaAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"), # SirnaAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_Main_Menu_Peter"),
# ChemicalAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"), # ChemicalAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_Main_Menu_Peter"),
# DocumentsAdaptor(fmConnString, fmUser, fmPass, "BOXIT_documents_Peter")] # DocumentsAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_documents_Peter")]
...@@ -642,7 +629,9 @@ adaptors = [ ...@@ -642,7 +629,9 @@ adaptors = [
#ChemicalAdaptor(fmConnString, fmUser, fmPass, "Weis_Chemicals") #ChemicalAdaptor(fmConnString, fmUser, fmPass, "Weis_Chemicals")
#OligoAdaptor(fmConnString, fmUser, fmPass, "Weis_Oligos"), #OligoAdaptor(fmConnString, fmUser, fmPass, "Weis_Oligos"),
#AntibodyAdaptor(fmConnString, fmUser, fmPass, "Weis _Antibodies") #AntibodyAdaptor(fmConnString, fmUser, fmPass, "Weis _Antibodies")
PlasmidAdaptor(fmConnString, fmUser, fmPass, "Weis_Plasmids") #PlasmidAdaptor(fmConnString, fmUser, fmPass, "Weis_Plasmids")
StrainAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains"),
StrainMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains")
] ]
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment