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 9993d96b4bcf8c6941d677575aa91060292d10ee..f5a3da472f05ce2c13b0cd4b5d35d4351eafa910 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
@@ -68,7 +68,7 @@ def setEntityProperties(tr, definition, entity, properties):
for propertyCode, propertyValue in properties.iteritems():
propertyDefinition = definitions.getPropertyDefinitionByCode(definition, propertyCode)
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:
date_val = datetime.strptime(propertyValue, "%Y")
@@ -129,9 +129,12 @@ def setEntityProperties(tr, definition, entity, properties):
entity.setPropertyValue("COMPANY", propertyValue)
else:
entity.setPropertyValue(propertyCode, propertyValue)
+
-def setEntityParents(tr, definition, entity, properties):
+
+
+def setPlasmidParents(tr, definition, entity, properties):
for propertyCode, propertyValue in properties.iteritems():
propertyDefinition = definitions.getPropertyDefinitionByCode(definition, propertyCode)
@@ -171,11 +174,8 @@ def setEntityParents(tr, definition, entity, properties):
else:
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):
#print "Cache Create " + sampleIdentifier + ":" + str(sampleType)
if sampleType == "ANTIBODY":
experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/ANTIBODIES", sampleType, tr)
- # elif sampleType == "STRAIN":
- # experiment = getExperimentForUpdate("/MATERIALS/YEASTS/YEAST_COLLECTION_1", sampleType, tr)
+ elif sampleType == "STRAIN":
+ experiment = getExperimentForUpdate("/MATERIALS/YEASTS/YEAST_COLLECTION_1", sampleType, tr)
elif sampleType == "PLASMID":
experiment = getExperimentForUpdate("/MATERIALS/PLASMIDS/PLASMID_COLLECTION_1", sampleType, tr)
elif sampleType == "CHEMICAL":
@@ -329,124 +329,107 @@ class FMPeterOpenBISDTO(OpenBISDTO):
print "* ERROR [" + str(code) + "] - Invalid Code found for '" + self.__class__.__name__ + "'"
raise Exception('Invalid Code found ' + str(code))
-class FMPeterBoxAdaptor(FileMakerEntityAdaptor):
- selectBoxQuery = None
+class FMPeterMultipleValuesAdaptor(FileMakerEntityAdaptor):
+ selectMultipleValuesQuery = None
entityIdFieldName = None
entityCodeFieldName = None
def addEntity(self, values):
- self.entities.append(FMPeterEntityBoxOpenBISDTO(values, self.definition))
+ self.entities.append(FMPeterEntityMultipleValuesOpenBISDTO(values, self.definition))
def init(self):
- #print "Reading boxes for: " + self.__class__.__name__
- emptyBox = 0
- boxes = {}
+ print "Reading MultipleValueses for: " + self.__class__.__name__
+ emptyMultipleValues = 0
+ MultipleValueses = {}
EntityAdaptor.init(self)
- preparedStatement = self.connection.prepareStatement(self.selectBoxQuery)
+ preparedStatement = self.connection.prepareStatement(self.selectMultipleValuesQuery)
result = preparedStatement.executeQuery()
while result.next():
entityId = unicode(result.getString(self.entityIdFieldName))
if entityId is not None:
if entityId in sampleID2Sample:
- antibodyNumber = sampleID2Sample[entityId][self.entityCodeFieldName]
- if antibodyNumber is not None:
+ entityNumber = sampleID2Sample[entityId][self.entityCodeFieldName]
+ if entityNumber is not None:
values = {}
- values["STORAGE_NAME"] = result.getString("location")
- values["STORAGE_ROW"] = None
- values["STORAGE_COLUMN"] = None
- values["STORAGE_BOX_NAME"] = result.getString("box label")
- values["STORAGE_USER"] = result.getString("frozen by")
- values["STORAGE_BOX_POSITION"] = result.getString("position")
+ values["DISRUPTIONS"] = result.getString("disruptions")
+ values["MARKERS"] = result.getString("markers")
+ values["UNMARKED_MUTATIONS"] = result.getString("unmarked mutations")
+
- allBoxes = []
- if antibodyNumber in boxes:
- allBoxes = boxes[antibodyNumber]
+ allMultipleValueses = []
+ if entityNumber in MultipleValueses:
+ allMultipleValueses = MultipleValueses[entityNumber]
else:
- boxes[antibodyNumber] = allBoxes
- allBoxes.append(values)
+ MultipleValueses[entityNumber] = allMultipleValueses
+ allMultipleValueses.append(values)
else:
- #The antibody is not there. What the *#%$&
- emptyBox += 1
+ #The entity is not there. What the *#%$&
+ emptyMultipleValues += 1
else:
- #The antibody is not there. What the *#%$&
- emptyBox += 1
+ #The entity is not there. What the *#%$&
+ 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({
"*CODE" : entiyCode,
- "*BOXESLIST" : allBoxes
+ "*MultipleValuesESLIST" : allMultipleValueses
})
result.close()
preparedStatement.close()
-class FMPeterEntityBoxOpenBISDTO(OpenBISDTO):
+class FMPeterEntityMultipleValuesOpenBISDTO(OpenBISDTO):
def getIdentifier(self, tr):
return self.values["*CODE"]
def write(self, tr):
sample = getSampleForUpdate("/MATERIALS/"+self.values["*CODE"], None, tr)
- print "* INFO Boxes size: " + str(len(self.values["*BOXESLIST"]))
- #Delete old boxes
- for boxNum in range(1, definitions.numberOfStorageGroups+1):
- for propertyCode in definitions.getStorageGroupPropertyCodes():
- sample.setPropertyValue(propertyCode + "_" + str(boxNum), None)
+ print "* INFO MultipleValueses size: " + str(len(self.values["*MultipleValuesESLIST"]))
+ #Delete old MultipleValueses
+ for MultipleValuesNum in range(1, definitions.numberOfRepetitions+1):
+ for propertyCode in definitions.getRepetitionPropertyCodes():
+ sample.setPropertyValue(propertyCode + "_" + str(MultipleValuesNum), None)
+
- #Add new boxes
- boxNum = 1
- for box in self.values["*BOXESLIST"]:
- boxNum += 1
- for propertyCode, propertyValue in box.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
+ #Add new MultipleValueses
+ MultipleValuesNum = 0
+ for MultipleValues in self.values["*MultipleValuesESLIST"]:
+ MultipleValuesNum += 1
+ for propertyCode, propertyValue in MultipleValues.iteritems():
if propertyValue is not None:
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)
if sample is not None:
- for boxNum in range(1, definitions.numberOfStorageGroups+1):
+ for MultipleValuesNum in range(1, definitions.numberOfRepetitions+1):
storedSignature = "";
- for propertyCode in definitions.getStorageGroupPropertyCodes():
- propertyValue = sample.getPropertyValue(propertyCode + "_" + str(boxNum))
+ 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
- if storedSignature == boxSignature:
- #print "Found Box " + storedSignature.encode('ascii', 'ignore')
+ storedSignature += propertyValue
+ if storedSignature == MultipleValuesSignature:
+ #print "Found MultipleValues " + storedSignature.encode('ascii', 'ignore')
return True
return False
def isInOpenBIS(self, tr):
- for box in self.values["*BOXESLIST"]:
- boxSignature = "";
- for propertyCode in definitions.getStorageGroupPropertyCodes():
- propertyValue = box[propertyCode]
- if propertyCode == "STORAGE_NAME":
- propertyValue = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("FREEZER", propertyValue)
- if propertyCode == "STORAGE_USER":
- propertyValue = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("LAB_MEMBERS_INITIALS", propertyValue)
-
+ for MultipleValues in self.values["*MultipleValuesESLIST"]:
+ MultipleValuesSignature = "";
+ for propertyCode in definitions.getRepetitionPropertyCodes():
+ propertyValue = MultipleValues[propertyCode]
+
if propertyValue is not None:
propertyValue = unicode(propertyValue)
- boxSignature += propertyValue
- if not self.isBoxPressent(boxSignature, tr):
+ MultipleValuesSignature += propertyValue
+ if not self.isMultipleValuesPressent(MultipleValuesSignature, tr):
return False
return True
##
@@ -486,7 +469,7 @@ class AntibodyOpenBISDTO(FMPeterOpenBISDTO):
class StrainAdaptor(FileMakerEntityAdaptor):
def init(self):
- self.selectQuery = "SELECT * FROM \"boxit strains\""
+ self.selectQuery = "SELECT * FROM \"Weis Lab Yeast Strains\""
self.definition = definitions.strainDefinition
FileMakerEntityAdaptor.init(self)
@@ -495,16 +478,20 @@ class StrainAdaptor(FileMakerEntityAdaptor):
class StrainOpenBISDTO(FMPeterOpenBISDTO):
def write(self, tr):
- code = self.values["STRAIN_ID_NR"]
+ code = self.values["NAME"]
if code is not None:
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):
- code = self.values["STRAIN_ID_NR"]
+ code = self.values["NAME"]
return code
-
+class StrainMultipleValuesAdaptor(FMPeterMultipleValuesAdaptor):
+ selectMultipleValuesQuery = "SELECT * FROM \"Weis Lab Yeast Strains\""
+ entityIdFieldName = "KWY number"
+ entityCodeFieldName = "NAME"
##
## Plasmids
##
@@ -524,8 +511,8 @@ class PlasmidOpenBISDTO(FMPeterOpenBISDTO):
if code is not None:
sample = getSampleForUpdate("/MATERIALS/"+code,"PLASMID", tr)
setEntityProperties(tr, self.definition, sample, self.values)
- setEntityParents(tr, self.definition, sample, self.values)
- print "SETPARENTS", setEntityParents(tr, self.definition, sample, self.values)
+ setPlasmidParents(tr, self.definition, sample, self.values)
+ print "SETPARENTS", setPlasmidParents(tr, self.definition, sample, self.values)
def getIdentifier(self, tr):
code = "PKW" +self.values["NAME"]
@@ -621,19 +608,19 @@ fmConnString = "jdbc:filemaker://127.0.0.1/"
fmUser= "admin"
fmPass = "nucleus"
-# adaptors = [ AntibodyAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibodies_Peter"),
-# AntibodyBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibody_boxes_Peter"),
-# PlasmidAdaptor(fmConnString, fmUser, fmPass, "BOXIT_plasmids_Peter"),
-# PlasmidBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_plasmid_boxes_Peter"),
-# StrainAdaptor(fmConnString, fmUser, fmPass, "BOXIT_strains_Peter"),
-# StrainBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_strain_boxes_Peter"),
-# OligoAdaptor(fmConnString, fmUser, fmPass, "BOXIT_oligos_Peter"),
-# OligoBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_oligo_boxes_Peter"),
-# CellAdaptor(fmConnString, fmUser, fmPass, "BOXIT_cells_Peter"),
-# CellBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_cell_boxes_Peter"),
-# SirnaAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),
-# ChemicalAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),
-# DocumentsAdaptor(fmConnString, fmUser, fmPass, "BOXIT_documents_Peter")]
+# 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")]
@@ -642,7 +629,9 @@ adaptors = [
#ChemicalAdaptor(fmConnString, fmUser, fmPass, "Weis_Chemicals")
#OligoAdaptor(fmConnString, fmUser, fmPass, "Weis_Oligos"),
#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")
]