def updateContainerSize(self, contID, contSize):
db = self.db
cursor = self.cursor # for easy access
ltHandler = LocationTypeHandler(db, cursor)
contSizeID = ltHandler.containerSizeToID(contSize)
cursor.execute("UPDATE Container_tbl SET contTypeID=" + `contSizeID` + " WHERE containerID=" + `contID` + " AND status='ACTIVE'")
def deleteContainerType(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
ltHandler = LocationTypeHandler(db, cursor)
#print "Content-type:text/html"
#print
#print `form`
contTypeID = form.getvalue("containerType")
#print contTypeID
ltHandler.deleteContainerType(contTypeID)
utils.redirect(hostname + "Location.php?View=6&Sub=4&Del=1")
def deleteContainerType(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
ltHandler = LocationTypeHandler(db, cursor)
#print "Content-type:text/html"
#print
#print `form`
contTypeID = form.getvalue("containerType")
#print contTypeID
ltHandler.deleteContainerType(contTypeID)
utils.redirect(hostname + "Location.php?View=6&Sub=4&Del=1")
def updateContainerType(self, contID, contType):
db = self.db
cursor = self.cursor # for easy access
ltHandler = LocationTypeHandler(db, cursor)
contTypeID = ltHandler.containerTypeToID(contType)
# container number needs to be updated too, since the container was moved into a new group
contNum = self.findNextContainerNumberInGroup(contTypeID)
cursor.execute("UPDATE Container_tbl SET contGroupCount=" + `contNum` + " WHERE containerID=" + `contID` + " AND status='ACTIVE'")
# AND container-type specific properties need to be changed too
self.updateContainerProperties(contID, contType)
# Finally change container type
cursor.execute("UPDATE Container_tbl SET contGroupID=" + `contTypeID` + " WHERE containerID=" + `contID` + " AND status='ACTIVE'")
def updateContainerInfo(self, contID, contType, contSize, contName, contDesc, contLab, storage_type, storage_name, storage_address, cont_shelf, cont_rack, cont_row, cont_col): db = self.db cursor = self.cursor # for easy access ltHandler = LocationTypeHandler(db, cursor) contTypeID = ltHandler.containerTypeToID(contType) contSizeID = ltHandler.containerSizeToID(contSize) # Compare old container properties to new values and only update those that have actually changed oldContType = self.findContainerType(contID) oldContSize = self.findContainerSize(contID) oldContName = self.findContainerName(contID) oldContDesc = self.findContainerDescription(contID) oldLabID = self.findContainerLabID(contID) oldBarcode = self.findContainerBarcode(contID) # Update barcode IFF container type, lab or size were changed!!!! if oldBarcode == '' or oldContType != contType or oldContSize != contSize or oldLabID != contLab: # only in this case recompute barcode contNum = self.findNextContainerBarcodeNumber(contTypeID, contSizeID, contLab) newBarcode = self.generateBarcode(contTypeID, contSizeID, contNum, contLab) self.updateContainerBarcode(contID, newBarcode) # Update the rest of the container properties if old and new values differ: if contType != oldContType: self.updateContainerType(contID, contType) if contSize != oldContSize: self.updateContainerSize(contID, contSize) if contName != oldContName: self.updateContainerName(contID, contName) if contDesc != oldContDesc: self.updateContainerDescription(contID, contDesc) if contLab != oldLabID: self.updateContainerLab(contID, contLab)
def updateContainerType(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
ltHandler = LocationTypeHandler(db, cursor)
contTypeID = form.getvalue("containerType")
contName = ""
contDesc = ""
#print "Content-type:text/html"
#print
#print `form`
contTypeID = int(form.getvalue("containerType"))
contGroupName = form.getvalue("cont_group_name_field")
contGroupCode = form.getvalue("cont_cont_code_field")
if form.has_key("cont_cont_isolateActive_radio"):
if form.getvalue("cont_cont_isolateActive_radio").upper() == 'YES':
isoActive = form.getvalue(
"cont_cont_isolateActive_radio").upper()
#print isoActive
else:
isoActive = "NO"
else:
isoActive = ltHandler.findIsolateActive(contTypeID)
newContTypeFeatures = form.getlist("container_features")
reagentTypes = form.getlist("reagent_types") # feb. 9/10
#print `reagentTypes`
ltHandler.updateContainerType(contTypeID, contGroupName, contGroupCode,
isoActive, newContTypeFeatures,
reagentTypes)
utils.redirect(hostname + "Location.php?View=6&Sub=4&contTypeID=" +
` contTypeID `)
def generateBarcode(self, cTypeID, cSizeID, contNum, cLab): db = self.db cursor = self.cursor # for easy access # Get the lab code that corresponds to lab ID lHandler = LabHandler(db, cursor) labCode = lHandler.findLabCode(cLab) ltHandler = LocationTypeHandler(db, cursor) # Find the container size contSize = ltHandler.findNumContainerSamples(cSizeID) # Find the container group code contTypeCode = ltHandler.findContainerTypeCode(cTypeID) # Produce a string barcode barcode = labCode + `contSize` + contTypeCode + `contNum` return barcode
def updateContainerType(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
ltHandler = LocationTypeHandler(db, cursor)
contTypeID = form.getvalue("containerType")
contName = ""
contDesc = ""
#print "Content-type:text/html"
#print
#print `form`
contTypeID = int(form.getvalue("containerType"))
contGroupName = form.getvalue("cont_group_name_field")
contGroupCode = form.getvalue("cont_cont_code_field")
if form.has_key("cont_cont_isolateActive_radio"):
if form.getvalue("cont_cont_isolateActive_radio").upper() == 'YES':
isoActive = form.getvalue("cont_cont_isolateActive_radio").upper()
#print isoActive
else:
isoActive = "NO"
else:
isoActive = ltHandler.findIsolateActive(contTypeID)
newContTypeFeatures = form.getlist("container_features")
reagentTypes = form.getlist("reagent_types") # feb. 9/10
#print `reagentTypes`
ltHandler.updateContainerType(contTypeID, contGroupName, contGroupCode, isoActive, newContTypeFeatures, reagentTypes)
utils.redirect(hostname + "Location.php?View=6&Sub=4&contTypeID=" + `contTypeID`)
def insertContainer(self, contTypeID, cSize, cName, cDesc, cLab, storage_type, storage_name, storage_address, cont_shelf, cont_rack, cont_row, cont_col):
db = self.db
cursor = self.cursor # for easy access
ltHandler = LocationTypeHandler(db, cursor)
# find 'container type' and 'container size' foreign keys
#contTypeID = ltHandler.containerTypeToID(cType)
cType = ltHandler.findContainerTypeName(contTypeID)
contSizeID = ltHandler.containerSizeToID(cSize)
# find the next available number in this container group to assign to the new container
contNum = self.findNextContainerNumberInGroup(contTypeID)
# check if this is an isolate active container
isoActive = ltHandler.isIsoActive(contTypeID)
# generate barcode
bcNum = self.findNextContainerBarcodeNumber(contTypeID, contSizeID, cLab)
barcode = self.generateBarcode(contTypeID, contSizeID, bcNum, cLab)
cursor.execute("INSERT INTO Container_tbl(contGroupID, contTypeID, contGroupCount, name, container_desc, labID, barcode, location, locationName, address, shelf, rack, row_number, col_number) VALUES(" + `contTypeID` + ", " + `contSizeID` + ", " + `contNum` + ", " + `cName` + ", " + `cDesc` + ", " + `cLab` + ", " + `barcode` + ", " + `storage_type` + ", " + `storage_name` + ", " + `storage_address` + ", " + `cont_shelf` + ", " + `cont_rack` + ", " + `cont_row` + ", " + `cont_col` + ")")
newContID = int(db.insert_id())
# Store container-specific properties
nRows = ltHandler.findNumRows(contSizeID)
nCols = ltHandler.findNumCols(contSizeID)
container = Container(cType, cSize, nRows, nCols, cName, cLab, cDesc)
#props = container.getContainerProperties()
props = ltHandler.findContainerTypeProperties(contTypeID)
#print "Content-type:text/html"
#print
#print storage_type
#print `props`
self.insertContainerProperties(newContID, props)
return newContID
def addContainerType(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
ltHandler = LocationTypeHandler(db, cursor)
# some form values may be blank, so initialize as empty
contName = ""
contDesc = ""
#print "Content-type:text/html"
#print
#print `form`
contGroupName = form.getvalue("cont_group_name_field")
contGroupCode = form.getvalue("cont_cont_code_field")
if form.has_key("cont_cont_isolateActive_radio"):
if form.getvalue("cont_cont_isolateActive_radio").upper() == 'YES':
isoActive = form.getvalue(
"cont_cont_isolateActive_radio").upper()
else:
isoActive = "NO"
newContTypeFeatures = form.getlist("container_features")
#print `newContTypeFeatures`
newContTypeID = ltHandler.insertContainerType(contGroupName, isoActive,
contGroupCode)
ltHandler.addContainerTypeFeatures(newContTypeID, newContTypeFeatures)
reagentTypes = form.getlist("cont_cont_group_selection") # feb. 16/10
#print `reagentTypes`
ltHandler.updateContainerReagentTypes(newContTypeID, reagentTypes)
utils.redirect(hostname + "Location.php?View=6&Sub=4&contTypeID=" +
` newContTypeID `)
def addContainerType(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
ltHandler = LocationTypeHandler(db, cursor)
# some form values may be blank, so initialize as empty
contName = ""
contDesc = ""
#print "Content-type:text/html"
#print
#print `form`
contGroupName = form.getvalue("cont_group_name_field")
contGroupCode = form.getvalue("cont_cont_code_field")
if form.has_key("cont_cont_isolateActive_radio"):
if form.getvalue("cont_cont_isolateActive_radio").upper() == 'YES':
isoActive = form.getvalue("cont_cont_isolateActive_radio").upper()
else:
isoActive = "NO"
newContTypeFeatures = form.getlist("container_features")
#print `newContTypeFeatures`
newContTypeID = ltHandler.insertContainerType(contGroupName, isoActive, contGroupCode)
ltHandler.addContainerTypeFeatures(newContTypeID, newContTypeFeatures)
reagentTypes = form.getlist("cont_cont_group_selection") # feb. 16/10
#print `reagentTypes`
ltHandler.updateContainerReagentTypes(newContTypeID, reagentTypes)
utils.redirect(hostname + "Location.php?View=6&Sub=4&contTypeID=" + `newContTypeID`)
def exportPlate(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
lHandler = LocationHandler(db, cursor)
ltHandler = LocationTypeHandler(db, cursor)
rHandler = ReagentHandler(db, cursor)
prepPropMapper = PrepPropertyMapper(db, cursor)
cTypeMapper = ContainerTypeMapper(db, cursor)
prepProp_Name_ID_Map = prepPropMapper.mapPrepPropNameToID()
prepProp_ID_Name_Map = prepPropMapper.mapPrepPropIDToName()
contType_Name_ID_Map = cTypeMapper.mapContainerTypeNameToID()
contID = int(form.getvalue("contID"))
contName = lHandler.findContainerName(contID)
contArray = contName.split(" ")
fname = string.join(contArray, "_") + ".csv"
wells = lHandler.findContainerWells(contID)
content = ""
# debug
#print "Content-type:text/html"
#print
contType = lHandler.findContainerType(contID)
contTypeID = contType_Name_ID_Map[contType]
contProps = ltHandler.findContainerTypeProperties(
contTypeID) # array of names
iso_active = ltHandler.isIsoActive(contTypeID)
if iso_active == 'YES':
isoActive = True
else:
isoActive = False
#print `contProps`
# Header
if isoActive:
content = "Well,OpenFreezer ID,Selected Isolate,Flag,Reference,Comments,"
else:
content = "Well,OpenFreezer ID,Flag,Reference,Comments,"
contPropIDs_sorted = []
for cPropName in contProps:
cPropID = prepProp_Name_ID_Map[cPropName]
contPropIDs_sorted.append(cPropID)
contPropIDs_sorted.sort()
for cPropID in contPropIDs_sorted:
cPropName = prepProp_ID_Name_Map[cPropID]
content += cPropName + ','
content += '\n'
numRows = lHandler.getNumRows(contID)
numCols = lHandler.getNumCols(contID)
plate = {}
for well in wells:
wellRowNum = well.getWellRowNumber()
#print wellRowNum
if plate.has_key(wellRowNum):
plate[wellRowNum].append(well)
else:
tmp_ar = []
tmp_ar.append(well)
plate[wellRowNum] = tmp_ar
plate.keys().sort()
for rowNum in range(1, numRows + 1):
if plate.has_key(rowNum):
wellRow = plate[rowNum]
wellRowNum = rowNum
wellRowLetter = Well.convertRowNumberToChar(wellRowNum)
wellRow.sort()
#print "ROW " + `rowNum`
for colNum in range(1, numCols + 1):
for well in wellRow:
wellID = well.getWellID()
#print wellID
wellCol = well.getWellColumn()
if wellCol == colNum:
#print "COLUMN " + `wellCol`
wellCoords = wellRowLetter + ":" + ` wellCol `
# get prep, reference, comments, flag
prepID = lHandler.findPrepIDInWell(wellID)
#print prepID
prepRef = lHandler.findPrepReference(prepID)
#print prepRef
if not prepRef:
prepRef = ""
prepComms = lHandler.findPrepComments(prepID)
#print prepComms
if not prepComms:
prepComms = ""
prepFlag = lHandler.findPrepFlag(prepID)
#print prepFlag
# get isolate number, selected isolate
isoID = lHandler.findPrepIsolateID(prepID)
isoNum = lHandler.findIsolateNumber(isoID)
isoSelected = lHandler.isSelectedIsolate(isoID)
# get prep property values
prepPropValues = lHandler.findAllPrepProperties(
prepID)
# find the LIMS ID of the reagent stored in this well
expID = lHandler.findExperimentIDByIsolate(isoID)
rID = lHandler.findReagentIDByExperiment(expID)
limsID = rHandler.convertDatabaseToReagentID(rID)
# Output: Well , Reagent-isolate , Selected , Flag , Reference , Comments , Attributes [name1 , name2 , name3....]
if isoActive:
content += wellCoords + ',' + limsID + "-" + ` isoNum ` + ',' + isoSelected + ',' + prepFlag + ',' + prepRef + ',' + prepComms + ","
else:
content += wellCoords + ',' + limsID + ',' + prepFlag + ',' + prepRef + ',' + prepComms + ","
prepPropIDs_sorted = {}
prepProps = {}
for pProp in prepPropValues:
pName = pProp.getPropName()
pVal = pProp.getPropValue()
prepProps[pName] = pVal
prepProps.keys().sort(
) # might not be necessary but still
for cPropID in contPropIDs_sorted:
cPropName = prepProp_ID_Name_Map[cPropID]
if prepProps.has_key(cPropName):
pVal = prepProps[cPropName]
content += pVal + ','
else:
content += ','
content += '\n'
print "Content-type: application/octet-stream"
print "Content-Disposition: attachment; name=" + fname
print
print content
