def findWellCoordinates(self, wellID): db = self.db cursor = self.cursor # for easy access wellRowNum = self.findWellRowNumber(wellID) wellCol = self.findWellColumn(wellID) wellRowLetter = Well.convertRowNumberToChar(wellRowNum) wellCoords = wellRowLetter + ":" + `wellCol` return wellCoords
def findContainerWells(self, contID):
db = self.db
cursor = self.cursor # for easy access
wells = []
cursor.execute("SELECT wellID, wellRow, wellCol FROM Wells_tbl WHERE containerID=" + `contID` + " AND status='ACTIVE'")
results = cursor.fetchall()
for result in results:
wellID = int(result[0])
wellRow = int(result[1])
wellCol = int(result[2])
tmpWell = Well(wellID, wellRow, wellCol, contID)
wells.append(tmpWell)
return wells
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