def load(self, attNames):
'''load attributes specified into nexus master dictionary. Should be callable multiple times
during Nexus lifetime'''
#print 'loading', attNames
#update selected attribute names
[self._loadedAttNames.append(x) for x in attNames if x not in self._loadedAttNames]
#make entry in master dictionary
[self.updateMasterDict([x]) for x in attNames if x not in self._attName_id_value]
#open file and binary skip to correct line if packet
dataFile = cgFile.cgFile(self._dataFileName)
if self._packetInfo:
dataFile.seekToLineStart(self._packetInfo[0])
#transcribe values
currentID = 0
for line in dataFile.file:
ls = line.strip().split('\t')
#get ID
if self.hasIDs:
id = int(ls[0]) #id is always first slot
else:
id = currentID
currentID += 1
#stop if at end of range
if self._packetInfo:
if id == self._packetInfo[1]:
break
#transcribe
#Note lots of copying is SLOW (10x)
#only copy if list?
#for listed stuff, do not use copy,
#make new fxn that will just return a copy...faster
for attName in attNames:
colPosition = self._attName_columnPosition[attName]
if colPosition < self.numSlots:
if ls[colPosition] != '.':
self._attName_id_value[attName][id] = self._attName_casteFromFxn[attName](ls[colPosition])
elif 'List' in self._attName__formatInfo[attName][1]: #change "in" to ==[-4:]?
self._attName_id_value[attName][id] = self._attName_defaultValue[attName][:]
else:
self._attName_id_value[attName][id] = copy(self._attName_defaultValue[attName])
else:
self._attName_id_value[attName][id] = self._attName_defaultValue[attName] #no need for copy on primitive types
dataFile.file.close()
def save(self, outFN=None):
if outFN == None: outFN = self._dataFileName
if self._packetInfo:
outFN += '.range.%s.%s' % (self._packetInfo[0],
self._packetInfo[1])
dataFile = cgFile.cgFile(self._dataFileName)
if self._packetInfo:
dataFile.seekToLineStart(self._packetInfo[0])
#create new file contents
currentID = 0
newLines = []
for line in dataFile.file:
ls = line.strip().split('\t')
if self.hasIDs:
id = int(ls[0])
else:
id = currentID
currentID += 1
if self._packetInfo:
if id == self._packetInfo[1]: break
#save the rest
#TODO: lineUpdate with multiple injections
for attName in self._selectedAttNames:
newVal = self._attName_casteToFxn[attName](
self._attName_id_value[attName][id])
ls = lineUpdate(ls, newVal,
self._attName_columnPosition[attName])
#only one newLine no matter the amount of attributes updated
newLines.append('%s\n' % '\t'.join(ls))
dataFile.file.close()
#output file
newLines = ''.join(
newLines
) #might cause less clogging if there is only one write operation...
f = open(outFN, 'w')
f.write(newLines)
f.close()
#exit signal for parallel processes
if self._packetInfo or self._splitRunFlag:
f = open(outFN + '.exitSignal', 'w')
f.write('DONE')
f.close()
def save(self, outFN = None):
if outFN == None: outFN = self._dataFileName
if self._packetInfo:
outFN += '.range.%s.%s' % (self._packetInfo[0], self._packetInfo[1])
dataFile = cgFile.cgFile(self._dataFileName)
if self._packetInfo:
dataFile.seekToLineStart(self._packetInfo[0])
#create new file contents
currentID = 0
newLines = []
for line in dataFile.file:
ls = line.strip().split('\t')
#id = int(ls[0]) if self.hasIDs else currentID
if self.hasIDs:
id = int(ls[0])
else:
id = currentID
currentID += 1
if self._packetInfo:
if id == self._packetInfo[1]: break
#save the rest
colPos__vals = [(self._attName_columnPosition[x], self._attName_casteToFxn[x](self._attName_id_value[x][id])) for x in self._loadedAttNames]
ls = lineUpdate(ls, colPos__vals)
#only one newLine no matter the amount of attributes updated
newLines.append('%s\n' % '\t'.join(ls))
dataFile.file.close()
#output file
#TODO have to write as you update...test if causes I/O clogging. Can buffer it anyways...
#update line --> write to temp file --> rename file after writing complete
newLines = ''.join(newLines) #might cause less clogging if there is only one write operation...
f = open(outFN, 'w')
f.write(newLines)
f.close()
#exit signal for parallel processes
if self._packetInfo or self._splitRunFlag:
f = open(outFN + '.exitSignal', 'w')
f.write('DONE')
f.close()
def save(self, outFN = None):
if outFN == None: outFN = self._dataFileName
if self._packetInfo:
outFN += '.range.%s.%s' % (self._packetInfo[0], self._packetInfo[1])
dataFile = cgFile.cgFile(self._dataFileName)
if self._packetInfo:
dataFile.seekToLineStart(self._packetInfo[0])
#create new file contents
currentID = 0
newLines = []
for line in dataFile.file:
ls = line.strip().split('\t')
if self.hasIDs:
id = int(ls[0])
else:
id = currentID
currentID += 1
if self._packetInfo:
if id == self._packetInfo[1]: break
#save the rest
#TODO: lineUpdate with multiple injections
for attName in self._selectedAttNames:
newVal = self._attName_casteToFxn[attName](self._attName_id_value[attName][id])
ls = lineUpdate(ls, newVal, self._attName_columnPosition[attName])
#only one newLine no matter the amount of attributes updated
newLines.append('%s\n' % '\t'.join(ls))
dataFile.file.close()
#output file
newLines = ''.join(newLines) #might cause less clogging if there is only one write operation...
f = open(outFN, 'w')
f.write(newLines)
f.close()
#exit signal for parallel processes
if self._packetInfo or self._splitRunFlag:
f = open(outFN + '.exitSignal', 'w')
f.write('DONE')
f.close()
def load(self, attNames, paraInfo=[None, None]):
'''paraInfo is [runNumber, numberOfRuns]'''
#t = bioLibCG.cgTimer()
#stage_cumTime = dict( (x, 0.0) for x in (''))
#t.start()
if paraInfo == ['splitRun', 'splitRun']:
self._splitRunFlag = True
paraInfo = [None,
None] # now treat paraInfo as if there was nothing...
if paraInfo != [None, None]:
paraInfo[0] = int(paraInfo[0])
paraInfo[1] = int(paraInfo[1])
self._packetInfo = cgFile.getPacketInfo(
self._dataFileName, paraInfo[1])[paraInfo[0] - 1]
#if running parallel or specific range, mark range info
self._selectedAttNames = attNames
#get casting and column info
self.loadTranscriptionInfo(attNames)
#init master dictionaries
self.initializeMasterDict()
#get number of slots
numSlots = self.getNumberOfSlots()
#open file and binary skip to correct line if packet
dataFile = cgFile.cgFile(self._dataFileName)
if self._packetInfo:
dataFile.seekToLineStart(self._packetInfo[0])
#print 'before loop', t.split()
#transcribe values
currentID = 0
for line in dataFile.file:
ls = line.strip().split('\t')
#get ID
if self.hasIDs:
id = int(ls[0]) #id is always first slot
else:
id = currentID
currentID += 1
#stop if at end of range
if self._packetInfo:
if id == self._packetInfo[1]:
break
#transcribe
#Note lots of copying is SLOW (10x)
#only copy if list?
for attName in attNames:
colPosition = self._attName_columnPosition[attName]
if colPosition < numSlots:
if ls[colPosition] != '.':
self._attName_id_value[attName][
id] = self._attName_casteFromFxn[attName](
ls[colPosition])
else:
self._attName_id_value[attName][id] = copy(
self._attName_defaultValue[attName])
else:
self._attName_id_value[attName][id] = copy(
self._attName_defaultValue[attName])
#print 'after loop', t.split()
dataFile.file.close()
#bind attribute names to dictionaries
self.bindAttributes(attNames)
#bind id attribute to first attribute, they all have the same ids...
self.linkIDsToColumn()
def load(self, attNames, paraInfo = [None, None]):
'''paraInfo is [runNumber, numberOfRuns]'''
#t = bioLibCG.cgTimer()
#stage_cumTime = dict( (x, 0.0) for x in (''))
#t.start()
if paraInfo == ['splitRun', 'splitRun']:
self._splitRunFlag = True
paraInfo = [None, None] # now treat paraInfo as if there was nothing...
if paraInfo != [None, None]:
paraInfo[0] = int(paraInfo[0])
paraInfo[1] = int(paraInfo[1])
self._packetInfo = cgFile.getPacketInfo(self._dataFileName, paraInfo[1])[paraInfo[0] - 1]
#if running parallel or specific range, mark range info
self._selectedAttNames = attNames
#get casting and column info
self.loadTranscriptionInfo(attNames)
#init master dictionaries
self.initializeMasterDict()
#get number of slots
numSlots = self.getNumberOfSlots()
#open file and binary skip to correct line if packet
dataFile = cgFile.cgFile(self._dataFileName)
if self._packetInfo:
dataFile.seekToLineStart(self._packetInfo[0])
#print 'before loop', t.split()
#transcribe values
currentID = 0
for line in dataFile.file:
ls = line.strip().split('\t')
#get ID
if self.hasIDs:
id = int(ls[0]) #id is always first slot
else:
id = currentID
currentID += 1
#stop if at end of range
if self._packetInfo:
if id == self._packetInfo[1]:
break
#transcribe
#Note lots of copying is SLOW (10x)
#only copy if list?
for attName in attNames:
colPosition = self._attName_columnPosition[attName]
if colPosition < numSlots:
if ls[colPosition] != '.':
self._attName_id_value[attName][id] = self._attName_casteFromFxn[attName](ls[colPosition])
else:
self._attName_id_value[attName][id] = copy(self._attName_defaultValue[attName])
else:
self._attName_id_value[attName][id] = copy(self._attName_defaultValue[attName])
#print 'after loop', t.split()
dataFile.file.close()
#bind attribute names to dictionaries
self.bindAttributes(attNames)
#bind id attribute to first attribute, they all have the same ids...
self.linkIDsToColumn()
