def flushDirectories(directoryList):
suffix = 2
usedNum = False
for pos in range(len(directoryList)):
flushDirectory = directoryList[pos].replace(' ', '')
if len(flushDirectory) == 0:
flushDirectory = "polyrun"
print "Flushing directory %s: %s" % (pos, flushDirectory)
if os.path.exists(flushDirectory):
print "*** Warning, preparing to flush path:", flushDirectory, " - continue? (yes/no/num/quit) ***"
print "-num will suffix the output directories with a number"
print "-no will output over the prior directory without cleanup"
while True:
response = str(raw_input(":")).lower()
if response == "n" or response == "no" or response == "y" or response == "yes" or response == "num" or response == "quit":
answer = RollVac.isYes(response, "null")
break
else:
print "Invalid Response, please enter yes, no, or num"
if answer == True:
shutil.rmtree(flushDirectory)
print " cleared succesfully"
elif response == 'quit':
print "Quitting now....\n\n"
quit()
elif response == 'num':
copyNum = 2
if os.path.exists(flushDirectory):
while os.path.exists(flushDirectory + str(copyNum)):
copyNum += 1
suffix = max(copyNum, suffix)
usedNum = True
else:
print "not found, skipping"
suffix = str(suffix)
if usedNum:
print "Duplicate directories found, will append suffix '%s' to output directories" % (
suffix)
return str(suffix)
else:
return ""
def flushDirectories(directoryList):
suffix = 2
usedNum = False
for pos in range(len(directoryList)):
flushDirectory= directoryList[pos].replace(' ','')
if len(flushDirectory) == 0:
flushDirectory = "polyrun"
print "Flushing directory %s: %s" % (pos, flushDirectory)
if os.path.exists(flushDirectory):
print "*** Warning, preparing to flush path:", flushDirectory, " - continue? (yes/no/num/quit) ***"
print "-num will suffix the output directories with a number"
print "-no will output over the prior directory without cleanup"
while True:
response = str(raw_input(":")).lower()
if response == "n" or response == "no" or response == "y" or response == "yes" or response == "num" or response == "quit":
answer = RollVac.isYes(response, "null")
break
else:
print "Invalid Response, please enter yes, no, or num"
if answer == True:
shutil.rmtree(flushDirectory)
print " cleared succesfully"
elif response == 'quit':
print "Quitting now....\n\n"
quit()
elif response == 'num':
copyNum = 2
if os.path.exists(flushDirectory):
while os.path.exists(flushDirectory + str(copyNum)):
copyNum += 1
suffix = max(copyNum, suffix)
usedNum = True
else:
print "not found, skipping"
suffix = str(suffix)
if usedNum:
print "Duplicate directories found, will append suffix '%s' to output directories" % (suffix)
return str(suffix)
else:
return ""
def main():
# USED TO DEFINE LOADING POSITIONS, MUST BE CONSERVED IN SOURCE AND GDOC
paramsStart = "Study Name Prefix (optional),Diagnosis Based"
startWord = "Subpopulation,Day/'enum',Length of Spread"
vacsRolled = 0
totalVars = 0
varList = []
varSets = []
suffixes = []
directorySuffix = ""
filteredIDs = [{"directory":'null','ids':[]}]
popSizes = dict()
# positions = []
# PARSING COMMAND LINE ARGUMENTS FOR PUBLIC/ PRIVATE FILE ACCESS
if len(sys.argv) > 2:
if len(sys.argv) == 3:
sys.argv.insert(2,'null')
else:
print "Ignoring", len(sys.argv) - 2, "excess arguments\n"
elif len(sys.argv) == 2:
sys.argv.insert(1,'null')
sys.argv.insert(1,'null')
script = gDocsImport.getScript(sys.argv[1], sys.argv[2], sys.argv[3], 0, -1, "default", False, [])
directoryLines = gDocsImport.getScript(sys.argv[1], sys.argv[2], sys.argv[3], paramsStart, startWord, "default", False,[])
sys.argv = None
# ERASES DIRECTORY NAMES GIVEN BY GDOC
directories = []
for directory in directoryLines:
dirToFlush =(directory[2] + '/' + directory[0]).replace('//','/')
if not dirToFlush in directories:
directories.append(dirToFlush)
directorySuffix = flushDirectories(directories)
# CREATES LISTS OF ALL EXPERIMENTAL VARIABLES ITERATED OVER
length = len(script)
print "Searching list for experimentally iterated variables"
for item in script:
temp = getPoly(item)
if temp[0] != 'null':
if temp[0] not in varSets:
totalVars += 1
varList.append(temp[0])
varSets.append(temp[0])
suffixes.append(temp[1])
varList.sort()
length = len(varSets)
varMatrix = [[] for x in xrange(totalVars)]
suffixMatrix = [[] for x in xrange(totalVars)]
# positionMatrix = [[] for x in xrange(totalVars)]
# CREATES MATRICES OF SUFFIXES, VARIABLE ID, AND LIST POSITION FOR ITERATION
for pos2 in range(totalVars):
for pos1 in range(length):
if varSets[pos1] == varList[pos2] and (suffixes[pos1] not in suffixMatrix[pos2]):
varMatrix[pos2].append(varSets[pos1])
suffixMatrix[pos2].append(suffixes[pos1])
# positionMatrix[pos2].append(positions[pos1])
# SETS UP RUN BOUNDS
runTracker = [0] * totalVars
done = False
totalRuns = 1
ends = []
for pos in range(totalVars):
totalRuns *= len(varMatrix[pos])
ends.append(len(varMatrix[pos])-1)
if pos >= 1:
ends[pos] += 1
# ITERATED RUN GENERATION, IF SCRIPT LINE CONTAINS CURRENT ITERATION RUN MARKERS OR NONE, SENT TO RollVac TO PARSE
while not done:
toRun = []
for pos in range(totalVars):
toRun.append(suffixMatrix[pos][runTracker[pos]])
length = len(script)
rollScript = []
print "Loading Script for line:", runTracker
for item in script:
if getPoly(item)[0] == 'null' or getPoly(item)[1] in toRun:
rollScript.append(filterPoly(item))
#if len(item.replace('"','').replace(',','').replace('\n','')) != 0:
# SUPPORT ADDED FOR MULTIPLE DIRECTORIES/ RUN
params = gDocsImport.getLine('null', 'null','null', paramsStart, True, rollScript)
folder = params[2] + '/' + params[0]
directory = appendSuffix(folder,directorySuffix)
# OUT DIRECTORY GENERATED VIA SUFFIX MATRIX
for pos in range(totalVars):
directory += suffixMatrix[pos][runTracker[pos]] + '/'
params = gDocsImport.loadNClean(False, rollScript, paramsStart, startWord, "single line")
print params
homeDir = appendSuffix(params[2] + '/' + params[0], directorySuffix)
explicit = appendSuffix(params[2], directorySuffix)
needsReplace = len(params[5]) > 0
noAVDiag = not RollVac.isYes(params[1],'null')
fileString = params[3]
filesToCopy = len(fileString) > 0
filteredIDs = RollVac.main('poly', directory, 'null', 'null', rollScript, filteredIDs, popSizes)
sleep(0.05)
qsubs = open(homeDir + 'qsublist', 'a+b')
qsubs.write(("qsub " + directory + 'qsub\n').replace('//','/'))
qsubs.close()
if noAVDiag:
extraCommands = ["Find = DiagnosisFile =",
"Replace = ",
"Find = AntiviralFile = ",
"Replace = "]
else:
extraCommands = 'null'
if needsReplace:
replaceFile = params[5]
else:
replaceFile = 'null'
if needsReplace or noAVDiag:
replaceScript = loadReplaceScript(replaceFile, extraCommands)
findNReplace(fileString, replaceScript, directory, vacsRolled, homeDir, explicit)
if filesToCopy and not needsReplace:
print fileString, directory
fileCopy(fileString, directory)
vacsRolled += 1
# POLYRUN MULTIDIMENSIONAL LOOP ITERATOR
if totalVars == 0:
print "No PolyRun iteration operators found, running in singular mode."
done = True
break
pos = 0
justRolled = False
while runTracker[pos] == ends[pos] and pos < totalVars - 1:
justRolled = True
runTracker[pos] = 0
runTracker[pos+1] += 1
pos += 1
if pos == totalVars - 1 and runTracker[pos] == ends[pos]:
print "Interventions Iterated =", vacsRolled
done = True
break
if not justRolled:
runTracker[0] += 1
print "Intervention iteration succesfully complete!"
def main():
# USED TO DEFINE LOADING POSITIONS, MUST BE CONSERVED IN SOURCE AND GDOC
paramsStart = "Study Name Prefix (optional),Diagnosis Based"
startWord = "Subpopulation,Day/'enum',Length of Spread"
vacsRolled = 0
totalVars = 0
varList = []
varSets = []
suffixes = []
directorySuffix = ""
filteredIDs = [{"directory": 'null', 'ids': []}]
popSizes = dict()
# positions = []
# PARSING COMMAND LINE ARGUMENTS FOR PUBLIC/ PRIVATE FILE ACCESS
if len(sys.argv) > 2:
if len(sys.argv) == 3:
sys.argv.insert(2, 'null')
else:
print "Ignoring", len(sys.argv) - 2, "excess arguments\n"
elif len(sys.argv) == 2:
sys.argv.insert(1, 'null')
sys.argv.insert(1, 'null')
script = gDocsImport.getScript(sys.argv[1], sys.argv[2], sys.argv[3], 0,
-1, "default", False, [])
directoryLines = gDocsImport.getScript(sys.argv[1], sys.argv[2],
sys.argv[3], paramsStart, startWord,
"default", False, [])
sys.argv = None
# ERASES DIRECTORY NAMES GIVEN BY GDOC
directories = []
for directory in directoryLines:
dirToFlush = (directory[2] + '/' + directory[0]).replace('//', '/')
if not dirToFlush in directories:
directories.append(dirToFlush)
directorySuffix = flushDirectories(directories)
# CREATES LISTS OF ALL EXPERIMENTAL VARIABLES ITERATED OVER
length = len(script)
print "Searching list for experimentally iterated variables"
print 'DEBOOO', script
for item in script:
temp = getPoly(item)
if temp[0] != 'null':
if temp[0] not in varSets:
totalVars += 1
varList.append(temp[0])
varSets.append(temp[0])
suffixes.append(temp[1])
varList.sort()
length = len(varSets)
varMatrix = [[] for x in xrange(totalVars)]
suffixMatrix = [[] for x in xrange(totalVars)]
# positionMatrix = [[] for x in xrange(totalVars)]
# CREATES MATRICES OF SUFFIXES, VARIABLE ID, AND LIST POSITION FOR ITERATION
for pos2 in range(totalVars):
for pos1 in range(length):
if varSets[pos1] == varList[pos2] and (suffixes[pos1]
not in suffixMatrix[pos2]):
varMatrix[pos2].append(varSets[pos1])
suffixMatrix[pos2].append(suffixes[pos1])
# positionMatrix[pos2].append(positions[pos1])
# SETS UP RUN BOUNDS
runTracker = [0] * totalVars
done = False
totalRuns = 1
ends = []
for pos in range(totalVars):
totalRuns *= len(varMatrix[pos])
ends.append(len(varMatrix[pos]) - 1)
if pos >= 1:
ends[pos] += 1
# ITERATED RUN GENERATION, IF SCRIPT LINE CONTAINS CURRENT ITERATION RUN MARKERS OR NONE, SENT TO RollVac TO PARSE
while not done:
toRun = []
for pos in range(totalVars):
toRun.append(suffixMatrix[pos][runTracker[pos]])
length = len(script)
rollScript = []
print "Loading Script for line:", runTracker
for item in script:
if getPoly(item)[0] == 'null' or getPoly(item)[1] in toRun:
rollScript.append(filterPoly(item))
#if len(item.replace('"','').replace(',','').replace('\n','')) != 0:
# SUPPORT ADDED FOR MULTIPLE DIRECTORIES/ RUN
params = gDocsImport.getLine('null', 'null', 'null', paramsStart, True,
rollScript)
folder = params[2] + '/' + params[0]
directory = appendSuffix(folder, directorySuffix)
# OUT DIRECTORY GENERATED VIA SUFFIX MATRIX
for pos in range(totalVars):
directory += suffixMatrix[pos][runTracker[pos]] + '/'
params = gDocsImport.loadNClean(False, rollScript, paramsStart,
startWord, "single line")
print params
homeDir = appendSuffix(params[2] + '/' + params[0], directorySuffix)
explicit = appendSuffix(params[2], directorySuffix)
needsReplace = len(params[5]) > 0
noAVDiag = not RollVac.isYes(params[1], 'null')
fileString = params[3]
filesToCopy = len(fileString) > 0
filteredIDs = RollVac.main('poly', directory, 'null', 'null',
rollScript, filteredIDs, popSizes)
sleep(0.05)
qsubs = open(homeDir + 'qsublist', 'a+b')
qsubs.write(("qsub " + directory + 'qsub\n').replace('//', '/'))
qsubs.close()
if noAVDiag:
extraCommands = [
"Find = DiagnosisFile =", "Replace = ",
"Find = AntiviralFile = ", "Replace = "
]
else:
extraCommands = 'null'
if needsReplace:
replaceFile = params[5]
else:
replaceFile = 'null'
if needsReplace or noAVDiag:
replaceScript = loadReplaceScript(replaceFile, extraCommands)
findNReplace(fileString, replaceScript, directory, vacsRolled,
homeDir, explicit)
if filesToCopy and not needsReplace:
print fileString, directory
fileCopy(fileString, directory)
vacsRolled += 1
# POLYRUN MULTIDIMENSIONAL LOOP ITERATOR
if totalVars == 0:
print "No PolyRun iteration operators found, running in singular mode."
done = True
break
pos = 0
justRolled = False
while runTracker[pos] == ends[pos] and pos < totalVars - 1:
justRolled = True
runTracker[pos] = 0
runTracker[pos + 1] += 1
pos += 1
if pos == totalVars - 1 and runTracker[pos] == ends[pos]:
print "Interventions Iterated =", vacsRolled
done = True
break
if not justRolled:
runTracker[0] += 1
print "Intervention iteration succesfully complete!"
