def main(arg1, arg2, arg3, arg4, polyScript, filteredIDs,popSizes):
print arg1, arg2, arg3, arg4
if __name__ != '__main__':
sys.argv = ['RollVac.py',arg1,arg2,arg3,arg4]
if arg1 == "poly":
del sys.argv[3:5]
trigger = 1
subnum = 0
path = ""
population = ""
useExplicit = False
explicitDirectory = ""
subpopDirectory = ""
useBase = False
useRaw = False
baseFile = ""
pos = 0
iCode = 0
vacTotal = 0
avTotal = 0
socialTotal = 0
workTotal = 0
schoolTotal = 0
sqTotal = 0
avTreatments = 0
try:
toFilterIDs = len(filteredIDs) > 0
except:
toFilterIDS = False
useNew = False
subpopsNew = []
actionsNew = []
totalsNew = {'vaccination':1000000000,'antiviral':1000000000}
interventionsNew = []
# LOADS PUBLIC/ PRIVATE DATA FROM GDOC IF PASSED
if len(sys.argv) < 3:
print "Missing arguments, quitting now"
quit()
outName = "Default"
elif len(sys.argv) > 3:
if sys.argv[1] == "gdoc" or sys.argv[1] == "poly":
arg = "gDoc"
if len(sys.argv) == 4:
sys.argv.insert(3,'null')
else:
print "Ignoring", len(sys.argv) - 3, "excess arguments\n"
elif len(sys.argv) == 3:
if sys.argv[1] == "gdoc" or sys.argv[1] == "poly":
arg = "gDoc"
sys.argv.insert(2,'null')
sys.argv.insert(2,'null')
else:
outName = sys.argv[2]
arg = sys.argv[1]
# LOADS AND WRITES AV/ DIAG SCRIPT FROM GOOGLE DOC, NOT IMPLEMENTED FOR USER/ LOCAL SCRIPT MODE
print sys.argv
if arg == "gDoc":
if sys.argv[1] == "poly":
isPoly = True
sys.argv[3] = 'null'
path = arg2
if os.path.exists(path):
shutil.rmtree(path)
os.makedirs(path)
os.makedirs(path + "/output")
else:
isPoly = False
loadType = "intervention script"
print sys.argv
script = gDocsImport.getScript(sys.argv[2], sys.argv[3], sys.argv[4], startWord, stopWord, loadType, isPoly, polyScript)
params = gDocsImport.getLine(sys.argv[2], sys.argv[3], sys.argv[4],paramsStart, isPoly, polyScript)
emptyblock = script == 'null'
explicitDirectory= params[2]
if len(explicitDirectory) > 0:
useExplicit = True
try:
shiftDates = int(params[8])
print "Date shift set to", shiftDates
except:
shiftDates = 0
print "Using default '0' date shift"
if isPoly:
outName = ""
baseFile = params[4]
subpopDirectory = params[6]
if len(baseFile) > 0:
if os.path.exists(baseFile):
print "Appending interventions to base file", baseFile
useBase = True
else:
print "Error, base file", baseFile, "not found"
quit()
else:
outName = params[0]
if len(outName) == 0:
print "No name prefix stored, using default intervention, antiviral, and diagnosis"
outName = ""
print "Will write to intervention file '%sIntervention'\n" % outName
diag = params[1]
diagnosis = isYes(diag, "diagnosis")
useNew = isYes(params[7], "new style")
try:
appendScript = gDocsImport.getScript(sys.argv[2], sys.argv[3], sys.argv[4], avStop, 0, loadType, isPoly, polyScript)
appendScript = appendRaw(appendScript)
useRaw = appendScript != 'null'
if useRaw:
print "\nRaw script footer loaded succesfully,", appendScript.count('\n') - 3, "lines to append"
except:
print "Error, raw script footer not loaded"
if not diagnosis:
sys.argv[3] = "null"
else:
loadType = "default"
avScript = gDocsImport.getScript(sys.argv[2], sys.argv[3], sys.argv[4], avStart, avStop, loadType, isPoly, polyScript)
diagParams = gDocsImport.getLine(sys.argv[2], sys.argv[3], sys.argv[4], stopWord, isPoly, polyScript)
sys.argv[3] = "null"
if not useNew:
if avScript == 'null':
print "No AV-Script found"
temp = open(path+'/Antiviral', 'w')
temp.write("#Null file: AV-Scripting enabled though no interventions found")
temp.close()
temp = open(path+'/Diagnosis', 'w')
temp.write("#Null file: AV-Scripting enabled though no interventions found")
temp.close()
avTreatments = 0
else:
avTreatments = writeAvScript(avScript, diagParams, outName, path, subpopDirectory, shiftDates)
# PREP NEW FORMAT DICTS
else:
if avScript == 'null':
print "No AV-Script found"
avTreatments = 0
else:
temp = prepNewAV(avScript, diagParams, outName, path, subpopDirectory, totalsNew, shiftDates)
subpopsNew += temp['subpops']
actionsNew += temp['actions']
interventionsNew += temp['interventions']
"""print subpopsNew
print actionsNew
print interventionsNew"""
avTreatments = len(actionsNew)
if arg != "user" and arg != "gDoc" and arg != "gdoc" and (not os.path.isfile(arg)):
print arg
print "Error, cannot open file or directory\n"
quit()
done = False
# LOCAL SCRIPT FILE LOADING
if arg != "user" and arg != "gDoc":
scriptfile = open(arg)
script = []
line = 0
gotPath = False
while True:
testline = scriptfile.readline()
if len(testline) == 0:
break
if not testline.startswith("#"):
if testline.startswith("Directory"):
gotPath = True
temp = testline.split()
if len(temp) <2:
path = ""
else:
path = testline.split()[1]
if (path == "local" or path == "Local"):
path = ""
else:
script.append(testline)
line += 1
if not gotPath:
path = ""
# FLUSH INTERVENTION FILE & COPY POLYRUN BASEFILE IF NEEDED
writePath = path + outName + 'Intervention'
if useNew:
writePath += 'New'
if useBase:
shutil.copy2(baseFile, writePath)
outFile = open(writePath)
temp = outFile.read()
outFile.close()
outFile = open(writePath, 'w')
outFile.write("# ----- PolyRun.Py Appended Intervention File -----\n\n")
outFile.write(temp)
outFile.write("\n\n# ----- End of Appended Intervention File -----\n\n")
else:
outFile = open(writePath, 'w')
if useNew:
outFile.write("# ----- RollVac.Py Autogenerated Intervention File New Version-----\n\n")
else:
outFile.write("# ----- RollVac.Py Autogenerated Intervention File Old Version-----\n\n")
outFile.close()
# GENERATING OUTPUT FILE LOOP
while not done and emptyblock == False:
subnum += 1
enum = False
# LOCAL SCRIPT/ GDOC CONTROLLED CHOPPING
if True:
if pos == len(script):
done = True
break
cmd = script[pos]
items = cmd.split()
population = (subpopDirectory + '/' + items[0]).replace('//','/')
try:
with open(population): pass
except:
print "Error: population file", population, "not found\n"
quit()
if str(items[1]) == 'enum':
enum = True
cmd = cmd.replace("enum","null null")
items = cmd.split()
pos += 1
enumList = script[pos].replace(";"," ; ")
if checkEnum(enumList):
enumList = parseEnum(enumList)
else:
print "Error: misformatted enumeration list", enumList
quit()
if not enum:
try:
day = int(items[1]) + shiftDates
if day <= 0:
print "Error, day must be an integer value\n"
quit()
except:
print "Error, day must be an integer greater than zero\n"
quit()
try:
length = int(items[2])
if length <= 0:
print "Error, length must be an integer greater than zero\n"
quit()
except:
print "Error, length must be an integer greater than zero\n"
quit()
temp = cmd.split()
print "Generating interventions with parameters:",cmd
method = temp[3]
arguments = len(temp)
if method == "Vaccination":
target = 7
meth = "v"
iCode = 0
if arguments == 7:
temp[5],temp[6] = temp[6],temp[5]
elif method == "Antiviral":
target = 8
meth = "av"
iCode = 1000
if arguments == 8:
temp[5],temp[6],temp[7] = temp[6],temp[7],temp[5]
elif method == "SocialDistancing":
target = 6
meth = "sd"
iCode = 2000
elif method == "WorkClosure":
target = 6
meth = "cw"
iCode = 3000
elif method == "SchoolClosure":
target = 6
meth = "cs"
iCode = 4000
elif method == "Sequestion":
target = 7
meth = "sq"
iCode = 6000
else:
print "Error:", method, "method not recognized\n"
quit()
if arguments != target:
print "Error:", len(temp), "parameters found,", target, "expected for intervention type", method, "\n"
quit()
interv = " ".join(temp[3:target])
intervNew = temp[3:target]
pos += 1
suffix = str(subnum) + meth
# ALL MODE CHOPPING EXECUTION
print population
if not useNew:
pos2 = 0
limit = len(filteredIDs)
found = False
while pos2 < limit:
if population in filteredIDs[pos2]['directory']:
found = True
runIDs = filteredIDs[pos2]['ids']
break
pos2 += 1
if not found:
filteredIDs.append(filterIDs(population))
runIDs = filteredIDs[-1]['ids']
if enum:
populationSize = checkSize(population,popSizes)
enumList = cleanEnum(percentEnum(enumList,populationSize))
holder = chopper.main(population,'e'," ".join(map(str, enumList)),suffix, path,runIDs)
returnSize = holder['count']
enumList = holder['enum']
length = chopper.getEnumSize(enumList)
else:
holder = chopper.main(population,'b',str(length),suffix, path, runIDs)
returnSize = holder['count']
else:
addSubpop(subpopsNew, population.split('/')[-1], population, 9000+ len(subpopsNew))
if enum:
populationSize = checkSize(population,popSizes)
temp = countEnum(enumList,populationSize)
enumList = chopper.trimEnum(cleanEnum(temp['enum']), populationSize)
length = chopper.getEnumSize(enumList)
returnSize = int(min(temp['total'],populationSize))
else:
populationSize = returnSize = checkSize(population,popSizes)
# NON TREATMENT BASED INTERVENTION TRACKING
if meth == "v":
vacTotal += returnSize
elif meth == "av":
avTotal += returnSize
elif meth == "sd":
socialTotal += returnSize
elif meth == "cw":
workTotal += returnSize
elif meth == "cs":
schoolTotal += returnSize
elif meth == "sq":
sqTotal += returnSize
# WRITING INTERVENTION FILE (AV TREATMENT & DIAG HANDLED SEPERATELY)
writePath = path + outName + 'Intervention'
pos2 = 0
popName = population.split('/')[-1]
if not useNew:
outFile = open(writePath, 'a+b')
if enum:
while pos2 < len(enumList):
subPopName = popName + 'd' + str(pos2/2) + 'i' + suffix
if ".txt" in subPopName:
subPopName = subPopName.replace('.txt','') + '.txt'
triggerOut = "* Trigger " + str(trigger+iCode) + " Date " + str(enumList[pos2] + shiftDates) + "\n"
if useExplicit:
tempPath = path + "/subpops/" + subPopName
else:
tempPath = "subpops/" + subPopName
intervOut = "* Action " + str(trigger+iCode) + " " + interv + " " + tempPath + "\n"
intervOut = intervOut.replace('//','/')
print triggerOut, intervOut.replace('\n','')
outFile.write(triggerOut)
outFile.write(intervOut)
trigger += 1
pos2 += 2
else:
while pos2 < length:
subPopName = popName + 'd' + str(pos2) + 'i' + suffix
if ".txt" in subPopName:
subPopName = subPopName.replace('.txt','') + '.txt'
triggerOut = "* Trigger " + str(trigger+iCode) + " Date " + str(day+pos2) + "\n"
if useExplicit:
tempPath = path + "/subpops/" + subPopName
else:
tempPath = "subpops/" + subPopName
intervOut = "* Action " + str(trigger+iCode) + " " + interv + " " + tempPath + "\n"
intervOut = intervOut.replace('//','/')
print triggerOut, intervOut.replace('\n','')
outFile.write(triggerOut)
outFile.write(intervOut)
trigger += 1
pos2 += 1
outFile.close()
print
else:
writePath += 'New'
tempAction = prepNewAction()
#tempInterv = [prepNewIntervention()]*len(enumList/2)
tempAction['actionID'] = actionID = str(trigger + iCode)
tempAction['actionType'] = method
if method == 'Antiviral':
method += "_Prophylaxis"
tempAction['actionDescription'] = method
tempAction['actionDelay'] = '0'
tempAction['actionDuration'] = intervNew[1]
conditionTotal = -1
if method == "Vaccination":
tempAction['actionEfficacy'] = intervNew[3]
conditionTotal = '9100'
elif method == "Antiviral":
tempAction['actionEfficacyIn'] = intervNew[3]
tempAction['actionEfficacyOut'] = intervNew[4]
conditionTotal = '9101'
elif method == "Sequestion":
tempAction['actionGroupSize'] = intervNew[3]
if enum:
tempInterv = []
while pos2 < len(enumList):
tempInterv.append(prepNewIntervention())
tempInterv[pos2/2]['interventionID'] = str(9300 + len(interventionsNew) + pos2/2)
tempInterv[pos2/2]['interventionType'] = "Offline"
if conditionTotal != -1:
tempInterv[pos2/2]['conditionTotal'] = conditionTotal
tempInterv[pos2/2]['conditionDate'] = str(enumList[pos2] + shiftDates) + '~' + str(enumList[pos2] + shiftDates)
tempInterv[pos2/2]['conditionMembership'] = getSubpopID(subpopsNew,popName)
tempInterv[pos2/2]['conditionCompliance'] = str(float(intervNew[2]) * enumList[pos2+1])
tempInterv[pos2/2]['action'] = actionID
pos2 += 2
else:
tempInterv = []
for pos2 in range(length):
tempInterv.append(prepNewIntervention())
tempInterv[pos2]['interventionID'] = str(9300 + len(interventionsNew) + pos2)
tempInterv[pos2]['interventionType'] = "Offline"
if conditionTotal != -1:
tempInterv[pos2]['conditionTotal'] = conditionTotal
tempInterv[pos2]['conditionDate'] = str(day+pos2+shiftDates) + '~' + str(day+pos2+shiftDates)
tempInterv[pos2]['conditionMembership'] = getSubpopID(subpopsNew,popName)
tempInterv[pos2]['conditionCompliance'] = str(float(intervNew[2]) / length)
tempInterv[pos2]['action'] = actionID
subPopName = popName + 'd' + str(pos2+1) + 'i' + suffix
if ".txt" in subPopName:
subPopName = subPopName.replace('.txt','') + '.txt'
actionsNew.append(tempAction)
interventionsNew += tempInterv
# AUTOGENERATE NEW FORMAT MUTEXES
if useNew:
vMutex = []; avMutex = []
sdMutex = []; cwMutex = []
csMutex = []; sqMutex = []
limit = len(actionsNew)
print "Generating", limit, "new format actions"
for pos in range(limit):
if actionsNew[pos]['actionType'] == "Vaccination":
if actionsNew[pos]['actionID'] not in vMutex:
vMutex.append(actionsNew[pos]['actionID'])
elif actionsNew[pos]['actionType'] == "Antiviral":
if actionsNew[pos]['actionID'] not in avMutex:
avMutex.append(actionsNew[pos]['actionID'])
elif actionsNew[pos]['actionType'] == "SocialDistancing":
if actionsNew[pos]['actionID'] not in sdMutex:
sdMutex.append(actionsNew[pos]['actionID'])
elif actionsNew[pos]['actionType'] == "CloseWork":
if actionsNew[pos]['actionID'] not in cwMutex:
cwMutex.append(actionsNew[pos]['actionID'])
elif actionsNew[pos]['actionType'] == "CloseSchools":
if actionsNew[pos]['actionID'] not in csMutex:
csMutex.append(actionsNew[pos]['actionID'])
elif actionsNew[pos]['actionType'] == "Sequestion":
if actionsNew[pos]['actionID'] not in sqMutex:
sqMutex.append(actionsNew[pos]['actionID'])
limit = len(interventionsNew)
print "Generating", limit, "new format interventions"
for pos in range(limit):
temp = getActionType(actionsNew,interventionsNew[pos]['action'])
if temp == "Vaccination":
interventionsNew[pos]['conditionMutex'] = ';'.join(vMutex)
elif temp == "Antiviral":
interventionsNew[pos]['conditionMutex'] = ';'.join(avMutex)
elif temp == "SocialDistancing":
interventionsNew[pos]['conditionMutex'] = ';'.join(sdMutex)
elif temp == "CloseWork":
interventionsNew[pos]['conditionMutex'] = ';'.join(cwMutex)
elif temp == "CloseSchools":
interventionsNew[pos]['conditionMutex'] = ';'.join(csMutex)
elif temp == "Sequestion":
interventionsNew[pos]['conditionMutex'] = ';'.join(sqMutex)
# APPENDING NON TREATMENT INTERVENTION TOTALS
outFile = open(writePath, 'a+b')
if useNew:
outFile.write(getOutputNew(subpopsNew, totalsNew, actionsNew, interventionsNew))
sumIntervs = vacTotal + avTotal + socialTotal + workTotal + schoolTotal + sqTotal + avTreatments
if sumIntervs == 0:
if useRaw:
print "No scripted interventions found, using iterated manual script"
outFile.write(appendScript)
else:
print "No scripted interventions or raw script found"
else:
if useRaw:
print "Appending manually iterated script"
outFile.write(appendScript)
outFile.write("\n#----- End of Generated Intervention File -----\n\n")
outFile.write("\n#Use only one intervention of each type per sub pop, using enumerated interventions for complex interventions.")
outFile.write("\n# Vaccination: " + str(vacTotal))
outFile.write("\n# Antiviral Prophylaxis: " + str(avTotal))
outFile.write("\n# Social Distancing: " + str(socialTotal))
outFile.write("\n# Close Work: " + str(workTotal))
outFile.write("\n# Close Schools: " + str(schoolTotal))
if useNew:
outFile.write("\n# Sequestered: " + str(sqTotal))
outFile.write("\n# AV Treatment Programs: " + str(avTreatments))
outFile.close()
print """RollVac.Py Pre Compliance Intervention Totals- calculated per output,
does not account for over-application to a given set of IDs.
Please apply only one of each type per sub pop, using enumerated
interventions for complex interventions."""
print "\nVaccination: " + str(vacTotal)
print "Antiviral Prophylaxis: " + str(avTotal)
print "Social Distancing: " + str(socialTotal)
print "Close Work: " + str(workTotal)
print "Close Schools:" + str(schoolTotal)
if useNew:
print "Sequestered:" + str(sqTotal)
print "AV Treatment Programs: " + str(avTreatments)
print
if toFilterIDs:
return filteredIDs
def giSpyGDILoad(gDocURL,directory):
"""Updates user config & lists for GDI seeker"""
gdi = {}
print "Loading user account info from local directory"
account = loadGDIAccount(gDocURL,directory)
public = account['public']
print "Loading email lists from local directory"
if not public:
emails = gd.getLine(account['userName'], account['password'], account['fileName'], gdiEmail, False, [])
else:
emails = gd.getLine('null', 'null', gDocURL, gdiEmail, False, [])
try:
gdi['Email'] = emails[0].replace(' ',',')
except:
gdi['Email'] = ""
try:
gdi['CC'] = emails[1].replace(' ',',')
except:
gdi['CC'] = ""
gdi['URL'] = gDocURL
gdi['UserName'] = account['userName']
gdi['Password'] = account['password']
gdi['FileName'] = account['fileName']
try:
gdi['Frequency'] = int(emails[2])
except:
gdi['Frequency'] = account['frequency']
print "Loading word lists from local directory"
if not public:
config = gd.getScript(account['userName'], account['password'], account['fileName'], gdiParams, gdiLists, "default", False, [])
else:
config = gd.getScript('null', 'null', gDocURL, gdiParams, gdiLists, "default", False, [])
cfg = getConfig(config)
cfg['OutDir'] = account['name'] + '/'
cfg['FileName'] = account['name']
cfg['Sanitize'] = account['sanitize']
if type(account['login']) is list:
cfg['Logins'] = account['login']
else:
cfg['Logins'] = [account['login']]
cfg['GDI'] = gdi
cfg['UseGDI'] = True
#if cfg['OnlyKeepNLP'] != False and cfg['OnlyKeepNLP'] != 'null':
# if type(cfg['OnlyKeepNLP']) != list:
# cfg['OnlyKeepNLP'] = [str(cfg['OnlyKeepNLP'])]
if not public:
uglyLists = gd.getScript(account['userName'], account['password'], account['fileName'], gdiLists, -1, "default", False, [])
else:
uglyLists = gd.getScript('null', 'null', gDocURL, gdiLists, -1, "default", False, [])
conditions = []
qualifiers = set()
exclusions = set()
for pos in range(len(uglyLists)):
row = uglyLists[pos]
if len(str(row[0])) != 0:
conditions.append(row[0])
if len(str(row[1])) != 0:
qualifiers.add(row[1])
if len(str(row[2])) != 0:
exclusions.add(row[2])
lists = {'conditions':conditions,'qualifiers':qualifiers,'exclusions':exclusions}
return {'lists':lists,'config':cfg,'login':account['login']}
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():
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')
params = gd.getLine(sys.argv[1], sys.argv[2], sys.argv[3], paramsLine, False, [])
script = gd.getScript(sys.argv[1], sys.argv[2], sys.argv[3], toFromLine, EFO6Line, "default", False, [])
directories = gd.getScript(sys.argv[1], sys.argv[2], sys.argv[3], EFO6Line, -1, "default", False, [])
sys.argv = None
outDir = prepDir(params[0])
subpopDir = prepDir(params[1])
filesOut = []
durations = {}
fromPops = []
for line in script:
if len(line[0]) == 0 or len(line[1]) == 0:
print "Error, missing to or from subpop name, line:", line
quit()
if line[1] not in fromPops:
fromPops.append(line[1])
for line in directories:
if len(line[0]) == 0 or len(line[1]) == 0:
print "Error, missing file or directory name, line:", line
quit()
if line[0] not in durations:
durations[line[0]] = 0
durations[line[0]] = max(durations[line[0]],getLength(line[1]))
if not os.path.isdir(outDir):
os.mkdir(outDir)
for line in directories:
if line[0] not in filesOut:
filesOut.append(line[0])
text = str(range(durations[line[0]])).replace('[','').replace(']',',\n').replace(' ','')
flush = open(outDir + 'CrossTalk_' + line[0],'w')
flush.write("directory,descriptor,toSubpop,toSize,fromSubpop,fromSize,iteration,isEpidemic," + text)
flush.close()
flush = open(outDir + 'RepNum_' + line[0],'w')
flush.write("directory,fromSubpop,fromSize,iteration,isEpidemic," + text)
flush.close()
if len(outDir) == 0:
print "Error, no output directory specified"
quit()
elif not os.path.isdir(subpopDir):
print "Error, subpop diretory", subpopDir, "does not exist"
quit()
elif len(filesOut) == 0:
print "Error, no analysis output directories specified"
quit()
print "Prepping experiment, parameters are:\n"
print "Analysis Directory:\n\t", outDir, "\nSubpop Directory:\n\t", subpopDir
print "Subpopulations to/ from:\n", printList(script)
print "Analyses:\n", printList(directories)
EFO6Files = getEFO6s(directories)
print EFO6Files.keys()
popSize = EFO6Files[directories[0][1]+'_size']
subpopFiles = getSubpops(script, subpopDir, popSize)
if "error" in subpopFiles:
print "Error termination"
quit()
allCurves = []
fromPopIsEpi = [0]*len(fromPops)
for experiment in directories:
for subpop in script:
crossTalkEFO6 = {'EFO6':EFO6Files[experiment[1]],'iterations':EFO6Files[experiment[1] +'_iterations']}
crossTalkSubs = {'toPop':subpopFiles[subpop[0]],
'toType':subpopFiles[subpop[0]+'_type'],
'toName':subpop[0],
'fromPop':subpopFiles[subpop[1]],
'fromType':subpopFiles[subpop[1] + '_type'],
'fromName':subpop[1]}
print "\nAnalizing crosstalk for", experiment[1], "\n\twith subpops", subpop[0:2]
crossTalk = loadCrossTalk(crossTalkEFO6, crossTalkSubs, durations[experiment[0]])
fromPopIsEpi[fromPops.index(subpop[1])] = crossTalk['isEpidemic']
statsOut = open(outDir + 'CrossTalk_' + experiment[0],'a+b')
statsOut.write(curvesToStringCT(crossTalk['meanCrossTalkCurve'],
crossTalk['crossTalkCurves'],
crossTalk['isEpidemic'],
experiment[1].replace(outDir.replace('Analysis/',''),'').replace('/EFO6',''),
subpop[0],
subpopFiles[subpop[0]+'_popSize'],
subpop[1],
subpopFiles[subpop[1]+'_popSize']))
statsOut.close()
#allCurves.append(crossTalk)
print printList(crossTalk['crossTalkCurves'])
print "CrossTalk Analysis Complete, beginning reproductive number analysis"
for experiment in directories:
for pos in range(len(fromPops)):
pop = fromPops[pos]
repNumStats = loadRepNum(pop,
subpopFiles[pop],
subpopFiles[pop + '_type'],
EFO6Files[experiment[1]],
EFO6Files[experiment[1]+'_iterations'],
durations[experiment[0]],
fromPopIsEpi[pos])
print '\n', printList(repNumStats['meanRepNumCurve'])
statsOut = open(outDir + 'RepNum_' + experiment[0],'a+b')
statsOut.write(curvesToStringRN(repNumStats['meanRepNumCurve'],
repNumStats['repNumCurves'],
fromPopIsEpi[pos],
experiment[1].replace(outDir.replace('Analysis/',''),'').replace('/EFO6',''),
pop,
subpopFiles[pop+'_popSize']))
statsOut.close()
print "Analysis complete, quitting now..."
def main(arg1, arg2, arg3, arg4, polyScript, filteredIDs, popSizes):
print arg1, arg2, arg3, arg4
if __name__ != '__main__':
sys.argv = ['RollVac.py', arg1, arg2, arg3, arg4]
if arg1 == "poly":
del sys.argv[3:5]
trigger = 1
subnum = 0
path = ""
population = ""
useExplicit = False
explicitDirectory = ""
subpopDirectory = ""
useBase = False
useRaw = False
baseFile = ""
pos = 0
iCode = 0
vacTotal = 0
avTotal = 0
socialTotal = 0
workTotal = 0
schoolTotal = 0
sqTotal = 0
avTreatments = 0
try:
toFilterIDs = len(filteredIDs) > 0
except:
toFilterIDS = False
useNew = False
subpopsNew = []
actionsNew = []
totalsNew = {'vaccination': 1000000000, 'antiviral': 1000000000}
interventionsNew = []
# LOADS PUBLIC/ PRIVATE DATA FROM GDOC IF PASSED
if len(sys.argv) < 3:
print "Missing arguments, quitting now"
quit()
outName = "Default"
elif len(sys.argv) > 3:
if sys.argv[1] == "gdoc" or sys.argv[1] == "poly":
arg = "gDoc"
if len(sys.argv) == 4:
sys.argv.insert(3, 'null')
else:
print "Ignoring", len(sys.argv) - 3, "excess arguments\n"
elif len(sys.argv) == 3:
if sys.argv[1] == "gdoc" or sys.argv[1] == "poly":
arg = "gDoc"
sys.argv.insert(2, 'null')
sys.argv.insert(2, 'null')
else:
outName = sys.argv[2]
arg = sys.argv[1]
# LOADS AND WRITES AV/ DIAG SCRIPT FROM GOOGLE DOC, NOT IMPLEMENTED FOR USER/ LOCAL SCRIPT MODE
print sys.argv
if arg == "gDoc":
if sys.argv[1] == "poly":
isPoly = True
sys.argv[3] = 'null'
path = arg2
if os.path.exists(path):
shutil.rmtree(path)
os.makedirs(path)
os.makedirs(path + "/output")
else:
isPoly = False
loadType = "intervention script"
print sys.argv
script = gDocsImport.getScript(sys.argv[2], sys.argv[3], sys.argv[4],
startWord, stopWord, loadType, isPoly,
polyScript)
params = gDocsImport.getLine(sys.argv[2], sys.argv[3], sys.argv[4],
paramsStart, isPoly, polyScript)
print "debooo script", script
emptyblock = (script
== 'null') or len(''.join(''.join(script).split())) < 2
explicitDirectory = params[2]
if len(explicitDirectory) > 0:
useExplicit = True
try:
shiftDates = int(params[8])
print "Date shift set to", shiftDates
except:
shiftDates = 0
print "Using default '0' date shift"
if isPoly:
outName = ""
baseFile = params[4]
subpopDirectory = params[6]
if len(baseFile) > 0:
if os.path.exists(baseFile):
print "Appending interventions to base file", baseFile
useBase = True
else:
print "Error, base file", baseFile, "not found"
quit()
else:
outName = params[0]
if len(outName) == 0:
print "No name prefix stored, using default intervention, antiviral, and diagnosis"
outName = ""
print "Will write to intervention file '%sIntervention'\n" % outName
diag = params[1]
diagnosis = isYes(diag, "diagnosis")
useNew = isYes(params[7], "new style")
try:
appendScript = gDocsImport.getScript(sys.argv[2], sys.argv[3],
sys.argv[4], avStop, 0,
loadType, isPoly, polyScript)
appendScript = appendRaw(appendScript)
useRaw = appendScript != 'null'
if useRaw:
print "\nRaw script footer loaded succesfully,", appendScript.count(
'\n') - 3, "lines to append"
except:
print "Error, raw script footer not loaded"
if not diagnosis:
sys.argv[3] = "null"
else:
loadType = "default"
avScript = gDocsImport.getScript(sys.argv[2], sys.argv[3],
sys.argv[4], avStart, avStop,
loadType, isPoly, polyScript)
diagParams = gDocsImport.getLine(sys.argv[2], sys.argv[3],
sys.argv[4], stopWord, isPoly,
polyScript)
sys.argv[3] = "null"
if not useNew:
if avScript == 'null':
print "No AV-Script found"
temp = open(path + '/Antiviral', 'w')
temp.write(
"#Null file: AV-Scripting enabled though no interventions found"
)
temp.close()
temp = open(path + '/Diagnosis', 'w')
temp.write(
"#Null file: AV-Scripting enabled though no interventions found"
)
temp.close()
avTreatments = 0
else:
avTreatments = writeAvScript(avScript, diagParams, outName,
path, subpopDirectory,
shiftDates)
# PREP NEW FORMAT DICTS
else:
if avScript == 'null':
print "No AV-Script found"
avTreatments = 0
else:
temp = prepNewAV(avScript, diagParams, outName, path,
subpopDirectory, totalsNew, shiftDates)
subpopsNew += temp['subpops']
actionsNew += temp['actions']
interventionsNew += temp['interventions']
"""print subpopsNew
print actionsNew
print interventionsNew"""
avTreatments = len(actionsNew)
if arg != "user" and arg != "gDoc" and arg != "gdoc" and (
not os.path.isfile(arg)):
print arg
print "Error, cannot open file or directory\n"
quit()
done = False
# LOCAL SCRIPT FILE LOADING
if arg != "user" and arg != "gDoc":
scriptfile = open(arg)
script = []
line = 0
gotPath = False
while True:
testline = scriptfile.readline()
if len(testline) == 0:
break
if not testline.startswith("#"):
if testline.startswith("Directory"):
gotPath = True
temp = testline.split()
if len(temp) < 2:
path = ""
else:
path = testline.split()[1]
if (path == "local" or path == "Local"):
path = ""
else:
script.append(testline)
line += 1
if not gotPath:
path = ""
# FLUSH INTERVENTION FILE & COPY POLYRUN BASEFILE IF NEEDED
writePath = path + outName + 'Intervention'
if useNew:
writePath += 'New'
if useBase:
shutil.copy2(baseFile, writePath)
outFile = open(writePath)
temp = outFile.read()
outFile.close()
outFile = open(writePath, 'w')
outFile.write(
"# ----- PolyRun.Py Appended Intervention File -----\n\n")
outFile.write(temp)
outFile.write(
"\n\n# ----- End of Appended Intervention File -----\n\n")
else:
outFile = open(writePath, 'w')
if useNew:
outFile.write(
"# ----- RollVac.Py Autogenerated Intervention File New Version-----\n\n"
)
else:
outFile.write(
"# ----- RollVac.Py Autogenerated Intervention File Old Version-----\n\n"
)
outFile.close()
# GENERATING OUTPUT FILE LOOP
while not done and emptyblock == False:
subnum += 1
enum = False
# LOCAL SCRIPT/ GDOC CONTROLLED CHOPPING
if True:
if pos == len(script):
done = True
break
cmd = script[pos]
items = cmd.split()
population = (subpopDirectory + '/' + items[0]).replace('//', '/')
try:
with open(population):
pass
except:
print "Error: population file", population, "not found\n"
quit()
if str(items[1]) == 'enum':
enum = True
cmd = cmd.replace("enum", "null null")
items = cmd.split()
pos += 1
enumList = script[pos].replace(";", " ; ")
if checkEnum(enumList):
enumList = parseEnum(enumList)
else:
print "Error: misformatted enumeration list", enumList
quit()
if not enum:
try:
day = int(items[1]) + shiftDates
if day <= 0:
print "Error, day must be an integer value\n"
quit()
except:
print "Error, day must be an integer greater than zero\n"
quit()
try:
length = int(items[2])
if length <= 0:
print "Error, length must be an integer greater than zero\n"
quit()
except:
print "Error, length must be an integer greater than zero\n"
quit()
temp = cmd.split()
print "Generating interventions with parameters:", cmd
method = temp[3]
arguments = len(temp)
if method == "Vaccination":
target = 7
meth = "v"
iCode = 0
if arguments == 7:
temp[5], temp[6] = temp[6], temp[5]
elif method == "Antiviral":
target = 8
meth = "av"
iCode = 1000
if arguments == 8:
temp[5], temp[6], temp[7] = temp[6], temp[7], temp[5]
elif method == "SocialDistancing":
target = 6
meth = "sd"
iCode = 2000
elif method == "WorkClosure":
target = 6
meth = "cw"
iCode = 3000
elif method == "SchoolClosure":
target = 6
meth = "cs"
iCode = 4000
elif method == "Sequestion":
target = 7
meth = "sq"
iCode = 6000
else:
print "Error:", method, "method not recognized\n"
quit()
if arguments != target:
print "Error:", len(
temp
), "parameters found,", target, "expected for intervention type", method, "\n"
quit()
interv = " ".join(temp[3:target])
intervNew = temp[3:target]
pos += 1
suffix = str(subnum) + meth
# ALL MODE CHOPPING EXECUTION
print population
if not useNew:
pos2 = 0
limit = len(filteredIDs)
found = False
while pos2 < limit:
if population in filteredIDs[pos2]['directory']:
found = True
runIDs = filteredIDs[pos2]['ids']
break
pos2 += 1
if not found:
filteredIDs.append(filterIDs(population))
runIDs = filteredIDs[-1]['ids']
if enum:
populationSize = checkSize(population, popSizes)
enumList = cleanEnum(percentEnum(enumList, populationSize))
holder = chopper.main(population, 'e',
" ".join(map(str, enumList)), suffix,
path, runIDs)
returnSize = holder['count']
enumList = holder['enum']
length = chopper.getEnumSize(enumList)
else:
holder = chopper.main(population, 'b', str(length), suffix,
path, runIDs)
returnSize = holder['count']
else:
addSubpop(subpopsNew,
population.split('/')[-1], population,
9000 + len(subpopsNew))
if enum:
populationSize = checkSize(population, popSizes)
temp = countEnum(enumList, populationSize)
enumList = chopper.trimEnum(cleanEnum(temp['enum']),
populationSize)
length = chopper.getEnumSize(enumList)
returnSize = int(min(temp['total'], populationSize))
else:
populationSize = returnSize = checkSize(population, popSizes)
# NON TREATMENT BASED INTERVENTION TRACKING
if meth == "v":
vacTotal += returnSize
elif meth == "av":
avTotal += returnSize
elif meth == "sd":
socialTotal += returnSize
elif meth == "cw":
workTotal += returnSize
elif meth == "cs":
schoolTotal += returnSize
elif meth == "sq":
sqTotal += returnSize
# WRITING INTERVENTION FILE (AV TREATMENT & DIAG HANDLED SEPERATELY)
writePath = path + outName + 'Intervention'
pos2 = 0
popName = population.split('/')[-1]
if not useNew:
outFile = open(writePath, 'a+b')
if enum:
while pos2 < len(enumList):
subPopName = popName + 'd' + str(pos2 / 2) + 'i' + suffix
if ".txt" in subPopName:
subPopName = subPopName.replace('.txt', '') + '.txt'
triggerOut = "* Trigger " + str(
trigger + iCode) + " Date " + str(enumList[pos2] +
shiftDates) + "\n"
if useExplicit:
tempPath = path + "/subpops/" + subPopName
else:
tempPath = "subpops/" + subPopName
intervOut = "* Action " + str(
trigger + iCode) + " " + interv + " " + tempPath + "\n"
intervOut = intervOut.replace('//', '/')
print triggerOut, intervOut.replace('\n', '')
outFile.write(triggerOut)
outFile.write(intervOut)
trigger += 1
pos2 += 2
else:
while pos2 < length:
subPopName = popName + 'd' + str(pos2) + 'i' + suffix
if ".txt" in subPopName:
subPopName = subPopName.replace('.txt', '') + '.txt'
triggerOut = "* Trigger " + str(
trigger + iCode) + " Date " + str(day + pos2) + "\n"
if useExplicit:
tempPath = path + "/subpops/" + subPopName
else:
tempPath = "subpops/" + subPopName
intervOut = "* Action " + str(
trigger + iCode) + " " + interv + " " + tempPath + "\n"
intervOut = intervOut.replace('//', '/')
print triggerOut, intervOut.replace('\n', '')
outFile.write(triggerOut)
outFile.write(intervOut)
trigger += 1
pos2 += 1
outFile.close()
print
else:
writePath += 'New'
tempAction = prepNewAction()
#tempInterv = [prepNewIntervention()]*len(enumList/2)
tempAction['actionID'] = actionID = str(trigger + iCode)
tempAction['actionType'] = method
if method == 'Antiviral':
method += "_Prophylaxis"
tempAction['actionDescription'] = method
tempAction['actionDelay'] = '0'
tempAction['actionDuration'] = intervNew[1]
conditionTotal = -1
if method == "Vaccination":
tempAction['actionEfficacy'] = intervNew[3]
conditionTotal = '9100'
elif method == "Antiviral":
tempAction['actionEfficacyIn'] = intervNew[3]
tempAction['actionEfficacyOut'] = intervNew[4]
conditionTotal = '9101'
elif method == "Sequestion":
tempAction['actionGroupSize'] = intervNew[3]
if enum:
tempInterv = []
while pos2 < len(enumList):
tempInterv.append(prepNewIntervention())
tempInterv[pos2 / 2]['interventionID'] = str(
9300 + len(interventionsNew) + pos2 / 2)
tempInterv[pos2 / 2]['interventionType'] = "Offline"
if conditionTotal != -1:
tempInterv[pos2 / 2]['conditionTotal'] = conditionTotal
tempInterv[pos2 / 2]['conditionDate'] = str(
enumList[pos2] +
shiftDates) + '~' + str(enumList[pos2] + shiftDates)
tempInterv[pos2 / 2]['conditionMembership'] = getSubpopID(
subpopsNew, popName)
tempInterv[pos2 / 2]['conditionCompliance'] = str(
float(intervNew[2]) * enumList[pos2 + 1])
tempInterv[pos2 / 2]['action'] = actionID
pos2 += 2
else:
tempInterv = []
for pos2 in range(length):
tempInterv.append(prepNewIntervention())
tempInterv[pos2]['interventionID'] = str(
9300 + len(interventionsNew) + pos2)
tempInterv[pos2]['interventionType'] = "Offline"
if conditionTotal != -1:
tempInterv[pos2]['conditionTotal'] = conditionTotal
tempInterv[pos2]['conditionDate'] = str(
day + pos2 + shiftDates) + '~' + str(day + pos2 +
shiftDates)
tempInterv[pos2]['conditionMembership'] = getSubpopID(
subpopsNew, popName)
tempInterv[pos2]['conditionCompliance'] = str(
float(intervNew[2]) / length)
tempInterv[pos2]['action'] = actionID
subPopName = popName + 'd' + str(pos2 + 1) + 'i' + suffix
if ".txt" in subPopName:
subPopName = subPopName.replace('.txt', '') + '.txt'
actionsNew.append(tempAction)
interventionsNew += tempInterv
# AUTOGENERATE NEW FORMAT MUTEXES
if useNew:
vMutex = []
avMutex = []
sdMutex = []
cwMutex = []
csMutex = []
sqMutex = []
limit = len(actionsNew)
print "Generating", limit, "new format actions"
for pos in range(limit):
if actionsNew[pos]['actionType'] == "Vaccination":
if actionsNew[pos]['actionID'] not in vMutex:
vMutex.append(actionsNew[pos]['actionID'])
elif actionsNew[pos]['actionType'] == "Antiviral":
if actionsNew[pos]['actionID'] not in avMutex:
avMutex.append(actionsNew[pos]['actionID'])
elif actionsNew[pos]['actionType'] == "SocialDistancing":
if actionsNew[pos]['actionID'] not in sdMutex:
sdMutex.append(actionsNew[pos]['actionID'])
elif actionsNew[pos]['actionType'] == "CloseWork":
if actionsNew[pos]['actionID'] not in cwMutex:
cwMutex.append(actionsNew[pos]['actionID'])
elif actionsNew[pos]['actionType'] == "CloseSchools":
if actionsNew[pos]['actionID'] not in csMutex:
csMutex.append(actionsNew[pos]['actionID'])
elif actionsNew[pos]['actionType'] == "Sequestion":
if actionsNew[pos]['actionID'] not in sqMutex:
sqMutex.append(actionsNew[pos]['actionID'])
limit = len(interventionsNew)
print "Generating", limit, "new format interventions"
for pos in range(limit):
temp = getActionType(actionsNew, interventionsNew[pos]['action'])
if temp == "Vaccination":
interventionsNew[pos]['conditionMutex'] = ';'.join(vMutex)
elif temp == "Antiviral":
interventionsNew[pos]['conditionMutex'] = ';'.join(avMutex)
elif temp == "SocialDistancing":
interventionsNew[pos]['conditionMutex'] = ';'.join(sdMutex)
elif temp == "CloseWork":
interventionsNew[pos]['conditionMutex'] = ';'.join(cwMutex)
elif temp == "CloseSchools":
interventionsNew[pos]['conditionMutex'] = ';'.join(csMutex)
elif temp == "Sequestion":
interventionsNew[pos]['conditionMutex'] = ';'.join(sqMutex)
# APPENDING NON TREATMENT INTERVENTION TOTALS
outFile = open(writePath, 'a+b')
if useNew:
outFile.write(
getOutputNew(subpopsNew, totalsNew, actionsNew, interventionsNew))
sumIntervs = vacTotal + avTotal + socialTotal + workTotal + schoolTotal + sqTotal + avTreatments
if sumIntervs == 0:
if useRaw:
print "No scripted interventions found, using iterated manual script"
outFile.write(appendScript)
else:
print "No scripted interventions or raw script found"
else:
if useRaw:
print "Appending manually iterated script"
outFile.write(appendScript)
outFile.write("\n#----- End of Generated Intervention File -----\n\n")
outFile.write(
"\n#Use only one intervention of each type per sub pop, using enumerated interventions for complex interventions."
)
outFile.write("\n# Vaccination: " + str(vacTotal))
outFile.write("\n# Antiviral Prophylaxis: " + str(avTotal))
outFile.write("\n# Social Distancing: " + str(socialTotal))
outFile.write("\n# Close Work: " + str(workTotal))
outFile.write("\n# Close Schools: " + str(schoolTotal))
if useNew:
outFile.write("\n# Sequestered: " + str(sqTotal))
outFile.write("\n# AV Treatment Programs: " + str(avTreatments))
outFile.close()
print """RollVac.Py Pre Compliance Intervention Totals- calculated per output,
does not account for over-application to a given set of IDs.
Please apply only one of each type per sub pop, using enumerated
interventions for complex interventions."""
print "\nVaccination: " + str(vacTotal)
print "Antiviral Prophylaxis: " + str(avTotal)
print "Social Distancing: " + str(socialTotal)
print "Close Work: " + str(workTotal)
print "Close Schools:" + str(schoolTotal)
if useNew:
print "Sequestered:" + str(sqTotal)
print "AV Treatment Programs: " + str(avTreatments)
print
if toFilterIDs:
return filteredIDs
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!"
def main():
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')
params = gd.getLine(sys.argv[1], sys.argv[2], sys.argv[3], paramsLine,
False, [])
script = gd.getScript(sys.argv[1], sys.argv[2], sys.argv[3], toFromLine,
EFO6Line, "default", False, [])
directories = gd.getScript(sys.argv[1], sys.argv[2], sys.argv[3], EFO6Line,
-1, "default", False, [])
sys.argv = None
outDir = prepDir(params[0])
subpopDir = prepDir(params[1])
filesOut = []
durations = {}
fromPops = []
for line in script:
if len(line[0]) == 0 or len(line[1]) == 0:
print "Error, missing to or from subpop name, line:", line
quit()
if line[1] not in fromPops:
fromPops.append(line[1])
for line in directories:
if len(line[0]) == 0 or len(line[1]) == 0:
print "Error, missing file or directory name, line:", line
quit()
if line[0] not in durations:
durations[line[0]] = 0
durations[line[0]] = max(durations[line[0]], getLength(line[1]))
if not os.path.isdir(outDir):
os.mkdir(outDir)
for line in directories:
if line[0] not in filesOut:
filesOut.append(line[0])
text = str(range(durations[line[0]])).replace('[', '').replace(
']', ',\n').replace(' ', '')
flush = open(outDir + 'CrossTalk_' + line[0], 'w')
flush.write(
"directory,descriptor,toSubpop,toSize,fromSubpop,fromSize,iteration,isEpidemic,"
+ text)
flush.close()
flush = open(outDir + 'RepNum_' + line[0], 'w')
flush.write("directory,fromSubpop,fromSize,iteration,isEpidemic," +
text)
flush.close()
if len(outDir) == 0:
print "Error, no output directory specified"
quit()
elif not os.path.isdir(subpopDir):
print "Error, subpop diretory", subpopDir, "does not exist"
quit()
elif len(filesOut) == 0:
print "Error, no analysis output directories specified"
quit()
print "Prepping experiment, parameters are:\n"
print "Analysis Directory:\n\t", outDir, "\nSubpop Directory:\n\t", subpopDir
print "Subpopulations to/ from:\n", printList(script)
print "Analyses:\n", printList(directories)
EFO6Files = getEFO6s(directories)
print EFO6Files.keys()
popSize = EFO6Files[directories[0][1] + '_size']
subpopFiles = getSubpops(script, subpopDir, popSize)
if "error" in subpopFiles:
print "Error termination"
quit()
allCurves = []
fromPopIsEpi = [0] * len(fromPops)
for experiment in directories:
for subpop in script:
crossTalkEFO6 = {
'EFO6': EFO6Files[experiment[1]],
'iterations': EFO6Files[experiment[1] + '_iterations']
}
crossTalkSubs = {
'toPop': subpopFiles[subpop[0]],
'toType': subpopFiles[subpop[0] + '_type'],
'toName': subpop[0],
'fromPop': subpopFiles[subpop[1]],
'fromType': subpopFiles[subpop[1] + '_type'],
'fromName': subpop[1]
}
print "\nAnalizing crosstalk for", experiment[
1], "\n\twith subpops", subpop[0:2]
crossTalk = loadCrossTalk(crossTalkEFO6, crossTalkSubs,
durations[experiment[0]])
fromPopIsEpi[fromPops.index(subpop[1])] = crossTalk['isEpidemic']
statsOut = open(outDir + 'CrossTalk_' + experiment[0], 'a+b')
statsOut.write(
curvesToStringCT(
crossTalk['meanCrossTalkCurve'],
crossTalk['crossTalkCurves'], crossTalk['isEpidemic'],
experiment[1].replace(outDir.replace('Analysis/', ''),
'').replace('/EFO6', ''), subpop[0],
subpopFiles[subpop[0] + '_popSize'], subpop[1],
subpopFiles[subpop[1] + '_popSize']))
statsOut.close()
#allCurves.append(crossTalk)
print printList(crossTalk['crossTalkCurves'])
print "CrossTalk Analysis Complete, beginning reproductive number analysis"
for experiment in directories:
for pos in range(len(fromPops)):
pop = fromPops[pos]
repNumStats = loadRepNum(pop, subpopFiles[pop],
subpopFiles[pop + '_type'],
EFO6Files[experiment[1]],
EFO6Files[experiment[1] + '_iterations'],
durations[experiment[0]],
fromPopIsEpi[pos])
print '\n', printList(repNumStats['meanRepNumCurve'])
statsOut = open(outDir + 'RepNum_' + experiment[0], 'a+b')
statsOut.write(
curvesToStringRN(
repNumStats['meanRepNumCurve'],
repNumStats['repNumCurves'], fromPopIsEpi[pos],
experiment[1].replace(outDir.replace('Analysis/', ''),
'').replace('/EFO6', ''), pop,
subpopFiles[pop + '_popSize']))
statsOut.close()
print "Analysis complete, quitting now..."