#### Initialize the FRED SIMS
fred = FRED()
key = opts.key
run = opts.run
try:
int(run)
except:
if run != "ave" and run != "all":
print "Invalid parameter for run, needs to be an integer, all or ave"
sys.exit(1)
fred_run = FRED_RUN(fred, key)
numberDays = int(fred_run.get_param("days"))
outputsAve = fred_run.outputsAve
apolloDBs = [apollo.ApolloDB(host_=x) for x in DBHosts]
for apolloDB in apolloDBs:
apolloDB.connect()
concString = ""
m5hash = ""
### create a string of the concatenated input files
exclusionList = ['dbfile.txt', 'defaults']
fred_work_dir = fred_run.run_work_dir
if os.path.exists(fred_work_dir) is True:
workingFiles = glob.glob(fred_work_dir + "/*")
### concatenate params file first
### find it and add it to the exclusionList
#### Initialize the FRED SIMS
fred = FRED()
key = opts.key
run = opts.run
try:
int(run)
except:
if run != "ave" and run != "all":
print "Invalid parameter for run, needs to be an integer, all or ave"
sys.exit(1)
fred_run = FRED_RUN(fred, key)
numberDays = int(fred_run.get_param("days"))
outputsAve = fred_run.outputsAve
apolloDB = apollo.ApolloDB()
apolloDB.connect()
#for day in outputsAve:
# print "Day = %d I = %d"%(day['Day'],day['I'])
#ApolloConn = MySQLdb.connect(host="warhol-fred.psc.edu",
# user="******",
# db="apollo")
#ApolloCursor = ApolloConn.cursor()
## Fill in the run table
vizType = opts.type
vizVariable = opts.variable
vizOp = opts.op
movFormat = opts.movformat
imgFormat = "png"
if vizType == "animated":
imgFormat = "gif"
percentsString = ""
if opts.percents is True:
percentsString = "_percents"
### Find the FRED run in this SIMS
fred_run = FRED_RUN(fred, key)
### Find the Population File
time1 = time.time()
countyList = []
#if fred_run.params_dict['city'] is not None:
# print fred_run.params_dict['city']
# countyList = [fred.cityDict[fred_run.params_dict['city']]]
# elif fred_run.params_dict['county'] is not None:
# countyList = [fred.countyDict[fred_run.params_dict['county']]]
# else:
#synth_pop_dir = fred_run.get_param("synthetic_population_directory")
#synth_pop_id = fred_run.get_param("synthetic_population_id")
#synth_pop_prefix = os.path.expandvars(synth_pop_dir + "/" + synth_pop_id + "/" + synth_pop_id)
#### Initialize the FRED SIMS
fred = FRED()
key = opts.key
run = opts.run
try:
int(run)
except:
if run != "ave" and run != "all":
print "Invalid parameter for run, needs to be an integer, all or ave"
sys.exit(1)
fred_run = FRED_RUN(fred,key)
numberDays = int(fred_run.get_param("days"))
outputsAve = fred_run.outputsAve
apolloDBs = [ apollo.ApolloDB(host_=x) for x in DBHosts ]
for apolloDB in apolloDBs:
apolloDB.connect()
concString = ""
m5hash = ""
### create a string of the concatenated input files
exclusionList = ['dbfile.txt','defaults']
fred_work_dir = fred_run.run_work_dir
if os.path.exists(fred_work_dir) is True:
workingFiles = glob.glob(fred_work_dir + "/*")
### concatenate params file first
### find it and add it to the exclusionList
vizType = opts.type
vizVariable = opts.variable
vizOp = opts.op
movFormat = opts.movformat
imgFormat = "png"
if vizType == "animated":
imgFormat = "gif"
percentsString = ""
if opts.percents is True:
percentsString = "_percents"
### Find the FRED run in this SIMS
fred_run = FRED_RUN(fred,key)
### Find the Population File
time1 = time.time()
if opts.taiwan is True:
countyList = None
else:
countyList = []
#if fred_run.params_dict['city'] is not None:
# print fred_run.params_dict['city']
# countyList = [fred.cityDict[fred_run.params_dict['city']]]
# elif fred_run.params_dict['county'] is not None:
# countyList = [fred.countyDict[fred_run.params_dict['county']]]
# else:
#synth_pop_dir = fred_run.get_param("synthetic_population_directory")
DBHosts = ["warhol-fred.psc.edu"]
### This only currently works for allegheny county
#### Initialize the FRED SIMS
fred = FRED()
key = opts.key
run = opts.run
simulationRunId = opts.runId
statusFile = "./starttime"
if simulationRunId is None:
error_exit("Need to specify an Apollo SimulationRunId to use this program")
try:
fred_run = FRED_RUN(fred,key)
numberDays = int(fred_run.get_param("days"))
outputsAve = fred_run.outputsAve
except Exception as e:
error_exit(str(e))
try:
apolloDBs = [ apollo.ApolloDB(host_=x) for x in DBHosts ]
for apolloDB in apolloDBs:
print "working on DB: " + str(apolloDB._host)
apolloDB.connect()
### Get the runId from the database
locationList = [fred_run.get_param('fips')]
### This only currently works for allegheny county
#### Initialize the FRED SIMS
fred = FRED()
key = opts.key
run = opts.run
simulationRunId = opts.runId
statusFile = "./starttime"
if simulationRunId is None:
error_exit(
"Need to specify an Apollo SimulationRunId to use this program")
try:
fred_run = FRED_RUN(fred, key)
numberDays = int(fred_run.get_param("days"))
outputsAve = fred_run.outputsAve
except Exception as e:
error_exit(str(e))
try:
apolloDBs = [apollo.ApolloDB(host_=x) for x in DBHosts]
for apolloDB in apolloDBs:
print "working on DB: " + str(apolloDB._host)
apolloDB.connect()
### Get the runId from the database
locationList = [fred_run.get_param('fips')]
#### Initialize the FRED SIMS
fred = FRED()
key = opts.key
run = opts.run
try:
int(run)
except:
if run != "ave" and run != "all":
print "Invalid parameter for run, needs to be an integer, all or ave"
sys.exit(1)
fred_run = FRED_RUN(fred,key)
numberDays = int(fred_run.get_param("days"))
outputsAve = fred_run.outputsAve
apolloDB = apollo.ApolloDB()
apolloDB.connect()
## Fill in the run table
SQLString = 'INSERT INTO run set label = "' + key + '"'
apolloDB.query(SQLString)
runInsertID = apolloDB.insertID()
stateList = {'S':'susceptible','E':'exposed','I':'infectious','R':'recovered'}
locationList = ['42003'] # need to replace with an automatic way of getting this info
stateInsertIDDict = {}