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
SQLString = 'INSERT INTO run set label = "' + key + '"'
apolloDB.query(SQLString)
runInsertID = apolloDB.insertID()
# print "Run ID = " + str(runInsertID)
""")
parser.add_option("-d","--debug",action="store_true")
parser.add_option("-i","--runId",type="string",
help="The Apollo RunId for this call")
parser.add_option("-H", "--dbHost", type="string", default="warhol-fred.psc.edu")
parser.add_option("-D", "--dbName", type="string", default="test")
parser.add_option("-U", "--dbUser", type="string", default="apolloext")
parser.add_option("-P", "--dbPword", type="string")
parser.add_option("-n", "--no_db", action="store_true", default=False)
opts,args=parser.parse_args()
try:
apolloDB = apollo.ApolloDB(host_=opts.dbHost, dbname_=opts.dbName, user_=opts.dbUser, password_=opts.dbPword)
apolloDB.connect()
except Exception as e:
error_exit(str(e))
try:
stateToDataFileDict = {'S':'susceptible.txt','E':'exposed.txt','I':'infectious.txt','T':'temp_immuned.txt',
'R':'recovered.txt','M':'immuned.txt','C':'newly_exposed.txt','MS':'mosquito_susceptible.txt',
'ME':'mosquito_exposed.txt','MI':'mosquito_infectious.txt','MC':'mosquito_newly_exposed.txt'}
stateMap = {'Day':0,'S':2,'E':3,'I':4,'T':5,'R':7,'M':6,'C':8,'MS':9,'ME':10,'MI':11,'MC':12}
location = "00000"
fileList = []
with open('Apollo/out-1.seir','rb') as f:
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')]
for state, fileName in apolloDB.stateToDataFileDict.items():
stateStringList = []
if state == "C": continue
for location in locationList:
for day in outputsAve:
state_dis = "%s_0" % state
if state_dis in day.keys():
type="string",
help="The status to send to the database")
parser.add_option("-m",
"--message",
type="string",
help="The message to send to the database")
parser.add_option("-H",
"--dbHost",
type="string",
default="warhol-fred.psc.edu")
parser.add_option("-D", "--dbName", type="string", default="test")
parser.add_option("-U", "--dbUser", type="string", default="apolloext")
parser.add_option("-P", "--pword", type="string")
opts, args = parser.parse_args()
try:
DBHosts = opts.dbHost
apolloDB = apollo.ApolloDB(host_=DBHosts,
dbname_=opts.dbName,
user_=opts.dbUser,
password_=opts.pword)
apolloDB.connect()
# ## Add timestamp to this.
d = datetime.datetime.now()
thisMessage = "%s: %s" % (d.strftime('%B %d, %Y %I:%M%p'),
opts.message)
apolloDB.setRunStatus(opts.runId, opts.status, opts.message)
except Exception as e:
sys.stderr.write(str(e))
sys.exit(1)
def main():
parser = optparse.OptionParser(usage="""
%prog [--help][-k key][-r run_number][-t vis_type]
-k or --key Fred Key
-r or --run The run number of vizualize
ave = produce an average result
all = produce an input for all runs
-w or --time Turn on profiling
-d or --debug Turn on debug printing
""")
# parser.add_option("-k","--key",type="string",
# help="The FRED key for the run you wish to visualize")
parser.add_option("-o", "--outputdir", type="string", default="OUT")
parser.add_option("-i",
"--runId",
type="string",
help="The Apollo RunId for this call")
# parser.add_option("-r","--run",type="string",
# help="The number of the run you would like to visualize (number,ave, or all)",
# default=1)
parser.add_option("-w", "--time", action="store_true", default=False)
parser.add_option("-d", "--debug", action="store_true", default=False)
parser.add_option("-H",
"--dbHost",
type="string",
default="warhol-fred.psc.edu")
parser.add_option("-D", "--dbName", type="string", default="test")
parser.add_option("-U", "--dbUser", type="string", default="apolloext")
parser.add_option("-P", "--dbPword", type="string")
parser.add_option("-n", "--no_db", action="store_true", default=False)
opts, args = parser.parse_args()
DBHosts = [opts.dbHost]
simulationRunId = opts.runId
statusFile = "./starttime"
if simulationRunId is None:
error_exit(
"Need to specify an Apollo SimulationRunId to use this program")
try:
numberDays, outputKeys, averageOuts = FREDAverageOuts(opts.outputdir)
#averageOutputs = FREDAverageOuts(opts.outputdir)
#sys.exit()
# 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,
dbname_=opts.dbName,
user_=opts.dbUser,
password_=opts.dbPword) for x in DBHosts
]
for apolloDB in apolloDBs:
apolloDB.connect()
for state, filename in apolloDB.stateToDataFileDict.items():
sio = StringIO()
csvsio = StringIO()
csvsio.write("BlockGroup,Day,{0}".format(state))
if state in outputKeys:
for fips, days in averageOuts.items():
for i in range(len(days)):
#print "US{0} {1} {2}:1\n".format(fips,days[i][outputKeys.index(state)],i)
sio.write("US{0} {1} {2}:1\n".format(
fips,
int(round(days[i][outputKeys.index(state)],
0)), i))
m = hashlib.md5()
m.update(sio.getvalue())
m5hash = m.hexdigest()
runDataContentId = -1
hashvar = apolloDB.checkMD5HashExistence(m5hash)
if hashvar > -1:
runDataContentId = hashvar
else:
SQLString = 'INSERT INTO run_data_content (text_content, md5_hash_of_content) values ("%s","%s")' % (
sio.getvalue(), m5hash)
if (opts.no_db is False):
apolloDB.query(SQLString)
runDataContentId = apolloDB.insertID()
runDataDescriptionIdTS = apolloDB.getRunDataDescriptionId(
label_=filename)
SQLString = 'INSERT INTO run_data (run_id, description_id, content_id) values '\
'("%s","%s","%s")' % (simulationRunId, runDataDescriptionIdTS, runDataContentId)
if (opts.no_db is False):
apolloDB.query(SQLString)
if state == "C":
runDataDescriptionIdGAIA = apolloDB.getRunDataDescriptionId(
label_="newly_exposed.txt", destination_software_=5)
SQLString = "INSERT INTO run_data(run_Id,description_id,content_id) values ('%s','%d','%d')" % (
simulationRunId, runDataDescriptionIdGAIA,
runDataContentId)
SQLString = "INSERT INTO run_data(run_Id,description_id,content_id) values ('%s','%d','%d')" % (
simulationRunId, runDataDescriptionIdGAIA,
runDataContentId)
if (opts.no_db is False):
apolloDB.query(SQLString)
with open(filename, "wb") as f:
f.write('{0}'.format(sio.getvalue()))
apolloDB.close()
statusUpdate(
"LOG_FILES_WRITTEN", "%s" %
datetime.datetime.now().strftime("%a %b %d %H:%M:%S EDT %Y"))
except Exception as e:
error_exit(str(e))