def main():
# pdb.set_trace()
#***************** Setup Logging **************
logger = logging.getLogger('FinalJobber')
logger.setLevel(logging.INFO)
#logFileHandle = logging.FileHandler('/usgs/cdev/PDS/logs/Service.log')
logFileHandle = logging.FileHandler(pds_log + 'Service.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
#***************Look at Final queue for work************
RQ_final = RedisQueue('FinalQueue')
if int(RQ_final.QueueSize()) == 0:
# logger.info('NO Keys Found in FinalQueue')
print 'Nothing Found in Final Queue'
else:
FKey = RQ_final.QueueGet()
logger.info('Found %s in Final Queue', FKey)
# ** *************** HPC job stuff ***********************
logger.info('HPC Cluster job Submission Starting')
jobOBJ = HPCjob()
jobOBJ.setJobName(FKey + '_Final')
#jobOBJ.setStdOut('/usgs/cdev/PDS/output/' + FKey + '_%A_%a.out')
#jobOBJ.setStdError('/usgs/cdev/PDS/output/' + FKey + '_%A_%a.err')
jobOBJ.setStdOut(slurm_log + FKey + '_%A_%a.out')
jobOBJ.setStdError(slurm_log + FKey + '_%A_%a.err')
jobOBJ.setWallClock('24:00:00')
jobOBJ.setMemory('8192')
jobOBJ.setPartition('pds')
cmd = cmd_dir + 'ServiceFinal.py ' + FKey
jobOBJ.setCommand(cmd)
logger.info('HPC Command: %s', cmd)
#SBfile = '/scratch/pds_services/' + FKey + '/' + FKey + '_final.sbatch'
SBfile = scratch + FKey + '/' + FKey + '_final.sbatch'
jobOBJ.MakeJobFile(SBfile)
try:
sb = open(SBfile)
sb.close
logger.info('SBATCH File Creation: Success')
except IOError as e:
logger.error('SBATCH File %s Not Found', SBfile)
try:
jobOBJ.Run()
logger.info('Job Submission to HPC: Success')
except IOError as e:
logger.error('Jobs NOT Submitted to HPC')
def main():
# pdb.set_trace()
archiveID = {
16: '/pds_san/PDS_Archive/Mars_Reconnaissance_Orbiter/CTX/',
74: '/pds_san/PDS_Archive/Lunar_Reconnaissance_Orbiter/LROC/EDR/',
124: '/pds_san/PDS_Archive/Mars_Reconnaissance_Orbiter/HiRISE/',
101: '/pds_san/PDS_Archive/Apollo/Rock_Sample_Images/'
}
# ********* Set up logging *************
logger = logging.getLogger('DI_Process')
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler('/usgs/cdev/PDS/logs/DI.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info('Starting DI Process')
try:
# Throws away engine information
session, _ = db_connect(pds_db)
logger.info('DataBase Connecton: Success')
except:
logger.error('DataBase Connection: Error')
return 1
RQ = RedisQueue('ChecksumUpdate_Queue')
index = 0
count = 0
while int(RQ.QueueSize()) > 0:
inputfile = RQ.QueueGet()
Qelement = session.query(Files).filter(
Files.filename == inputfile).one()
cpfile = archiveID[Qelement.archiveid] + Qelement.filename
if os.path.isfile(cpfile):
"""
CScmd = 'md5sum ' + cpfile
process = subprocess.Popen(
CScmd, stdout=subprocess.PIPE, shell=True)
(stdout, stderr) = process.communicate()
temp_checksum = stdout.split()[0]
# temp_checksum = hashlib.md5(open(tempfile, 'rb').read()).hexdigest()
# os.remove(tempfile)
"""
# Calculate checksum in chunks of 4096
f_hash = hashlib.md5()
with open(cpfile, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
f_hash.update(chunk)
checksum = f_hash.hexdigest()
if checksum != Qelement.checksum:
Qelement.checksum = checksum
Qelement.di_pass = '******'
Qelement.di_date = datetime.datetime.now(
pytz.utc).strftime("%Y-%m-%d %H:%M:%S")
session.flush()
index = index + 1
count = count + 1
logger.info('Update Checksum %s: Success', inputfile)
if count > 25:
session.commit()
logger.info('Session Commit for 25 Records: Success')
count = 0
else:
logger.error('File %s Not Found', cpfile)
try:
session.commit()
except:
session.rollback()
logger.error('Error durint commit')
logger.info("End Commit DI process to Database: Success")
logger.info('Checksum for %s Files Updated', str(index))
def main():
# pdb.set_trace()
# ***************** Set up logging *****************
logger = logging.getLogger('ProjectionBrowse_Process')
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler('/usgs/cdev/PDS/logs/Process.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
RQ_main = RedisQueue('PilotB_ReadyQueue')
while int(RQ_main.QueueSize()) > 0:
inputfile = RQ_main.QueueGet()
if os.path.isfile(inputfile):
logger.info('Starting Process: %s', inputfile)
if 'Mars_Reconnaissance_Orbiter/CTX/' in inputfile:
mission = 'CTX'
# ********** Derived DIR path Stuff **********************
finalpath = makedir(inputfile)
recipeOBJ = Recipe()
recipe_json = recipeOBJ.getRecipeJSON(mission)
recipeOBJ.AddJsonFile(recipe_json, 'reduced')
infile = workarea + \
os.path.splitext(os.path.basename(inputfile))[
0] + '.Pinput.cub'
outfile = workarea + \
os.path.splitext(os.path.basename(inputfile))[
0] + '.Poutput.cub'
status = 'success'
for item in recipeOBJ.getProcesses():
if status == 'error':
break
elif status == 'success':
processOBJ = Process()
processR = processOBJ.ProcessFromRecipe(
item, recipeOBJ.getRecipe())
if '2isis' in item:
processOBJ.updateParameter('from_', inputfile)
processOBJ.updateParameter('to', outfile)
elif item == 'spiceinit':
processOBJ.updateParameter('from_', infile)
elif item == 'ctxevenodd':
label = pvl.load(infile)
SS = label['IsisCube']['Instrument']['SpatialSumming']
if SS != 1:
break
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif item == 'reduce':
label = pvl.load(infile)
Nline = label['IsisCube']['Core']['Dimensions']['Lines']
Nsample = label['IsisCube']['Core']['Dimensions']['Samples']
Sfactor = scaleFactor(Nline, Nsample)
processOBJ.updateParameter('lscale', Sfactor)
processOBJ.updateParameter('sscale', Sfactor)
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif item == 'isis2std':
outfile = finalpath + '/' + \
os.path.splitext(os.path.basename(inputfile))[
0] + '.projectionbrowse.png'
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
print processOBJ.getProcess()
for k, v in processOBJ.getProcess().items():
func = getattr(isis, k)
try:
func(**v)
logger.info('Process %s :: Success', k)
if os.path.isfile(outfile):
if '.cub' in outfile:
os.rename(outfile, infile)
status = 'success'
except ProcessError as e:
logger.error('Process %s :: Error', k)
status = 'error'
if status == 'success':
os.remove(infile)
logger.info('Browse Process Success: %s', inputfile)
else:
logger.error('File %s Not Found', inputfile)
def main():
args = Args()
args.parse_args()
override = args.override
# ********* Set up logging *************
logger = logging.getLogger('Ingest_Process')
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler(pds_log + 'Ingest.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info("Starting Process")
PDSinfoDICT = json.load(open(pds_info, 'r'))
RQ_main = RedisQueue('Ingest_ReadyQueue')
RQ_work = RedisQueue('Ingest_WorkQueue')
RQ_upc = RedisQueue('UPC_ReadyQueue')
RQ_thumb = RedisQueue('Thumbnail_ReadyQueue')
RQ_browse = RedisQueue('Browse_ReadyQueue')
#RQ_pilotB = RedisQueue('PilotB_ReadyQueue')
try:
session, _ = db_connect(pds_db)
logger.info('DataBase Connecton: Success')
except:
logger.error('DataBase Connection: Error')
index = 1
while int(RQ_main.QueueSize()) > 0:
item = literal_eval(RQ_main.QueueGet().decode("utf-8"))
inputfile = item[0]
archive = item[1]
RQ_work.QueueAdd(inputfile)
subfile = inputfile.replace(PDSinfoDICT[archive]['path'], '')
# Calculate checksum in chunks of 4096
f_hash = hashlib.md5()
with open(inputfile, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
f_hash.update(chunk)
filechecksum = f_hash.hexdigest()
QOBJ = session.query(Files).filter_by(filename=subfile).first()
runflag = False
if QOBJ is None:
runflag = True
elif filechecksum != QOBJ.checksum:
runflag = True
if runflag == True or override == True:
date = datetime.datetime.now(
pytz.utc).strftime("%Y-%m-%d %H:%M:%S")
fileURL = inputfile.replace(archive_base, web_base)
# If all upc requirements are in 'inputfile,' flag for upc
upcflag = all(x in inputfile for x in PDSinfoDICT[archive]['upc_reqs'])
filesize = os.path.getsize(inputfile)
try:
# If we found an existing file and want to overwrite the data
if QOBJ is not None and override == True:
testIN = QOBJ
# If the file was not found, create a new entry
else:
testIN = Files()
testIN.archiveid = PDSinfoDICT[archive]['archiveid']
testIN.filename = subfile
testIN.entry_date = date
testIN.checksum = filechecksum
testIN.upc_required = upcflag
testIN.validation_required = True
testIN.header_only = False
testIN.release_date = date
testIN.file_url = fileURL
testIN.file_size = filesize
testIN.di_pass = True
testIN.di_date = date
session.merge(testIN)
session.flush()
if upcflag == True:
RQ_upc.QueueAdd((inputfile, testIN.fileid, archive))
RQ_thumb.QueueAdd((inputfile, testIN.fileid, archive))
RQ_browse.QueueAdd((inputfile, testIN.fileid, archive))
#RQ_pilotB.QueueAdd((inputfile, testIN.fileid, archive))
RQ_work.QueueRemove(inputfile)
index = index + 1
except Exception as e:
print(e)
logger.error("Error During File Insert %s", subfile)
elif runflag == False:
RQ_work.QueueRemove(inputfile)
if index >= 250:
try:
session.commit()
logger.info("Commit 250 files to Database: Success")
index = 1
except:
session.rollback()
logger.error("Something Went Wrong During DB Insert")
else:
logger.info("No Files Found in Ingest Queue")
try:
session.commit()
logger.info("Commit to Database: Success")
except:
session.rollback()
if RQ_main.QueueSize() == 0 and RQ_work.QueueSize() == 0:
logger.info("Process Complete All Queues Empty")
elif RQ_main.QueueSize() == 0 and RQ_work.QueueSize() != 0:
logger.warning("Process Done Work Queue NOT Empty Contains %s Files", str(
RQ_work.QueueSize()))
logger.info("Ingest Complete")