def main():
RQ = RedisQueue('LinkQueue')
while int(RQ.QueueSize()) > 0:
# Grab a tuple of values from the redis queue
item = literal_eval(RQ.QueueGet().decode('utf-8'))
# Split tuple into two values
inputfile = item[0]
archive = item[1]
json_file_path = recipe_base + archive + '.json'
try:
with open(json_file_path, 'r') as f:
json_dict = json.load(f)
except (ValueError):
continue
link_src_path = json_dict['src']
voldesc = load_pvl(inputfile)
dataset_id = voldesc['VOLUME']['DATA_SET_ID']
volume_id = voldesc['VOLUME']['VOLUME_ID']
# if more than one dataset id exists, link each of them
if isinstance(dataset_id, (list, tuple, set)):
[link(link_src_path, link_dest, volume_id, x) for x in dataset_id]
else:
# Not container type
link(link_src_path, link_dest, volume_id, dataset_id)
def main():
args = Args()
args.parse_args()
logger = logging.getLogger('FinalJobber')
level = logging.getLevelName(args.log_level)
logger.setLevel(level)
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')
logger.info("Reddis Queue: %s", RQ_final.id_name)
if int(RQ_final.QueueSize()) == 0:
logging.info('Nothing Found in Final Queue')
else:
FKey = RQ_final.QueueGet()
logger.info('Found %s in Final Queue', str(FKey))
# ** *************** HPC job stuff ***********************
logger.info('HPC Cluster job Submission Starting')
jobOBJ = HPCjob()
jobOBJ.setJobName(FKey + '_Final')
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\n%s', e)
def main():
RQ = RedisQueue('LinkQueue')
args = Args()
args.parse_args()
logger = logging.getLogger('LINK_Process')
level = logging.getLevelName(args.log_level)
logger.setLevel(level)
logFileHandle = logging.FileHandler(pds_log + 'Link.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
while int(RQ.QueueSize()) > 0:
# Grab a tuple of values from the redis queue
item = literal_eval(RQ.QueueGet().decode('utf-8'))
# Split tuple into two values
inputfile = item[0]
archive = item[1]
json_file_path = recipe_base + archive + '.json'
try:
with open(json_file_path, 'r') as f:
json_dict = json.load(f)
except ValueError as e:
logging.warn(e)
continue
link_src_path = json_dict['src']
voldesc = load_pvl(inputfile)
dataset_id = voldesc['VOLUME']['DATA_SET_ID']
volume_id = voldesc['VOLUME']['VOLUME_ID']
# if more than one dataset id exists, link each of them
if isinstance(dataset_id, (list, tuple, set)):
[link(link_src_path, link_dest, volume_id, x) for x in dataset_id]
else:
# Not container type
link(link_src_path, link_dest, volume_id, dataset_id)
def main():
# pdb.set_trace()
Key = sys.argv[-1]
workarea = '/scratch/pds_services/' + Key + '/'
RQ_file = RedisQueue(Key + '_FileQueue')
RQ_work = RedisQueue(Key + '_WorkQueue')
RQ_zip = RedisQueue(Key + '_ZIP')
RQ_loggy = RedisQueue(Key + '_loggy')
RQ_final = RedisQueue('FinalQueue')
RHash = RedisHash(Key + '_info')
RHerror = RedisHash(Key + '_error')
if int(RQ_file.QueueSize()) == 0:
print "No Files Found in Redis Queue"
else:
print RQ_file.getQueueName()
jobFile = RQ_file.Qfile2Qwork(
RQ_file.getQueueName(), RQ_work.getQueueName())
# Setup system logging
basename = os.path.splitext(os.path.basename(jobFile))[0]
logger = logging.getLogger(Key + '.' + basename)
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler('/usgs/cdev/PDS/logs/Service.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info('Starting POW Processing')
# set up loggy
loggyOBJ = Loggy(basename)
# File Naming
if '+' in jobFile:
bandSplit = jobFile.split('+')
inputFile = bandSplit[0]
else:
inputFile = jobFile
infile = workarea + \
os.path.splitext(os.path.basename(jobFile))[0] + '.input.cub'
outfile = workarea + \
os.path.splitext(os.path.basename(jobFile))[0] + '.output.cub'
RQ_recipe = RedisQueue(Key + '_recipe')
status = 'success'
for element in RQ_recipe.RecipeGet():
if status == 'error':
break
elif status == 'success':
processOBJ = Process()
process = processOBJ.JSON2Process(element)
if 'gdal_translate' not in processOBJ.getProcessName():
print processOBJ.getProcessName()
if '2isis' in processOBJ.getProcessName():
processOBJ.updateParameter('from_', inputFile)
processOBJ.updateParameter('to', outfile)
elif 'cubeatt-band' in processOBJ.getProcessName():
if '+' in jobFile:
infileB = infile + '+' + bandSplit[1]
processOBJ.updateParameter('from_', infileB)
processOBJ.updateParameter('to', outfile)
processOBJ.ChangeProcess('cubeatt')
else:
continue
elif 'cubeatt-bit' in processOBJ.getProcessName():
if RHash.OutBit() == 'unsignedbyte':
temp_outfile = outfile + '+lsb+tile+attached+unsignedbyte+1:254'
elif RHash.OutBit() == 'signedword':
temp_outfile = outfile + '+lsb+tile+attached+signedword+-32765:32765'
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', temp_outfile)
processOBJ.ChangeProcess('cubeatt')
elif 'spice' in processOBJ.getProcessName():
processOBJ.updateParameter('from_', infile)
elif 'ctxevenodd' in processOBJ.getProcessName():
label = pvl.load(infile)
SS = label['IsisCube']['Instrument']['SpatialSumming']
print SS
if SS != 1:
continue
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif 'mocevenodd' in processOBJ.getProcessName():
label = pvl.load(infile)
CTS = label['IsisCube']['Instrument']['CrosstrackSumming']
print CTS
if CTS != 1:
continue
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif 'mocnoise50' in processOBJ.getProcessName():
label = pvl.load(infile)
CTS = label['IsisCube']['Instrument']['CrosstrackSumming']
if CTS != 1:
continue
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif 'cam2map' in processOBJ.getProcessName():
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
if RHash.getGRtype() == 'smart' or RHash.getGRtype() == 'fill':
subloggyOBJ = SubLoggy('cam2map')
camrangeOUT = workarea + basename + '_camrange.txt'
isis.camrange(from_=infile,
to=camrangeOUT)
cam = pvl.load(camrangeOUT)
if cam['UniversalGroundRange']['MaximumLatitude'] < float(RHash.getMinLat()) or \
cam['UniversalGroundRange']['MinimumLatitude'] > float(RHash.getMaxLat()) or \
cam['UniversalGroundRange']['MaximumLongitude'] < float(RHash.getMinLon()) or \
cam['UniversalGroundRange']['MinimumLongitude'] > float(RHash.getMaxLon()):
status = 'error'
eSTR = "Error Ground Range Outside Extent Range"
RHerror.addError(os.path.splitext(
os.path.basename(jobFile))[0], eSTR)
subloggyOBJ.setStatus('ERROR')
subloggyOBJ.errorOut(eSTR)
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
break
elif RHash.getGRtype() == 'smart':
if cam['UniversalGroundRange']['MinimumLatitude'] > float(RHash.getMinLat()):
minlat = cam['UniversalGroundRange']['MinimumLatitude']
else:
minlat = RHash.getMinLat()
if cam['UniversalGroundRange']['MaximumLatitude'] < float(RHash.getMaxLat()):
maxlat = cam['UniversalGroundRange']['MaximumLatitude']
else:
maxlat = RHash.getMaxLat()
if cam['UniversalGroundRange']['MinimumLongitude'] > float(RHash.getMinLon()):
minlon = cam['UniversalGroundRange']['MinimumLongitude']
else:
minlon = RHash.getMinLon()
if cam['UniversalGroundRange']['MaximumLongitude'] < float(RHash.getMaxLon()):
maxlon = cam['UniversalGroundRange']['MaximumLongitude']
else:
maxlon = RHash.getMaxLon()
elif RHash.getGRtype() == 'fill':
minlat = RHash.getMinLat()
maxlat = RHash.getMaxLat()
minlon = RHash.getMinLon()
maxlon = RHash.getMaxLon()
processOBJ.AddParameter('minlat', minlat)
processOBJ.AddParameter('maxlat', maxlat)
processOBJ.AddParameter('minlon', minlon)
processOBJ.AddParameter('maxlon', maxlon)
os.remove(camrangeOUT)
elif 'isis2pds' in processOBJ.getProcessName():
finalfile = infile.replace('.input.cub', '_final.img')
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', finalfile)
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
print processOBJ.getProcess()
for k, v in processOBJ.getProcess().items():
func = getattr(isis, k)
subloggyOBJ = SubLoggy(k)
try:
func(**v)
logger.info('Process %s :: Success', k)
subloggyOBJ.setStatus('SUCCESS')
subloggyOBJ.setCommand(processOBJ.LogCommandline())
subloggyOBJ.setHelpLink(processOBJ.LogHelpLink())
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
if os.path.isfile(outfile):
os.rename(outfile, infile)
status = 'success'
except ProcessError as e:
logger.error('Process %s :: Error', k)
logger.error(e)
status = 'error'
eSTR = 'Error Executing ' + k + \
' Standard Error: ' + str(e)
RHerror.addError(os.path.splitext(
os.path.basename(jobFile))[0], eSTR)
subloggyOBJ.setStatus('ERROR')
subloggyOBJ.setCommand(processOBJ.LogCommandline())
subloggyOBJ.setHelpLink(processOBJ.LogHelpLink())
subloggyOBJ.errorOut(eSTR)
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
else:
GDALcmd = ""
for process, v, in processOBJ.getProcess().items():
subloggyOBJ = SubLoggy(process)
GDALcmd += process
for key, value in v.items():
GDALcmd += ' ' + key + ' ' + value
if RHash.Format() == 'GeoTiff-BigTiff':
fileext = 'tif'
elif RHash.Format() == 'GeoJPEG-2000':
fileext = 'jp2'
elif RHash.Format() == 'JPEG':
fileext = 'jpg'
elif RHash.Format() == 'PNG':
fileext = 'png'
elif RHash.Format() == 'GIF':
fileext = 'gif'
logGDALcmd = GDALcmd + ' ' + basename + \
'.input.cub ' + basename + '_final.' + fileext
finalfile = infile.replace(
'.input.cub', '_final.' + fileext)
GDALcmd += ' ' + infile + ' ' + finalfile
print GDALcmd
result = subprocess.call(GDALcmd, shell=True)
if result == 0:
logger.info('Process GDAL translate :: Success')
status = 'success'
subloggyOBJ.setStatus('SUCCESS')
subloggyOBJ.setCommand(logGDALcmd)
subloggyOBJ.setHelpLink(
'http://www.gdal.org/gdal_translate.html')
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
os.remove(infile)
else:
errmsg = 'Error Executing GDAL translate: Error'
logger.error(errmsg)
status = 'error'
RHerror.addError(os.path.splitext(
os.path.basename(jobFile))[0], errmsg)
subloggyOBJ.setStatus('ERROR')
subloggyOBJ.setCommand(logGDALcmd)
subloggyOBJ.setHelpLink(
'http://www.gdal.org/gdal_translate.html')
subloggyOBJ.errorOut('Process GDAL translate :: Error')
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
if status == 'success':
if RHash.Format() == 'ISIS3':
finalfile = infile.replace('.input.cub', '_final.cub')
shutil.move(infile, finalfile)
if RHash.getStatus() != 'ERROR':
RHash.Status('SUCCESS')
try:
RQ_zip.QueueAdd(finalfile)
logger.info('File Added to ZIP Queue')
except:
logger.error('File NOT Added to ZIP Queue')
elif status == 'error':
RHash.Status('ERROR')
if os.path.isfile(infile):
os.remove(infile)
try:
RQ_loggy.QueueAdd(loggyOBJ.Loggy2json())
RQ_work.QueueRemove(jobFile)
logger.info('JSON Added to Loggy Queue')
except:
logger.error('JSON NOT Added to Loggy Queue')
if RQ_file.QueueSize() == 0 and RQ_work.QueueSize() == 0:
try:
RQ_final.QueueAdd(Key)
logger.info('Key %s Added to Final Queue: Success', Key)
logger.info('Both Queues Empty: filequeue = %s work queue = %s', str(
RQ_file.QueueSize()), str(RQ_work.QueueSize()))
logger.info('JOB Complete')
except:
logger.error('Key NOT Added to Final Queue')
elif RQ_file.QueueSize() == 0 and RQ_work.QueueSize() != 0:
logger.warning('Work Queue Not Empty: filequeue = %s work queue = %s', str(
RQ_file.QueueSize()), str(RQ_work.QueueSize()))
def main():
# pdb.set_trace()
args = Args()
args.parse_args()
logging.basicConfig(level=args.loglevel)
RQ_ingest = RedisQueue('Ingest_ReadyQueue')
RQ_linking = RedisQueue('LinkQueue')
# Set up logging
logger = logging.getLogger(args.archive + '_INGEST')
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)
if args.loglevel == logging.INFO:
print("Log File: {}Ingest.log".format(pds_log))
PDSinfoDICT = json.load(open(pds_info, 'r'))
try:
archivepath = PDSinfoDICT[args.archive]['path'][:-1]
except KeyError:
print("\nArchive '{}' not found in {}\n".format(
args.archive, pds_info))
print("The following archives are available:")
for k in PDSinfoDICT.keys():
print("\t{}".format(k))
logging.error("Unable to locate {}".format(args.archive))
exit()
if args.volume:
archivepath = archivepath + '/' + args.volume
logger.info('Starting Ingest for: %s', archivepath)
logger.info('Ingest Queue: {}'.format(str(RQ_ingest.id_name)))
logger.info('Linking Queue: {}'.format(str(RQ_linking.id_name)))
# Possible bug in RQ? Can't add to queue in "if fname == voldesc"
queue_size = RQ_ingest.QueueSize()
voldescs = []
for dirpath, dirs, files in os.walk(archivepath):
for filename in files:
fname = os.path.join(dirpath, filename)
if args.search:
if args.search in fname:
try:
if os.path.basename(fname) == "voldesc.cat":
voldescs.append(fname)
if args.ingest:
RQ_ingest.QueueAdd((fname, args.archive))
except:
logger.error('File %s NOT added to Ingest Queue',
fname)
else:
continue
else:
try:
if os.path.basename(fname) == "voldesc.cat":
voldescs.append(fname)
if args.ingest:
RQ_ingest.QueueAdd((fname, args.archive))
except:
logger.error('File %s NOT added to Ingest Queue', fname)
n_added = RQ_ingest.QueueSize() - queue_size
for fpath in voldescs:
RQ_linking.QueueAdd((fpath, args.archive))
logger.info('Files added to Ingest Queue: %s', n_added)
def main():
args = Args()
args.parse_args()
override = args.override
logger = logging.getLogger('Ingest_Process')
level = logging.getLevelName(args.log_level)
logger.setLevel(level)
logFileHandle = logging.FileHandler(pds_log + 'Ingest.log')
print("Log File: {}Ingest.log".format(pds_log))
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info("Starting Ingest Process")
PDSinfoDICT = json.load(open(pds_info, 'r'))
RQ_main = RedisQueue('Ingest_ReadyQueue')
RQ_lock = RedisLock(lock_obj)
RQ_lock.add({RQ_main.id_name: '1'})
RQ_work = RedisQueue('Ingest_WorkQueue')
RQ_upc = RedisQueue('UPC_ReadyQueue')
RQ_thumb = RedisQueue('Thumbnail_ReadyQueue')
RQ_browse = RedisQueue('Browse_ReadyQueue')
logger.info("UPC Queue: %s", RQ_upc.id_name)
logger.info("Thumbnail Queue: %s", RQ_thumb.id_name)
logger.info("Browse Queue: %s", RQ_browse.id_name)
try:
session, engine = db_connect(pds_db)
logger.info('DataBase Connecton: Success')
except:
logger.error('DataBase Connection: Error')
return 1
index = 1
while int(RQ_main.QueueSize()) > 0 and RQ_lock.available(RQ_main.id_name):
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 or filechecksum != QOBJ.checksum:
runflag = True
if runflag or override:
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:
ingest_entry = QOBJ
# If the file was not found, create a new entry
else:
ingest_entry = Files()
ingest_entry.archiveid = PDSinfoDICT[archive]['archiveid']
ingest_entry.filename = subfile
ingest_entry.entry_date = date
ingest_entry.checksum = filechecksum
ingest_entry.upc_required = upcflag
ingest_entry.validation_required = True
ingest_entry.header_only = False
ingest_entry.release_date = date
ingest_entry.file_url = fileURL
ingest_entry.file_size = filesize
ingest_entry.di_pass = True
ingest_entry.di_date = date
session.merge(ingest_entry)
session.flush()
if upcflag:
RQ_upc.QueueAdd((inputfile, ingest_entry.fileid, archive))
RQ_thumb.QueueAdd(
(inputfile, ingest_entry.fileid, archive))
RQ_browse.QueueAdd(
(inputfile, ingest_entry.fileid, archive))
#RQ_pilotB.QueueAdd((inputfile,ingest_entry.fileid, archive))
RQ_work.QueueRemove(inputfile)
index = index + 1
except Exception as e:
logger.error("Error During File Insert %s : %s", str(subfile),
str(e))
elif not runflag and not override:
RQ_work.QueueRemove(inputfile)
logger.warn(
"Not running ingest: file %s already present"
" in database and no override flag supplied", inputfile)
if index >= 250:
try:
session.commit()
logger.info("Commit 250 files to Database: Success")
index = 1
except Exception as e:
session.rollback()
logger.warn("Unable to commit to database: %s", str(e))
else:
logger.info("No Files Found in Ingest Queue")
try:
session.commit()
logger.info("Commit to Database: Success")
except Exception as e:
logger.error("Unable to commit to database: %s", str(e))
session.rollback()
# Close connection to database
session.close()
engine.dispose()
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")
def main():
# Connect to database - ignore engine information
pds_session, pds_engine = db_connect(pds_db)
# Connect to database - ignore engine information
session, upc_engine = db_connect(upc_db)
# ***************** Set up logging *****************
logger = logging.getLogger('UPC_Process')
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler(pds_log + 'Process.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
PDSinfoDICT = json.load(open(pds_info, 'r'))
# Redis Queue Objects
RQ_main = RedisQueue('UPC_ReadyQueue')
logger.info("UPC Processing Queue: %s", RQ_main.id_name)
RQ_lock = RedisLock(lock_obj)
# If the queue isn't registered, add it and set it to "running"
RQ_lock.add({RQ_main.id_name: '1'})
proc_date_tid = get_tid('processdate', session)
err_type_tid = get_tid('errortype', session)
err_msg_tid = get_tid('errormessage', session)
err_flag_tid = get_tid('error', session)
isis_footprint_tid = get_tid('isisfootprint', session)
isis_centroid_tid = get_tid('isiscentroid', session)
start_time_tid = get_tid('starttime', session)
stop_time_tid = get_tid('stoptime', session)
checksum_tid = get_tid('checksum', session)
# while there are items in the redis queue
while int(RQ_main.QueueSize()) > 0 and RQ_lock.available(RQ_main.id_name):
# get a file from the queue
item = literal_eval(RQ_main.QueueGet().decode("utf-8"))
inputfile = item[0]
fid = item[1]
archive = item[2]
#inputfile = (RQ_main.QueueGet()).decode('utf-8')
if os.path.isfile(inputfile):
pass
else:
print("{} is not a file\n".format(inputfile))
if os.path.isfile(inputfile):
logger.info('Starting Process: %s', inputfile)
# @TODO refactor this logic. We're using an object to find a path, returning it,
# then passing it back to the object so that the object can use it.
recipeOBJ = Recipe()
recipe_json = recipeOBJ.getRecipeJSON(archive)
#recipe_json = recipeOBJ.getRecipeJSON(getMission(str(inputfile)))
recipeOBJ.AddJsonFile(recipe_json, 'upc')
infile = workarea + os.path.splitext(
str(os.path.basename(inputfile)))[0] + '.UPCinput.cub'
outfile = workarea + os.path.splitext(
str(os.path.basename(inputfile)))[0] + '.UPCoutput.cub'
caminfoOUT = workarea + os.path.splitext(
str(os.path.basename(inputfile)))[0] + '_caminfo.pvl'
EDRsource = inputfile.replace(
'/pds_san/PDS_Archive/',
'https://pdsimage.wr.ugs.gov/Missions/')
status = 'success'
# Iterate through each process listed in the recipe
for item in recipeOBJ.getProcesses():
# If any of the processes failed, discontinue processing
if status.lower() == 'error':
break
elif status.lower() == 'success':
processOBJ = Process()
processOBJ.ProcessFromRecipe(item, recipeOBJ.getRecipe())
# Handle processing based on string description.
if '2isis' in item:
processOBJ.updateParameter('from_', inputfile)
processOBJ.updateParameter('to', outfile)
elif item == 'thmproc':
processOBJ.updateParameter('from_', inputfile)
processOBJ.updateParameter('to', outfile)
thmproc_odd = str(workarea) + str(
os.path.splitext(os.path.basename(inputfile))
[0]) + '.UPCoutput.raw.odd.cub'
thmproc_even = str(workarea) + str(
os.path.splitext(os.path.basename(inputfile))
[0]) + '.UPCoutput.raw.even.cub'
elif item == 'handmos':
processOBJ.updateParameter('from_', thmproc_even)
processOBJ.updateParameter('mosaic', thmproc_odd)
elif item == 'spiceinit':
processOBJ.updateParameter('from_', infile)
elif item == 'cubeatt':
band_infile = infile + '+' + str(1)
processOBJ.updateParameter('from_', band_infile)
processOBJ.updateParameter('to', outfile)
elif item == 'footprintinit':
processOBJ.updateParameter('from_', infile)
elif item == 'caminfo':
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', caminfoOUT)
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
pwd = os.getcwd()
# iterate through functions listed in process obj
for k, v in processOBJ.getProcess().items():
# load a function into func
func = getattr(isis, k)
try:
os.chdir(workarea)
# execute function
func(**v)
os.chdir(pwd)
if item == 'handmos':
if os.path.isfile(thmproc_odd):
os.rename(thmproc_odd, infile)
else:
if os.path.isfile(outfile):
os.rename(outfile, infile)
status = 'success'
if '2isis' in item:
label = pvl.load(infile)
infile_bandlist = label['IsisCube']['BandBin'][
PDSinfoDICT[archive]['bandbinQuery']]
infile_centerlist = label['IsisCube'][
'BandBin']['Center']
elif item == 'thmproc':
pass
elif item == 'handmos':
label = pvl.load(infile)
infile_bandlist = label['IsisCube']['BandBin'][
PDSinfoDICT[archive]['bandbinQuery']]
infile_centerlist = label['IsisCube'][
'BandBin']['Center']
except ProcessError as e:
print(e)
status = 'error'
processError = item
# keyword definitions
keywordsOBJ = None
if status.lower() == 'success':
try:
keywordsOBJ = UPCkeywords(caminfoOUT)
except:
with open(caminfoOUT, 'r') as f:
filedata = f.read()
filedata = filedata.replace(';', '-').replace('&', '-')
filedata = re.sub(r'\-\s+', r'', filedata, flags=re.M)
with open(caminfoOUT, 'w') as f:
f.write(filedata)
keywordsOBJ = UPCkeywords(caminfoOUT)
target_Qobj = session.query(upc_models.Targets).filter(
upc_models.Targets.targetname == keywordsOBJ.getKeyword(
'TargetName').upper()).first()
instrument_Qobj = session.query(upc_models.Instruments).filter(
upc_models.Instruments.instrument ==
keywordsOBJ.getKeyword('InstrumentId')).first()
if session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid == keywordsOBJ.getKeyword(
'IsisId')).first() is None:
test_input = upc_models.DataFiles(
isisid=keywordsOBJ.getKeyword('IsisId'),
productid=keywordsOBJ.getKeyword('ProductId'),
edr_source=EDRsource,
edr_detached_label='',
instrumentid=instrument_Qobj.instrumentid,
targetid=target_Qobj.targetid)
session.merge(test_input)
session.commit()
Qobj = session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid == keywordsOBJ.getKeyword(
'IsisId')).first()
UPCid = Qobj.upcid
print(UPCid)
# block to add band information to meta_bands
if isinstance(infile_bandlist, list):
index = 0
while index < len(infile_bandlist):
B_DBinput = upc_models.MetaBands(
upcid=UPCid,
filter=str(infile_bandlist[index]),
centerwave=infile_centerlist[index])
session.merge(B_DBinput)
index = index + 1
else:
try:
# If infile_centerlist is in "Units" format, grab the value
f_centerlist = float(infile_centerlist[0])
except TypeError:
f_centerlist = float(infile_centerlist)
B_DBinput = upc_models.MetaBands(upcid=UPCid,
filter=infile_bandlist,
centerwave=f_centerlist)
session.merge(B_DBinput)
session.commit()
# Block to add common keywords
testjson = json.load(open(keyword_def, 'r'))
for element_1 in testjson['instrument']['COMMON']:
keyvalue = ""
keytype = testjson['instrument']['COMMON'][element_1][
'type']
keyword = testjson['instrument']['COMMON'][element_1][
'keyword']
keyword_Qobj = session.query(upc_models.Keywords).filter(
and_(upc_models.Keywords.typename == element_1,
upc_models.Keywords.instrumentid == 1)).first()
if keyword_Qobj is None:
continue
else:
keyvalue = keywordsOBJ.getKeyword(keyword)
if keyvalue is None:
continue
keyvalue = db2py(keytype, keyvalue)
try:
DBinput = upc_models.create_table(
keytype,
upcid=UPCid,
typeid=keyword_Qobj.typeid,
value=keyvalue)
except Exception as e:
logger.warn("Unable to enter %s into table\n\n%s",
keytype, e)
continue
session.merge(DBinput)
try:
session.flush()
except:
logger.warn("Unable to flush database connection")
session.commit()
for element_1 in testjson['instrument'][archive]:
keyvalue = ""
keytype = testjson['instrument'][archive][element_1][
'type']
keyword = testjson['instrument'][archive][element_1][
'keyword']
keyword_Qobj = session.query(upc_models.Keywords).filter(
and_(
upc_models.Keywords.typename == element_1,
upc_models.Keywords.instrumentid.in_(
(1, instrument_Qobj.instrumentid)))).first()
if keyword_Qobj is None:
continue
else:
keyvalue = keywordsOBJ.getKeyword(keyword)
if keyvalue is None:
logger.debug("Keyword %s not found", keyword)
continue
keyvalue = db2py(keytype, keyvalue)
try:
DBinput = upc_models.create_table(
keytype,
upcid=UPCid,
typeid=keyword_Qobj.typeid,
value=keyvalue)
except Exception as e:
logger.warn("Unable to enter %s into database\n\n%s",
keytype, e)
continue
session.merge(DBinput)
try:
session.flush()
except:
logger.warn("Unable to flush database connection")
session.commit()
# geometry stuff
G_centroid = 'point ({} {})'.format(
str(keywordsOBJ.getKeyword('CentroidLongitude')),
str(keywordsOBJ.getKeyword('CentroidLatitude')))
G_keyword_Qobj = session.query(
upc_models.Keywords.typeid).filter(
upc_models.Keywords.typename ==
'isiscentroid').first()
G_footprint_Qobj = session.query(
upc_models.Keywords.typeid).filter(
upc_models.Keywords.typename ==
'isisfootprint').first()
G_footprint = keywordsOBJ.getKeyword('GisFootprint')
G_DBinput = upc_models.MetaGeometry(upcid=UPCid,
typeid=G_keyword_Qobj,
value=G_centroid)
session.merge(G_DBinput)
G_DBinput = upc_models.MetaGeometry(upcid=UPCid,
typeid=G_footprint_Qobj,
value=G_footprint)
session.merge(G_DBinput)
session.flush()
session.commit()
f_hash = hashlib.md5()
with open(inputfile, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
f_hash.update(chunk)
checksum = f_hash.hexdigest()
DBinput = upc_models.MetaString(upcid=UPCid,
typeid=checksum_tid,
value=checksum)
session.merge(DBinput)
DBinput = upc_models.MetaBoolean(upcid=UPCid,
typeid=err_flag_tid,
value=False)
session.merge(DBinput)
session.commit()
AddProcessDB(pds_session, fid, True)
os.remove(infile)
os.remove(caminfoOUT)
elif status.lower() == 'error':
try:
label = pvl.load(infile)
except Exception as e:
logger.info('%s', e)
continue
date = datetime.datetime.now(
pytz.utc).strftime("%Y-%m-%d %H:%M:%S")
if '2isis' in processError or processError == 'thmproc':
if session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.edr_source ==
EDRsource.decode("utf-8")).first() is None:
target_Qobj = session.query(upc_models.Targets).filter(
upc_models.Targets.targetname == str(
label['IsisCube']['Instrument']
['TargetName']).upper()).first()
instrument_Qobj = session.query(
upc_models.Instruments).filter(
upc_models.Instruments.instrument == str(
label['IsisCube']['Instrument']
['InstrumentId'])).first()
error1_input = upc_models.DataFiles(
isisid='1', edr_source=EDRsource)
session.merge(error1_input)
session.commit()
EQ1obj = session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.edr_source == EDRsource).first()
UPCid = EQ1obj.upcid
errorMSG = 'Error running {} on file {}'.format(
processError, inputfile)
DBinput = MetaTime(upcid=UPCid,
typeid=proc_date_tid,
value=date)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_type_tid,
value=processError)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_msg_tid,
value=errorMSG)
session.merge(DBinput)
DBinput = MetaBoolean(upcid=UPCid,
typeid=err_flag_tid,
value=True)
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_footprint_tid,
value='POINT(361 0)')
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_centroid_tid,
value='POINT(361 0)')
session.merge(DBinput)
session.commit()
else:
try:
label = pvl.load(infile)
except Exception as e:
logger.warn('%s', e)
continue
isisSerial = getISISid(infile)
if session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid ==
isisSerial).first() is None:
target_Qobj = session.query(upc_models.Targets).filter(
upc_models.Targets.targetname == str(
label['IsisCube']['Instrument']
['TargetName']).upper()).first()
instrument_Qobj = session.query(
upc_models.Instruments).filter(
upc_models.Instruments.instrument == str(
label['IsisCube']['Instrument']
['InstrumentId'])).first()
if target_Qobj is None or instrument_Qobj is None:
continue
error2_input = upc_models.DataFiles(
isisid=isisSerial,
productid=label['IsisCube']['Archive']
['ProductId'],
edr_source=EDRsource,
instrumentid=instrument_Qobj.instrumentid,
targetid=target_Qobj.targetid)
session.merge(error2_input)
session.commit()
try:
EQ2obj = session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid == isisSerial).first()
UPCid = EQ2obj.upcid
errorMSG = 'Error running {} on file {}'.format(
processError, inputfile)
DBinput = MetaTime(upcid=UPCid,
typeid=proc_date_tid,
value=date)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_type_tid,
value=processError)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_msg_tid,
value=errorMSG)
session.merge(DBinput)
DBinput = MetaBoolean(upcid=UPCid,
typeid=err_flag_tid,
value=True)
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_footprint_tid,
value='POINT(361 0)')
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_centroid_tid,
value='POINT(361 0)')
session.merge(DBinput)
except:
pass
try:
v = label['IsisCube']['Instrument']['StartTime']
except KeyError:
v = None
except:
continue
try:
DBinput = MetaTime(upcid=UPCid,
typeid=start_time_tid,
value=v)
session.merge(DBinput)
except:
continue
try:
v = label['IsisCube']['Instrument']['StopTime']
except KeyError:
v = None
DBinput = MetaTime(upcid=UPCid,
typeid=stop_time_tid,
value=v)
session.merge(DBinput)
session.commit()
AddProcessDB(pds_session, fid, False)
os.remove(infile)
# Disconnect from db sessions
pds_session.close()
session.close()
# Disconnect from the engines
pds_engine.dispose()
upc_engine.dispose()
logger.info("UPC processing exited successfully")
def main():
args = Args()
args.parse_args()
key = args.key
namespace = args.namespace
if namespace is None:
namespace is default_namespace
workarea = scratch + args.key + '/'
RQ_file = RedisQueue(key + '_FileQueue', namespace)
RQ_work = RedisQueue(key + '_WorkQueue', namespace)
RQ_zip = RedisQueue(key + '_ZIP', namespace)
RQ_loggy = RedisQueue(key + '_loggy', namespace)
RQ_final = RedisQueue('FinalQueue', namespace)
RHash = RedisHash(key + '_info')
RHerror = RedisHash(key + '_error')
RQ_lock = RedisLock(lock_obj)
RQ_lock.add({'MAP':'1'})
if int(RQ_file.QueueSize()) == 0 and RQ_lock.available('MAP'):
print("No Files Found in Redis Queue")
else:
jobFile = RQ_file.Qfile2Qwork(
RQ_file.getQueueName(), RQ_work.getQueueName()).decode('utf-8')
# Setup system logging
basename = os.path.splitext(os.path.basename(jobFile))[0]
logger = logging.getLogger(key + '.' + basename)
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler(pds_log + '/Service.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info('Starting MAP Processing')
loggyOBJ = Loggy(basename)
# File Naming
infile = workarea + \
os.path.splitext(os.path.basename(jobFile))[0] + '.input.cub'
outfile = workarea + \
os.path.splitext(os.path.basename(jobFile))[0] + '.output.cub'
# Recipe Stuff
RQ_recipe = RedisQueue(key + '_recipe')
status = 'success'
for element in RQ_recipe.RecipeGet():
if status == 'error':
break
elif status == 'success':
processOBJ = Process()
process = processOBJ.JSON2Process(element)
if 'gdal_translate' not in processOBJ.getProcessName():
if 'cubeatt-band' in processOBJ.getProcessName():
if '+' in jobFile:
processOBJ.updateParameter('from_', jobFile)
processOBJ.updateParameter('to', outfile)
processOBJ.ChangeProcess('cubeatt')
else:
continue
elif 'map2map' in processOBJ.getProcessName():
if '+' in jobFile:
processOBJ.updateParameter('from_', infile)
else:
processOBJ.updateParameter('from_', jobFile)
processOBJ.updateParameter('to', outfile)
elif 'cubeatt-bit' in processOBJ.getProcessName():
if RHash.OutBit().decode('utf-8') == 'unsignedbyte':
temp_outfile = outfile + '+lsb+tile+attached+unsignedbyte+1:254'
elif RHash.OutBit().decode('utf-8') == 'signedword':
temp_outfile = outfile + '+lsb+tile+attached+signedword+-32765:32765'
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', temp_outfile)
processOBJ.ChangeProcess('cubeatt')
elif 'isis2pds' in processOBJ.getProcessName():
# finalfile = infile.replace('.input.cub', '_final.img')
finalfile = workarea + RHash.getMAPname().decode('utf-8') + '.img'
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', finalfile)
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
print(processOBJ.getProcess())
for k, v in processOBJ.getProcess().items():
func = getattr(isis, k)
subloggyOBJ = SubLoggy(k)
try:
func(**v)
logger.info('Process %s :: Success', k)
subloggyOBJ.setStatus('SUCCESS')
subloggyOBJ.setCommand(processOBJ.LogCommandline())
subloggyOBJ.setHelpLink(processOBJ.LogHelpLink())
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
if os.path.isfile(outfile):
os.rename(outfile, infile)
status = 'success'
except ProcessError as e:
logger.error('Process %s :: Error', k)
logger.error(e)
status = 'error'
eSTR = 'Error Executing ' + k + \
' Standard Error: ' + str(e)
RHerror.addError(os.path.splitext(
os.path.basename(jobFile))[0], eSTR)
subloggyOBJ.setStatus('ERROR')
subloggyOBJ.setCommand(processOBJ.LogCommandline())
subloggyOBJ.setHelpLink(processOBJ.LogHelpLink())
subloggyOBJ.errorOut(eSTR)
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
else:
GDALcmd = ""
for process, v, in processOBJ.getProcess().items():
subloggyOBJ = SubLoggy(process)
GDALcmd += process
for key, value in v.items():
GDALcmd += ' ' + key + ' ' + value
img_format = RHash.Format().decode('utf-8')
if img_format == 'GeoTiff-BigTiff':
fileext = 'tif'
elif img_format == 'GeoJPEG-2000':
fileext = 'jp2'
elif img_format == 'JPEG':
fileext = 'jpg'
elif img_format == 'PNG':
fileext = 'png'
elif img_format == 'GIF':
fileext = 'gif'
logGDALcmd = GDALcmd + ' ' + basename + '.input.cub ' + RHash.getMAPname().decode('utf-8') + '.' + fileext
finalfile = workarea + RHash.getMAPname().decode('utf-8') + '.' + fileext
GDALcmd += ' ' + infile + ' ' + finalfile
print(GDALcmd)
try:
subprocess.call(GDALcmd, shell=True)
logger.info('Process GDAL translate :: Success')
status = 'success'
subloggyOBJ.setStatus('SUCCESS')
subloggyOBJ.setCommand(logGDALcmd)
subloggyOBJ.setHelpLink(
'www.gdal.org/gdal_translate.html')
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
os.remove(infile)
except OSError as e:
logger.error('Process GDAL translate :: Error')
logger.error(e)
status = 'error'
RHerror.addError(os.path.splitext(os.path.basename(jobFile))[0],
'Process GDAL translate :: Error')
subloggyOBJ.setStatus('ERROR')
subloggyOBJ.setCommand(logGDALcmd)
subloggyOBJ.setHelpLink(
'http://www.gdal.org/gdal_translate.html')
subloggyOBJ.errorOut(e)
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
if status == 'success':
if RHash.Format().decode('utf-8') == 'ISIS3':
finalfile = workarea + RHash.getMAPname().decode('utf-8') + '.cub'
shutil.move(infile, finalfile)
if RHash.getStatus() != b'ERROR':
RHash.Status('SUCCESS')
try:
RQ_zip.QueueAdd(finalfile)
logger.info('File Added to ZIP Queue')
except:
logger.error('File NOT Added to ZIP Queue')
try:
RQ_loggy.QueueAdd(loggyOBJ.Loggy2json())
logger.info('JSON Added to Loggy Queue')
except:
logger.error('JSON NOT Added to Loggy Queue')
RQ_work.QueueRemove(jobFile)
elif status == 'error':
RHash.Status('ERROR')
if os.path.isfile(infile):
os.remove(infile)
if RQ_file.QueueSize() == 0 and RQ_work.QueueSize() == 0:
try:
RQ_final.QueueAdd(key)
logger.info('Key %s Added to Final Queue: Success', key)
logger.info('Job Complete')
except:
logger.error('Key NOT Added to Final Queue')
else:
logger.warning('Queues Not Empty: filequeue = %s work queue = %s', str(
RQ_file.QueueSize()), str(RQ_work.QueueSize()))
def main():
# pdb.set_trace()
PDSinfoDICT = json.load(open(pds_info, 'r'))
# ********* Set up logging *************
logger = logging.getLogger('DI_Process')
logger.setLevel(logging.INFO)
#logFileHandle = logging.FileHandler('/usgs/cdev/PDS/logs/DI.log')
logFileHandle = logging.FileHandler(pds_log + 'DI.log')
#logFileHandle = logging.FileHandler('/home/arsanders/PDS-Pipelines/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:
# ignores engine information
session, _ = db_connect(pds_db)
logger.info('DataBase Connecton: Success')
except:
logger.error('DataBase Connection: Error')
RQ = RedisQueue('DI_ReadyQueue')
index = 0
while int(RQ.QueueSize()) > 0:
item = literal_eval(RQ.QueueGet().decode("utf-8"))
inputfile = item[0]
archive = item[1]
try:
Qelement = session.query(Files).filter(
Files.filename == inputfile).one()
except:
logger.error('Query for File: %s', inputfile)
archive_path = PDSinfoDICT[archive]['path']
cpfile = archive_path + Qelement.filename
if os.path.isfile(cpfile):
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.di_pass = True
else:
Qelement.di_pass = False
Qelement.di_date = datetime.datetime.now(
pytz.utc).strftime("%Y-%m-%d %H:%M:%S")
session.flush()
index = index + 1
if index > 50:
session.commit()
logger.info('Session Commit for 50 Records: Success')
index = 0
else:
logger.error('File %s Not Found', cpfile)
try:
session.commit()
logger.info("End Commit DI process to Database: Success")
index = 1
except:
session.rollback()
def main():
# pdb.set_trace()
##***************** Set up logging *****************
logger = logging.getLogger('Browse_Process')
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler(pds_log + 'Process.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
RQ_main = RedisQueue('Browse_ReadyQueue')
PDSinfoDICT = json.load(open(pds_info, 'r'))
pds_session, _ = db_connect(pds_db)
upc_session, _ = db_connect(upc_db)
tid = get_tid('fullimageurl', upc_session)
while int(RQ_main.QueueSize()) > 0:
item = literal_eval(RQ_main.QueueGet().decode("utf-8"))
inputfile = item[0]
fid = item[1]
archive = item[2]
if os.path.isfile(inputfile):
logger.info('Starting Process: %s', inputfile)
finalpath = makedir(inputfile)
recipeOBJ = Recipe()
recip_json = recipeOBJ.getRecipeJSON(archive)
recipeOBJ.AddJsonFile(recip_json, 'reduced')
infile = workarea + os.path.splitext(
os.path.basename(inputfile))[0] + '.Binput.cub'
outfile = workarea + os.path.splitext(
os.path.basename(inputfile))[0] + '.Boutput.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 == 'cubeatt':
label = pvl.load(infile)
bands = PDSinfoDICT[archive]['bandorder']
query_bands = label['IsisCube']['BandBin'][
PDSinfoDICT[archive]['bandbinQuery']]
# Create a set from the list / single value
try:
query_band_set = set(query_bands)
except:
query_band_set = set([query_bands])
# Iterate through 'bands' and grab the first value that is present in the
# set defined by 'bandbinquery' -- if not present, default to 1
exband = next(
(band for band in bands if band in query_band_set),
1)
band_infile = infile + '+' + str(exband)
processOBJ.updateParameter('from_', band_infile)
processOBJ.updateParameter('to', outfile)
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']
Nline = int(Nline)
Nsample = int(Nsample)
Sfactor = scaleFactor(Nline, Nsample, recip_json)
processOBJ.updateParameter('lscale', Sfactor)
processOBJ.updateParameter('sscale', Sfactor)
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif item == 'isis2std':
final_outfile = finalpath + '/' + os.path.splitext(
os.path.basename(inputfile))[0] + '.browse.jpg'
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', final_outfile)
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
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'
if '2isis' in item:
isisSerial = getISISid(infile)
except ProcessError as e:
print(e)
logger.error('Process %s :: Error', k)
status = 'error'
if status == 'success':
DB_addURL(upc_session, isisSerial, final_outfile, tid)
os.remove(infile)
logger.info('Browse Process Success: %s', inputfile)
AddProcessDB(pds_session, fid, 't')
else:
logger.error('File %s Not Found', inputfile)
def main():
# pdb.set_trace()
DBQO = PDS_DBquery('JOBS')
Key = DBQO.jobKey()
# Key = '2d7379497fed4c092046b2a06f5471a5'
DBQO.setJobsQueued(Key)
#*************** Setup logging ******************
logger = logging.getLogger(Key)
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler('/usgs/cdev/PDS/logs/Service.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info('Starting Process')
xmlOBJ = jobXML(DBQO.jobXML4Key(Key))
# ********** Test if Directory exists and make it if not *******
directory = '/scratch/pds_services/' + Key
if not os.path.exists(directory):
os.makedirs(directory)
logger.info('Working Area: %s', directory)
# ******************** Setup Redis Hash for ground range *********
RedisH = RedisHash(Key + '_info')
RedisH.RemoveAll()
RedisErrorH = RedisHash(Key + '_error')
RedisErrorH.RemoveAll()
RedisH_DICT = {}
RedisH_DICT['service'] = xmlOBJ.getProcess()
RedisH_DICT['fileformat'] = xmlOBJ.getOutFormat()
RedisH_DICT['outbit'] = xmlOBJ.getOutBit()
if xmlOBJ.getRangeType() is not None:
RedisH_DICT['grtype'] = xmlOBJ.getRangeType()
RedisH_DICT['minlat'] = xmlOBJ.getMinLat()
RedisH_DICT['maxlat'] = xmlOBJ.getMaxLat()
RedisH_DICT['minlon'] = xmlOBJ.getMinLon()
RedisH_DICT['maxlon'] = xmlOBJ.getMaxLon()
if RedisH.IsInHash('service'):
pass
else:
RedisH.AddHash(RedisH_DICT)
if RedisH.IsInHash('service'):
logger.info('Redis info Hash: Success')
else:
logger.error('Redis info Hash Not Found')
# ***end ground range **
RQ_recipe = RedisQueue(Key + '_recipe')
RQ_recipe.RemoveAll()
RQ_file = RedisQueue(Key + '_FileQueue')
RQ_file.RemoveAll()
RQ_WorkQueue = RedisQueue(Key + '_WorkQueue')
RQ_WorkQueue.RemoveAll()
RQ_loggy = RedisQueue(Key + '_loggy')
RQ_loggy.RemoveAll()
RQ_zip = RedisQueue(Key + '_ZIP')
RQ_zip.RemoveAll()
if xmlOBJ.getProcess() == 'POW':
fileList = xmlOBJ.getFileListWB()
elif xmlOBJ.getProcess() == 'MAP2':
fileList = xmlOBJ.getMFileListWB()
for List_file in fileList:
######### Input and output file naming and path stuff ############
if xmlOBJ.getProcess() == 'POW':
if xmlOBJ.getInst() == 'THEMIS_IR':
Input_file = List_file.replace('odtie1_', 'odtir1_')
Input_file = Input_file.replace('xxedr', 'xxrdr')
Input_file = Input_file.replace('EDR.QUB', 'RDR.QUB')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/',
'/pds_san/PDS_Archive/')
elif xmlOBJ.getInst() == 'ISSNA':
Input_file = List_file.replace('.IMG', '.LBL')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/',
'/pds_san/PDS_Archive/')
elif xmlOBJ.getInst() == 'ISSWA':
Input_file = List_file.replace('.IMG', '.LBL')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/',
'/pds_san/PDS_Archive/')
elif xmlOBJ.getInst() == 'SOLID STATE IMAGING SYSTEM':
Input_file = List_file.replace('.img', '.lbl')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/',
'/pds_san/PDS_Archive/')
else:
Input_file = List_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/',
'/pds_san/PDS_Archive/')
elif xmlOBJ.getProcess() == 'MAP2':
Input_file = List_file.replace('file://pds_san', '/pds_san')
if '+' in Input_file:
tempsplit = Input_file.split('+')
tempFile = tempsplit[0]
else:
tempFile = Input_file
label = pvl.load(tempFile)
#*********Output final file naming **************
Tbasename = os.path.splitext(os.path.basename(tempFile))[0]
splitBase = Tbasename.split('_')
labP = xmlOBJ.getProjection()
if labP == 'INPUT':
lab_proj = label['IsisCube']['Mapping']['ProjectionName'][0:4]
else:
lab_proj = labP[0:4]
if xmlOBJ.getClat() is None or xmlOBJ.getClon() is None:
basefinal = splitBase[0] + splitBase[1] + \
splitBase[2] + '_MAP2_' + lab_proj.upper()
else:
lab_clat = float(xmlOBJ.getClat())
if lab_clat >= 0:
labH = 'N'
elif lab_clat < 0:
labH = 'S'
lab_clon = float(xmlOBJ.getClon())
basefinal = splitBase[0] + splitBase[1] + splitBase[
2] + '_MAP2_' + str(lab_clat) + labH + str(
lab_clon) + '_' + lab_proj.upper()
RedisH.MAPname(basefinal)
try:
RQ_file.QueueAdd(Input_file)
logger.info('File %s Added to Redis Queue', Input_file)
except Exception as e:
logger.warn('File %s NOT Added to Redis Queue', Input_file)
print('Redis Queue Error', e)
RedisH.FileCount(RQ_file.QueueSize())
logger.info('Count of Files Queue: %s', str(RQ_file.QueueSize()))
# ************* Map Template Stuff ******************
logger.info('Making Map File')
mapOBJ = MakeMap()
if xmlOBJ.getProcess() == 'MAP2' and xmlOBJ.getProjection() == 'INPUT':
proj = label['IsisCube']['Mapping']['ProjectionName']
mapOBJ.Projection(proj)
else:
mapOBJ.Projection(xmlOBJ.getProjection())
if xmlOBJ.getClon() is not None:
mapOBJ.CLon(float(xmlOBJ.getClon()))
if xmlOBJ.getClat() is not None:
mapOBJ.CLat(float(xmlOBJ.getClat()))
if xmlOBJ.getFirstParallel() is not None:
mapOBJ.FirstParallel(float(xmlOBJ.getFirstParallel()))
if xmlOBJ.getSecondParallel() is not None:
mapOBJ.SecondParallel(float(xmlOBJ.getSecondParallel()))
if xmlOBJ.getResolution() is not None:
mapOBJ.PixelRes(float(xmlOBJ.getResolution()))
if xmlOBJ.getTargetName() is not None:
mapOBJ.Target(xmlOBJ.getTargetName())
if xmlOBJ.getERadius() is not None:
mapOBJ.ERadius(float(xmlOBJ.getERadius()))
if xmlOBJ.getPRadius() is not None:
mapOBJ.PRadius(float(xmlOBJ.getPRadius()))
if xmlOBJ.getLatType() is not None:
mapOBJ.LatType(xmlOBJ.getLatType())
if xmlOBJ.getLonDirection() is not None:
mapOBJ.LonDirection(xmlOBJ.getLonDirection())
if xmlOBJ.getLonDomain() is not None:
mapOBJ.LonDomain(int(xmlOBJ.getLonDomain()))
if xmlOBJ.getProcess() == 'MAP2':
if xmlOBJ.getMinLat() is not None:
mapOBJ.MinLat(float(xmlOBJ.getMinLat()))
if xmlOBJ.getMaxLat() is not None:
mapOBJ.MaxLat(float(xmlOBJ.getMaxLat()))
if xmlOBJ.getMinLon() is not None:
mapOBJ.MinLon(float(xmlOBJ.getMinLon()))
if xmlOBJ.getMaxLon() is not None:
mapOBJ.MaxLon(float(xmlOBJ.getMaxLon()))
mapOBJ.Map2pvl()
MAPfile = directory + "/" + Key + '.map'
mapOBJ.Map2File(MAPfile)
try:
f = open(MAPfile)
f.close
logger.info('Map File Creation: Success')
except IOError as e:
logger.error('Map File %s Not Found', MAPfile)
# ** End Map Template Stuff **
# *************************************************
logger.info('Building Recipe')
recipeOBJ = Recipe()
if xmlOBJ.getProcess() == 'POW':
recipeOBJ.AddJsonFile(recipe_dict[xmlOBJ.getInst()])
elif xmlOBJ.getProcess() == 'MAP2':
recipeOBJ.AddJsonFile(recipe_dict['MAP'])
# ************** Test for stretch and add to recipe **********************
# if MAP2 and 8 or 16 bit run stretch to set range
if xmlOBJ.getOutBit() == 'input':
testBitType = str(label['IsisCube']['Core']['Pixels']['Type']).upper()
else:
testBitType = xmlOBJ.getOutBit().upper()
if xmlOBJ.getProcess() == 'MAP2' and xmlOBJ.STR_Type() is None:
if str(label['IsisCube']['Core']['Pixels']['Type']).upper(
) != xmlOBJ.getOutBit().upper() and str(
label['IsisCube']['Core']['Pixels']['Type']).upper() != 'REAL':
if str(label['IsisCube']['Core']['Pixels']
['Type']).upper() == 'SIGNEDWORD':
strpairs = '0:-32765 0:-32765 100:32765 100:32765'
elif str(label['IsisCube']['Core']['Pixels']
['Type']).upper() == 'UNSIGNEDBYTE':
strpairs = '0:1 0:1 100:254 100:254'
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('stretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('usepercentages', 'yes')
STRprocessOBJ.AddParameter('pairs', strpairs)
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
strType = xmlOBJ.STR_Type()
if strType == 'StretchPercent' and xmlOBJ.STR_PercentMin(
) is not None and xmlOBJ.STR_PercentMax(
) is not None and testBitType != 'REAL':
if float(xmlOBJ.STR_PercentMin()) != 0 and float(
xmlOBJ.STR_PercentMax()) != 100:
if testBitType == 'UNSIGNEDBYTE':
strpairs = '0:1 ' + xmlOBJ.STR_PercentMin() + ':1 ' + \
xmlOBJ.STR_PercentMax() + ':254 100:254'
elif testBitType == 'SIGNEDWORD':
strpairs = '0:-32765 ' + xmlOBJ.STR_PercentMin() + ':-32765 ' + \
xmlOBJ.STR_PercentMax() + ':32765 100:32765'
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('stretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('usepercentages', 'yes')
STRprocessOBJ.AddParameter('pairs', strpairs)
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'GaussStretch':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('gaussstretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('gsigma', xmlOBJ.STR_GaussSigma())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'HistogramEqualization':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('histeq')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
if xmlOBJ.STR_PercentMin() is None:
STRprocessOBJ.AddParameter('minper', '0')
else:
STRprocessOBJ.AddParameter('minper', xmlOBJ.STR_PercentMin())
if xmlOBJ.STR_PercentMax() is None:
STRprocessOBJ.AddParameter('maxper', '100')
else:
STRprocessOBJ.AddParameter('maxper', xmlOBJ.STR_PercentMax())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'SigmaStretch':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('sigmastretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('variance', xmlOBJ.STR_SigmaVariance())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
# ************* Test for output bit type and add to recipe *************
if xmlOBJ.getProcess() == 'POW':
if xmlOBJ.getOutBit().upper() == 'UNSIGNEDBYTE' or xmlOBJ.getOutBit(
).upper() == 'SIGNEDWORD':
CAprocessOBJ = Process()
CAprocessOBJ.newProcess('cubeatt-bit')
CAprocessOBJ.AddParameter('from_', 'value')
CAprocessOBJ.AddParameter('to', 'value')
recipeOBJ.AddProcess(CAprocessOBJ.getProcess())
elif xmlOBJ.getProcess() == 'MAP2':
if xmlOBJ.getOutBit().upper() != 'INPUT':
if xmlOBJ.getOutBit().upper(
) == 'UNSIGNEDBYTE' or xmlOBJ.getOutBit().upper() == 'SIGNEDWORD':
if str(label['IsisCube']['Core']['Pixels']
['Type']).upper() != xmlOBJ.getOutBit().upper():
CAprocessOBJ = Process()
CAprocessOBJ.newProcess('cubeatt-bit')
CAprocessOBJ.AddParameter('from_', 'value')
CAprocessOBJ.AddParameter('to', 'value')
recipeOBJ.AddProcess(CAprocessOBJ.getProcess())
# **************** Add Grid(MAP2) *************
if xmlOBJ.getGridInterval() is not None:
GprocessOBJ = Process()
GprocessOBJ.newProcess('grid')
GprocessOBJ.AddParameter('from_', 'value')
GprocessOBJ.AddParameter('to', 'value')
GprocessOBJ.AddParameter('latinc', xmlOBJ.getGridInterval())
GprocessOBJ.AddParameter('loninc', xmlOBJ.getGridInterval())
GprocessOBJ.AddParameter('outline', 'yes')
GprocessOBJ.AddParameter('boundary', 'yes')
GprocessOBJ.AddParameter('linewidth', '3')
recipeOBJ.AddProcess(GprocessOBJ.getProcess())
# ********OUTPUT FORMAT ***************
# ************* Test for GDAL and add to recipe *************************
Oformat = xmlOBJ.getOutFormat()
if Oformat == 'GeoTiff-BigTiff' or Oformat == 'GeoJPEG-2000' or Oformat == 'JPEG' or Oformat == 'PNG':
if Oformat == 'GeoJPEG-2000':
Oformat = 'JP2KAK'
if Oformat == 'GeoTiff-BigTiff':
Oformat = 'GTiff'
GDALprocessOBJ = Process()
# GDALprocessOBJ.newProcess('/usgs/dev/contrib/bin/FWTools-linux-x86_64-3.0.3/bin_safe/gdal_translate')
GDALprocessOBJ.newProcess('/usgs/apps/anaconda/bin/gdal_translate')
if xmlOBJ.getOutBit() != 'input':
GDALprocessOBJ.AddParameter(
'-ot', GDALprocessOBJ.GDAL_OBit(xmlOBJ.getOutBit()))
GDALprocessOBJ.AddParameter('-of', Oformat)
if Oformat == 'GTiff' or Oformat == 'JP2KAK' or Oformat == 'JPEG':
GDALprocessOBJ.AddParameter('-co',
GDALprocessOBJ.GDAL_Creation(Oformat))
recipeOBJ.AddProcess(GDALprocessOBJ.getProcess())
# **************** set up pds2isis and add to recipe
elif Oformat == 'PDS':
pdsProcessOBJ = Process()
pdsProcessOBJ.newProcess('isis2pds')
pdsProcessOBJ.AddParameter('from_', 'value')
pdsProcessOBJ.AddParameter('to', 'value')
if xmlOBJ.getOutBit() == 'unsignedbyte':
pdsProcessOBJ.AddParameter('bittype', '8bit')
elif xmlOBJ.getOutBit() == 'signedword':
pdsProcessOBJ.AddParameter('bittype', 's16bit')
recipeOBJ.AddProcess(pdsProcessOBJ.getProcess())
for item in recipeOBJ.getProcesses():
processOBJ = Process()
processOBJ.ProcessFromRecipe(item, recipeOBJ.getRecipe())
if item == 'cam2map':
processOBJ.updateParameter('map', MAPfile)
if xmlOBJ.getResolution() is None:
processOBJ.updateParameter('pixres', 'CAMERA')
else:
processOBJ.updateParameter('pixres', 'MAP')
if xmlOBJ.getRangeType() is None:
processOBJ.updateParameter('defaultrange', 'MINIMIZE')
elif xmlOBJ.getRangeType() == 'smart' or xmlOBJ.getRangeType(
) == 'fill':
processOBJ.updateParameter('defaultrange', 'CAMERA')
processOBJ.AddParameter('trim', 'YES')
elif item == 'map2map':
processOBJ.updateParameter('map', MAPfile)
if xmlOBJ.getResolution() is None:
processOBJ.updateParameter('pixres', 'FROM')
else:
processOBJ.updateParameter('pixres', 'MAP')
if xmlOBJ.OutputGeometry() is not None:
processOBJ.updateParameter('defaultrange', 'MAP')
processOBJ.AddParameter('trim', 'YES')
else:
processOBJ.updateParameter('defaultrange', 'FROM')
processJSON = processOBJ.Process2JSON()
try:
RQ_recipe.QueueAdd(processJSON)
logger.info('Recipe Element Added to Redis: %s : Success', item)
except Exception as e:
logger.warn('Recipe Element NOT Added to Redis: %s', item)
# ** *************** HPC job stuff ***********************
logger.info('HPC Cluster job Submission Starting')
jobOBJ = HPCjob()
jobOBJ.setJobName(Key + '_Service')
jobOBJ.setStdOut('/usgs/cdev/PDS/output/' + Key + '_%A_%a.out')
jobOBJ.setStdError('/usgs/cdev/PDS/output/' + Key + '_%A_%a.err')
jobOBJ.setWallClock('24:00:00')
# jobOBJ.setMemory('8192')
# jobOBJ.setMemory('16384')
jobOBJ.setMemory('24576')
jobOBJ.setPartition('pds')
JAsize = RQ_file.QueueSize()
jobOBJ.setJobArray(JAsize)
logger.info('Job Array Size : %s', str(JAsize))
jobOBJ.addPath('/usgs/apps/anaconda/bin')
if xmlOBJ.getProcess() == 'POW':
cmd = '/usgs/cdev/PDS/bin/POWprocess.py ' + Key
elif xmlOBJ.getProcess() == 'MAP2':
cmd = '/usgs/cdev/PDS/bin/MAPprocess.py ' + Key
logger.info('HPC Command: %s', cmd)
jobOBJ.setCommand(cmd)
SBfile = directory + '/' + Key + '.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')
DBQO.setJobsStarted(Key)
except IOError as e:
logger.error('Jobs NOT Submitted to HPC')
def main():
PDSinfoDICT = json.load(open(pds_info, 'r'))
args = Args()
args.parse_args()
# Set up logging
logger = logging.getLogger('DI_Process')
level = logging.getLevelName(args.log_level)
logger.setLevel(level)
logFileHandle = logging.FileHandler(pds_log + '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:
session, engine = db_connect(pds_db)
logger.info('DataBase Connecton: Success')
except Exception as e:
logger.error('DataBase Connection Error: %s', str(e))
return 1
RQ = RedisQueue('DI_ReadyQueue')
RQ_lock = RedisLock(lock_obj)
RQ_lock.add({RQ.id_name: '1'})
index = 0
logger.info("DI Queue: %s", RQ.id_name)
while int(RQ.QueueSize()) > 0 and RQ_lock.available(RQ.id_name):
item = literal_eval(RQ.QueueGet().decode("utf-8"))
inputfile = item[0]
archive = item[1]
try:
Qelement = session.query(Files).filter(
Files.filename == inputfile).one()
except Exception as e:
logger.warn('Filename query failed for inputfile %s: %s',
inputfile, str(e))
continue
archive_path = PDSinfoDICT[archive]['path']
cpfile = archive_path + Qelement.filename
if os.path.isfile(cpfile):
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()
Qelement.di_pass = checksum == Qelement.checksum
Qelement.di_date = datetime.datetime.now(
pytz.utc).strftime("%Y-%m-%d %H:%M:%S")
session.flush()
index = index + 1
if index > 50:
session.commit()
logger.info('Session Commit for 50 Records: Success')
index = 0
else:
logger.warn('File %s Not Found', cpfile)
try:
session.commit()
logger.info("End Commit DI process to Database: Success")
index = 1
except Exception as e:
logger.warn("Unable to commit changes to database\n\n%s", e)
session.rollback()
# Close connection to database
session.close()
engine.dispose()
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/'
}
args = Args()
args.parse_args()
logger = logging.getLogger('DI_Process')
level = argparse.getLevelName(args.log_level)
logger.setLevel(level)
logFileHandle = logging.FileHandler(pds_log + '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):
# 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 during commit')
logger.info("End Commit DI process to Database: Success")
logger.info('Checksum for %s Files Updated', str(index))
def main():
args = Args()
args.parse_args()
key = args.key
namespace = args.namespace
if namespace is None:
namespace = default_namespace
# Set up logging
logger = logging.getLogger(key)
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler(pds_log + 'Service.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
# Connect to database and access 'jobs' table
DBQO = PDS_DBquery('JOBS')
if key is None:
# If no key is specified, grab the first key
key = DBQO.jobKey()
try:
# Set the 'queued' column to current time i.e. prep for processing
DBQO.setJobsQueued(key)
except KeyError as e:
logger.error('%s', e)
exit(1)
logger.info('Starting Process')
xmlOBJ = jobXML(DBQO.jobXML4Key(key))
# Make directory if it doesn't exist
directory = scratch + key
if not os.path.exists(directory):
os.makedirs(directory)
logger.info('Working Area: %s', directory)
# Set up Redis Hash for ground range
RedisH = RedisHash(key + '_info')
RedisH.RemoveAll()
RedisErrorH = RedisHash(key + '_error')
RedisErrorH.RemoveAll()
RedisH_DICT = {}
RedisH_DICT['service'] = xmlOBJ.getProcess()
RedisH_DICT['fileformat'] = xmlOBJ.getOutFormat()
RedisH_DICT['outbit'] = xmlOBJ.getOutBit()
if xmlOBJ.getRangeType() is not None:
RedisH_DICT['grtype'] = xmlOBJ.getRangeType()
RedisH_DICT['minlat'] = xmlOBJ.getMinLat()
RedisH_DICT['maxlat'] = xmlOBJ.getMaxLat()
RedisH_DICT['minlon'] = xmlOBJ.getMinLon()
RedisH_DICT['maxlon'] = xmlOBJ.getMaxLon()
if RedisH.IsInHash('service'):
pass
else:
RedisH.AddHash(RedisH_DICT)
if RedisH.IsInHash('service'):
logger.info('Redis info Hash: Success')
else:
logger.error('Redis info Hash Not Found')
# End ground range
RQ_recipe = RedisQueue(key + '_recipe', namespace)
RQ_recipe.RemoveAll()
RQ_file = RedisQueue(key + '_FileQueue', namespace)
RQ_file.RemoveAll()
RQ_WorkQueue = RedisQueue(key + '_WorkQueue', namespace)
RQ_WorkQueue.RemoveAll()
RQ_loggy = RedisQueue(key + '_loggy', namespace)
RQ_loggy.RemoveAll()
RQ_zip = RedisQueue(key + '_ZIP', namespace)
RQ_zip.RemoveAll()
if xmlOBJ.getProcess() == 'POW':
fileList = xmlOBJ.getFileListWB()
elif xmlOBJ.getProcess() == 'MAP2':
fileList = xmlOBJ.getMFileListWB()
for List_file in fileList:
# Input and output file naming and path stuff
if xmlOBJ.getProcess() == 'POW':
if xmlOBJ.getInst() == 'THEMIS_IR':
Input_file = List_file.replace('odtie1_', 'odtir1_')
Input_file = Input_file.replace('xxedr', 'xxrdr')
Input_file = Input_file.replace('EDR.QUB', 'RDR.QUB')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/', archive_base)
elif xmlOBJ.getInst() == 'ISSNA':
Input_file = List_file.replace('.IMG', '.LBL')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/', archive_base)
elif xmlOBJ.getInst() == 'ISSWA':
Input_file = List_file.replace('.IMG', '.LBL')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/', archive_base)
elif xmlOBJ.getInst() == 'SOLID STATE IMAGING SYSTEM':
Input_file = List_file.replace('.img', '.lbl')
Input_file = Input_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/', archive_base)
else:
Input_file = List_file.replace(
'http://pdsimage.wr.usgs.gov/Missions/', archive_base)
elif xmlOBJ.getProcess() == 'MAP2':
Input_file = List_file.replace('file://pds_san', '/pds_san')
if '+' in Input_file:
tempsplit = Input_file.split('+')
tempFile = tempsplit[0]
else:
tempFile = Input_file
label = pvl.load(tempFile)
# Output final file naming
Tbasename = os.path.splitext(os.path.basename(tempFile))[0]
splitBase = Tbasename.split('_')
labP = xmlOBJ.getProjection()
if labP == 'INPUT':
lab_proj = label['IsisCube']['Mapping']['ProjectionName'][0:4]
else:
lab_proj = labP[0:4]
if xmlOBJ.getClat() is None or xmlOBJ.getClon() is None:
basefinal = splitBase[0] + splitBase[1] + \
splitBase[2] + '_MAP2_' + lab_proj.upper()
else:
lab_clat = float(xmlOBJ.getClat())
if lab_clat >= 0:
labH = 'N'
elif lab_clat < 0:
labH = 'S'
lab_clon = float(xmlOBJ.getClon())
basefinal = splitBase[0] + splitBase[1] + splitBase[
2] + '_MAP2_' + str(lab_clat) + labH + str(
lab_clon) + '_' + lab_proj.upper()
RedisH.MAPname(basefinal)
try:
RQ_file.QueueAdd(Input_file)
logger.info('File %s Added to Redis Queue', Input_file)
except Exception as e:
logger.warn('File %s NOT Added to Redis Queue', Input_file)
print('Redis Queue Error', e)
RedisH.FileCount(RQ_file.QueueSize())
logger.info('Count of Files Queue: %s', str(RQ_file.QueueSize()))
# Map Template Stuff
logger.info('Making Map File')
mapOBJ = MakeMap()
if xmlOBJ.getProcess() == 'MAP2' and xmlOBJ.getProjection() == 'INPUT':
proj = label['IsisCube']['Mapping']['ProjectionName']
mapOBJ.Projection(proj)
else:
mapOBJ.Projection(xmlOBJ.getProjection())
if xmlOBJ.getClon() is not None:
mapOBJ.CLon(float(xmlOBJ.getClon()))
if xmlOBJ.getClat() is not None:
mapOBJ.CLat(float(xmlOBJ.getClat()))
if xmlOBJ.getFirstParallel() is not None:
mapOBJ.FirstParallel(float(xmlOBJ.getFirstParallel()))
if xmlOBJ.getSecondParallel() is not None:
mapOBJ.SecondParallel(float(xmlOBJ.getSecondParallel()))
if xmlOBJ.getResolution() is not None:
mapOBJ.PixelRes(float(xmlOBJ.getResolution()))
if xmlOBJ.getTargetName() is not None:
mapOBJ.Target(xmlOBJ.getTargetName())
if xmlOBJ.getERadius() is not None:
mapOBJ.ERadius(float(xmlOBJ.getERadius()))
if xmlOBJ.getPRadius() is not None:
mapOBJ.PRadius(float(xmlOBJ.getPRadius()))
if xmlOBJ.getLatType() is not None:
mapOBJ.LatType(xmlOBJ.getLatType())
if xmlOBJ.getLonDirection() is not None:
mapOBJ.LonDirection(xmlOBJ.getLonDirection())
if xmlOBJ.getLonDomain() is not None:
mapOBJ.LonDomain(int(xmlOBJ.getLonDomain()))
if xmlOBJ.getProcess() == 'MAP2':
if xmlOBJ.getMinLat() is not None:
mapOBJ.MinLat(float(xmlOBJ.getMinLat()))
if xmlOBJ.getMaxLat() is not None:
mapOBJ.MaxLat(float(xmlOBJ.getMaxLat()))
if xmlOBJ.getMinLon() is not None:
mapOBJ.MinLon(float(xmlOBJ.getMinLon()))
if xmlOBJ.getMaxLon() is not None:
mapOBJ.MaxLon(float(xmlOBJ.getMaxLon()))
mapOBJ.Map2pvl()
MAPfile = directory + "/" + key + '.map'
mapOBJ.Map2File(MAPfile)
try:
f = open(MAPfile)
f.close
logger.info('Map File Creation: Success')
except IOError as e:
logger.error('Map File %s Not Found', MAPfile)
# ** End Map Template Stuff **
logger.info('Building Recipe')
recipeOBJ = Recipe()
if xmlOBJ.getProcess() == 'POW':
recipeOBJ.AddJsonFile(recipe_base + xmlOBJ.getCleanName() + '.json',
"pow")
elif xmlOBJ.getProcess() == 'MAP2':
recipeOBJ.AddJsonFile(recipe_base + "map2_process.json", "map")
# Test for stretch and add to recipe
# if MAP2 and 8 or 16 bit run stretch to set range
if xmlOBJ.getOutBit() == 'input':
testBitType = str(label['IsisCube']['Core']['Pixels']['Type']).upper()
else:
testBitType = xmlOBJ.getOutBit().upper()
if xmlOBJ.getProcess() == 'MAP2' and xmlOBJ.STR_Type() is None:
if str(label['IsisCube']['Core']['Pixels']['Type']).upper(
) != xmlOBJ.getOutBit().upper() and str(
label['IsisCube']['Core']['Pixels']['Type']).upper() != 'REAL':
if str(label['IsisCube']['Core']['Pixels']
['Type']).upper() == 'SIGNEDWORD':
strpairs = '0:-32765 0:-32765 100:32765 100:32765'
elif str(label['IsisCube']['Core']['Pixels']
['Type']).upper() == 'UNSIGNEDBYTE':
strpairs = '0:1 0:1 100:254 100:254'
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('stretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('usepercentages', 'yes')
STRprocessOBJ.AddParameter('pairs', strpairs)
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
strType = xmlOBJ.STR_Type()
if strType == 'StretchPercent' and xmlOBJ.STR_PercentMin(
) is not None and xmlOBJ.STR_PercentMax(
) is not None and testBitType != 'REAL':
if float(xmlOBJ.STR_PercentMin()) != 0 and float(
xmlOBJ.STR_PercentMax()) != 100:
if testBitType == 'UNSIGNEDBYTE':
strpairs = '0:1 ' + xmlOBJ.STR_PercentMin() + ':1 ' + \
xmlOBJ.STR_PercentMax() + ':254 100:254'
elif testBitType == 'SIGNEDWORD':
strpairs = '0:-32765 ' + xmlOBJ.STR_PercentMin() + ':-32765 ' + \
xmlOBJ.STR_PercentMax() + ':32765 100:32765'
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('stretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('usepercentages', 'yes')
STRprocessOBJ.AddParameter('pairs', strpairs)
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'GaussStretch':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('gaussstretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('gsigma', xmlOBJ.STR_GaussSigma())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'HistogramEqualization':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('histeq')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
if xmlOBJ.STR_PercentMin() is None:
STRprocessOBJ.AddParameter('minper', '0')
else:
STRprocessOBJ.AddParameter('minper', xmlOBJ.STR_PercentMin())
if xmlOBJ.STR_PercentMax() is None:
STRprocessOBJ.AddParameter('maxper', '100')
else:
STRprocessOBJ.AddParameter('maxper', xmlOBJ.STR_PercentMax())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
elif strType == 'SigmaStretch':
STRprocessOBJ = Process()
STRprocessOBJ.newProcess('sigmastretch')
STRprocessOBJ.AddParameter('from_', 'value')
STRprocessOBJ.AddParameter('to', 'value')
STRprocessOBJ.AddParameter('variance', xmlOBJ.STR_SigmaVariance())
recipeOBJ.AddProcess(STRprocessOBJ.getProcess())
# Test for output bit type and add to recipe
if xmlOBJ.getProcess() == 'POW':
if xmlOBJ.getOutBit().upper() == 'UNSIGNEDBYTE' or xmlOBJ.getOutBit(
).upper() == 'SIGNEDWORD':
CAprocessOBJ = Process()
CAprocessOBJ.newProcess('cubeatt-bit')
CAprocessOBJ.AddParameter('from_', 'value')
CAprocessOBJ.AddParameter('to', 'value')
recipeOBJ.AddProcess(CAprocessOBJ.getProcess())
elif xmlOBJ.getProcess() == 'MAP2':
if xmlOBJ.getOutBit().upper() != 'INPUT':
if xmlOBJ.getOutBit().upper(
) == 'UNSIGNEDBYTE' or xmlOBJ.getOutBit().upper() == 'SIGNEDWORD':
if str(label['IsisCube']['Core']['Pixels']
['Type']).upper() != xmlOBJ.getOutBit().upper():
CAprocessOBJ = Process()
CAprocessOBJ.newProcess('cubeatt-bit')
CAprocessOBJ.AddParameter('from_', 'value')
CAprocessOBJ.AddParameter('to', 'value')
recipeOBJ.AddProcess(CAprocessOBJ.getProcess())
# Add Grid(MAP2)
if xmlOBJ.getGridInterval() is not None:
GprocessOBJ = Process()
GprocessOBJ.newProcess('grid')
GprocessOBJ.AddParameter('from_', 'value')
GprocessOBJ.AddParameter('to', 'value')
GprocessOBJ.AddParameter('latinc', xmlOBJ.getGridInterval())
GprocessOBJ.AddParameter('loninc', xmlOBJ.getGridInterval())
GprocessOBJ.AddParameter('outline', 'yes')
GprocessOBJ.AddParameter('boundary', 'yes')
GprocessOBJ.AddParameter('linewidth', '3')
recipeOBJ.AddProcess(GprocessOBJ.getProcess())
# OUTPUT FORMAT
# Test for GDAL and add to recipe
Oformat = xmlOBJ.getOutFormat()
if Oformat == 'GeoTiff-BigTiff' or Oformat == 'GeoJPEG-2000' or Oformat == 'JPEG' or Oformat == 'PNG':
if Oformat == 'GeoJPEG-2000':
Oformat = 'JP2KAK'
if Oformat == 'GeoTiff-BigTiff':
Oformat = 'GTiff'
GDALprocessOBJ = Process()
# @TODO remove hard-coded path in favor of using whichever utilities are found within the conda environment --
# we need more information here to ensure that whichever utilities are found are capable of supporting GeoJPEG-2000.
GDALprocessOBJ.newProcess('/usgs/apps/anaconda/bin/gdal_translate')
if xmlOBJ.getOutBit() != 'input':
GDALprocessOBJ.AddParameter(
'-ot', GDALprocessOBJ.GDAL_OBit(xmlOBJ.getOutBit()))
GDALprocessOBJ.AddParameter('-of', Oformat)
if Oformat == 'GTiff' or Oformat == 'JP2KAK' or Oformat == 'JPEG':
GDALprocessOBJ.AddParameter('-co',
GDALprocessOBJ.GDAL_Creation(Oformat))
recipeOBJ.AddProcess(GDALprocessOBJ.getProcess())
# set up pds2isis and add to recipe
elif Oformat == 'PDS':
pdsProcessOBJ = Process()
pdsProcessOBJ.newProcess('isis2pds')
pdsProcessOBJ.AddParameter('from_', 'value')
pdsProcessOBJ.AddParameter('to', 'value')
if xmlOBJ.getOutBit() == 'unsignedbyte':
pdsProcessOBJ.AddParameter('bittype', '8bit')
elif xmlOBJ.getOutBit() == 'signedword':
pdsProcessOBJ.AddParameter('bittype', 's16bit')
recipeOBJ.AddProcess(pdsProcessOBJ.getProcess())
for item in recipeOBJ.getProcesses():
processOBJ = Process()
processOBJ.ProcessFromRecipe(item, recipeOBJ.getRecipe())
if item == 'cam2map':
processOBJ.updateParameter('map', MAPfile)
if xmlOBJ.getResolution() is None:
processOBJ.updateParameter('pixres', 'CAMERA')
else:
processOBJ.updateParameter('pixres', 'MAP')
if xmlOBJ.getRangeType() is None:
processOBJ.updateParameter('defaultrange', 'MINIMIZE')
elif xmlOBJ.getRangeType() == 'smart' or xmlOBJ.getRangeType(
) == 'fill':
processOBJ.updateParameter('defaultrange', 'CAMERA')
processOBJ.AddParameter('trim', 'YES')
elif item == 'map2map':
processOBJ.updateParameter('map', MAPfile)
if xmlOBJ.getResolution() is None:
processOBJ.updateParameter('pixres', 'FROM')
else:
processOBJ.updateParameter('pixres', 'MAP')
if xmlOBJ.OutputGeometry() is not None:
processOBJ.updateParameter('defaultrange', 'MAP')
processOBJ.AddParameter('trim', 'YES')
else:
processOBJ.updateParameter('defaultrange', 'FROM')
processJSON = processOBJ.Process2JSON()
try:
RQ_recipe.QueueAdd(processJSON)
logger.info('Recipe Element Added to Redis: %s : Success', item)
except Exception as e:
logger.warn('Recipe Element NOT Added to Redis: %s', item)
# HPC job stuff
logger.info('HPC Cluster job Submission Starting')
jobOBJ = HPCjob()
jobOBJ.setJobName(key + '_Service')
jobOBJ.setStdOut(slurm_log + key + '_%A_%a.out')
jobOBJ.setStdError(slurm_log + key + '_%A_%a.err')
jobOBJ.setWallClock('24:00:00')
jobOBJ.setMemory('24576')
jobOBJ.setPartition('pds')
JAsize = RQ_file.QueueSize()
jobOBJ.setJobArray(JAsize)
logger.info('Job Array Size : %s', str(JAsize))
# @TODO replace with source activate <env>
#jobOBJ.addPath('/usgs/apps/anaconda/bin')
# Whether or not we use the default namespace, this guarantees that the POW/MAP queues will match the namespace
# used in the job manager.
if xmlOBJ.getProcess() == 'POW':
cmd = cmd_dir + "POWprocess.py -k {} -n {}".format(key, namespace)
elif xmlOBJ.getProcess() == 'MAP2':
cmd = cmd_dir + "MAPprocess.py -k {} -n {}".format(key, namespace)
logger.info('HPC Command: %s', cmd)
jobOBJ.setCommand(cmd)
SBfile = directory + '/' + key + '.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')
DBQO.setJobsStarted(key)
except IOError as e:
logger.error('Jobs NOT Submitted to HPC')